Dataset and Motifs High-scoring Sequences Motif Diagrams Annotated Sequences Debugging Information


MAST - Motif Alignment and Search Tool

MAST version 3.0 (Release date: 2004/07/16 05:53:30)

For further information on how to interpret these results or to get a copy of the MAST software please access http://meme.sdsc.edu.


REFERENCE

If you use this program in your research, please cite:

Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(48-54), 1998.


DATABASE AND MOTIFS

	DATABASE /home/meme/meme.3.0.6/tests/farntrans5.s (peptide)
	Last updated on Fri Jul 16 15:53:55 2004
	Database contains 5 sequences, 1900 residues

	MOTIFS meme.farntrans5.tcm.4.Linuxx86_64.html (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    30   GGFQGRPNKEVHTCYTYWALAALAILNKLH
	  2    14   INKEKLIQWIKSCQ

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.22
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from non-redundant database):
	A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 
	L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 
	W 0.013 Y 0.033 

SECTION I: HIGH-SCORING SEQUENCES

LinksSequence NameDescriptionE-valueLength
D A ?
BET2_YEAST YPT1/SEC4 PROTEINS GERANY... 2.9e-27 325
D A ?
RATRABGERB Rat rab geranylgeranyl tr... 1.4e-25 331
D A ?
CAL1_YEAST RAS PROTEINS GERANYLGERAN... 9.7e-22 376
D A ?
PFTB_RAT PROTEIN FARNESYLTRANSFERA... 7.6e-21 437
D A ?
RAM1_YEAST PROTEIN FARNESYLTRANSFERA... 6.2e-20 431

SECTION II: MOTIF DIAGRAMS


LinksNameExpect   Motifs
S A ?
BET2_YEAST 2.9e-27

2
1
2
1
2
1
2
1
1
2
1
S A ?
RATRABGERB 1.4e-25

2
1
2
1
2
1
1
2
1
S A ?
CAL1_YEAST 9.7e-22

2
2
1
2
1
1
2
S A ?
PFTB_RAT 7.6e-21

2
1
2
1
2
1
2
1
2
1
S A ?
RAM1_YEAST 6.2e-20

1
2
1
2
1
2
1
2
1
2
SCALE
| | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450

SECTION III: ANNOTATED SEQUENCES


BET2_YEAST
S D ?

YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2.
LENGTH = 325 COMBINED P-VALUE = 5.77e-28 E-VALUE = 2.9e-27
DIAGRAM: 6-[2]-3-[1]-1-[2]-4-[1]-4-[2]-3-[1]-1-[2]-3-[1]-21-[1]-1-[2]-4-[1]-24
           [2]              [1]                            [2]               [1]
           5.2e-05          2.7e-10                        6.6e-10           5.9
           INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGF
             +++ +++++++     ++  + +++ +++ +++++ +++++++ + ++++++++++++++    + +
1    MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF

                                    [2]              [1]
     e-14                           4.8e-07          2.3e-17
     QGRPNKEVHTCYTYWALAALAILNKLH    INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILN
     +  +++++++  +  ++++++ +++++    +++ +++++++ ++   + ++++  +++++++ +++++++++++
76   APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG

         [2]              [1]                                                [1]
         5.1e-07          1.4e-18                                            4.6
     KLH INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH                     GGF
     +++ ++++ ++++++++    ++++  ++++++++++++++++++++++++                     +++
151  ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL

                                 [2]               [1]
     e-22                        2.0e-13           3.8e-17
     QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNKL
     ++++ ++++++++++++++++++++++ ++ +++++++++++    ++++++++++++++++ ++++++++++ +
226  NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD

     
     
     H
     +
301  NLVPIDPIYCMPKSVTSKFKKYPYK



RATRABGERB
S D ?

Rat rab geranylgeranyl transferase beta-subunit
LENGTH = 331 COMBINED P-VALUE = 2.83e-26 E-VALUE = 1.4e-25
DIAGRAM: 65-[2]-3-[1]-1-[2]-3-[1]-1-[2]-3-[1]-18-[1]-1-[2]-4-[1]-26
                                                                      [2]
                                                                      1.0e-11
                                                                      INKEKLIQWI
                                                                      +++++++ ++
1    MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFI

            [1]                            [2]              [1]
            1.6e-14                        1.4e-09          5.4e-19
     KSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWAL
     ++++   ++ +  +++++++ ++  ++++++++++++ +++++++ ++++++   + ++++++++++++++++++
76   KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV

                [2]              [1]
                3.8e-12          4.8e-19
     AALAILNKLH INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH
     ++++++++++ ++++++++++++++   ++++++++ ++++++++++++ ++++++++
151  ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP

      [1]                            [2]               [1]
      3.9e-21                        1.2e-12           9.6e-18
      GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAI
      +++++++++++++++++++++++ ++++++ ++++++++++++++    ++++++++++++ +++ ++++++++
226  SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL

     
     
     LNKLH
     +++++
301  LGEEQIKPVSPVFCMPEEVLQRVNVQPELVS



CAL1_YEAST
S D ?

RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
LENGTH = 376 COMBINED P-VALUE = 1.94e-22 E-VALUE = 9.7e-22
DIAGRAM: 125-[2]-50-[2]-1-[1]-4-[2]-22-[1]-22-[1]-5-[2]-1

                                                       [2]
                                                       1.8e-08
                                                       INKEKLIQWIKSCQ
                                                        +++++++++++++
76   LDDTENTVISGFVGSLVMNIPHATTINLPNTLFALLSMIMLRDYEYFETILDKRSLARFVSKCQRPDRGSFVSCL

                                            [2]            [1]
                                            4.8e-10        8.7e-14
                                            INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALA
                                            +++++++ ++++++  + + + +++++ +++ ++++
151  DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS

                  [2]                                 [1]
                  5.9e-08                             5.9e-20
     ALAILNKLH    INKEKLIQWIKSCQ                      GGFQGRPNKEVHTCYTYWALAALAIL
     +++++++++      ++++++++++++                      +++++++++ +++++++++++++ ++
226  TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL

                               [1]                                [2]
                               4.0e-13                            2.1e-07
     NKLH                      GGFQGRPNKEVHTCYTYWALAALAILNKLH     INKEKLIQWIKSCQ
     ++++                      ++++ + ++++++++++ + +++++++        + ++ +++++++++
301  TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC



PFTB_RAT
S D ?

PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
LENGTH = 437 COMBINED P-VALUE = 1.53e-21 E-VALUE = 7.6e-21
DIAGRAM: 120-[2]-3-[1]-4-[2]-3-[1]-1-[2]-3-[1]-1-[2]-4-[1]-14-[2]-4-[1]-60

                                                  [2]              [1]
                                                  1.3e-07          2.8e-19
                                                  INKEKLIQWIKSCQ   GGFQGRPNKEVHT
                                                  ++ ++++++++ ++   +++++++++ +++
76   EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL

                          [2]              [1]                            [2]
                          2.3e-09          2.1e-14                        1.8e-0
     CYTYWALAALAILNKLH    INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKL
     + +++++++++++++++    ++++++++++ +++   + + ++ +++++++ +++++++++++++++ +  +++
151  APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT

                [1]                            [2]               [1]
     8          7.4e-20                        1.8e-08           2.2e-16
     IQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCY
     ++++ +++   +++++ +++++++++++++++++ ++++++  + +++++++++++    ++++++ ++++++++
226  AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY

                                  [2]               [1]
                                  5.0e-08           3.1e-15
     TYWALAALAILNKLH              INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNK
     ++++++ + ++++                ++++++++++++++    +++ +++++  +++++++++++++++++
301  SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH

     
     
     LH
     +
376  FGSGAMLHDVVMGVPENVLQPTHPVYNIGPDKVIQATTHFLQKPVPGFEECEDAVTSDPATD



RAM1_YEAST
S D ?

PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
LENGTH = 431 COMBINED P-VALUE = 1.24e-20 E-VALUE = 6.2e-20
DIAGRAM: 144-[1]-5-[2]-4-[1]-1-[2]-4-[1]-1-[2]-4-[1]-4-[2]-5-[1]-35-[2]-4

                                                                          [1]
                                                                          8.8e-1
                                                                          GGFQGR
                                                                          + ++++
76   PALTKEFHKMYLDVAFEISLPPQMTALDASQPWMLYWIANSLKVMDRDWLSDDTKRKIVVKLFTISPSGGPFGGG

                                  [2]               [1]
     7                            6.4e-07           1.0e-13
     PNKEVHTCYTYWALAALAILNKLH     INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNK
     ++++++++ ++++++++++ ++++     ++++++++++ +++    +  ++ ++++++++ +++++++++++++
151  PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI

        [2]               [1]                            [2]               [1]
        2.5e-08           3.1e-17                        4.7e-11           2.4e-
     LH INKEKLIQWIKSCQ    GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGFQG
     ++ + ++++++++++++    +  ++  +++++++++++++++++++++++ ++++++++++++++     ++ +
226  LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG

                                  [2]                [1]
     16                           4.9e-09            2.7e-13
     RPNKEVHTCYTYWALAALAILNKLH    INKEKLIQWIKSCQ     GGFQGRPNKEVHTCYTYWALAALAILN
     + ++++++++++++ +++++++++     +++++++++++ ++      +++++++++++++++ +++ ++++++
301  RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE

                                           [2]
                                           9.8e-05
     KLH                                   INKEKLIQWIKSCQ
     +                                     +++++++ + +++
376  SSYSCTPNDSPHNIKCTPDRLIGSSKLTDVNPVYGLPIENVRKIIHYFKSNLSSPS

Debugging Information




CPU: chromo
Time 0.030000 secs.

mast meme.farntrans5.tcm.4.Linuxx86_64.html -stdout

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E
Links to Entrez database at NCBI
S
Links to sequence scores (section I)
D
Links to motif diagrams (section II)
A
Links to sequence/motif annotated alignments (section III)
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