Query psy3929
Match_columns 120
No_of_seqs 72 out of 74
Neff 2.9
Searched_HMMs 46136
Date Fri Aug 16 20:58:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3929.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3929hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3541|consensus 99.5 1.6E-14 3.4E-19 126.1 2.1 88 29-116 15-107 (477)
2 smart00229 RasGEFN Guanine nuc 99.2 2.4E-11 5.3E-16 84.5 4.4 55 37-92 2-56 (127)
3 PF00618 RasGEF_N: RasGEF N-te 99.1 6E-11 1.3E-15 80.3 2.7 50 40-90 2-51 (104)
4 cd06224 REM Guanine nucleotide 98.7 2E-08 4.4E-13 68.4 5.2 49 44-93 1-49 (122)
5 KOG3541|consensus 97.9 1.1E-05 2.5E-10 71.3 4.2 60 28-87 179-238 (477)
6 KOG3629|consensus 96.4 0.012 2.6E-07 54.4 7.1 54 37-91 64-117 (728)
7 KOG3542|consensus 84.9 0.82 1.8E-05 44.3 3.0 47 40-87 424-471 (1283)
8 KOG2378|consensus 58.8 13 0.00028 34.4 3.8 54 39-92 69-126 (573)
9 PF04520 Senescence_reg: Senes 42.6 13 0.00028 28.5 1.1 13 72-84 104-116 (152)
10 PF15008 DUF4518: Domain of un 26.3 89 0.0019 26.3 3.5 37 60-96 61-101 (262)
11 KOG1752|consensus 23.9 76 0.0016 22.8 2.4 48 3-51 40-87 (104)
No 1
>KOG3541|consensus
Probab=99.46 E-value=1.6e-14 Score=126.05 Aligned_cols=88 Identities=28% Similarity=0.233 Sum_probs=78.8
Q ss_pred CCcceeeecCCCCCcCHHHHHHHHccCCCCCccH--HHHHHHHhhccCccChHHHHHHHHHHHHHHhhhcCCCCcchHHH
Q psy3929 29 RSWALVYREGHLVSGTLDALIQHIVPTIDYYPDR--AYLFAFLLSSRLFIKPHELLGRVIALCDVQQKLTDKTPHGKKEL 106 (120)
Q Consensus 29 ~~~~LvY~dg~lvSGsLeaLI~hLvPT~dyypD~--syiFaFLLssRLFI~PhELL~kv~q~C~~qq~~~~~~~~~dk~~ 106 (120)
+++....++|...|||.|+++.|||||+|++||+ .|||+++.++|.|++||++|++|.|.|+.+.+....+..+-+++
T Consensus 15 ~~~~~~~~~g~~~sgsrda~~~hlvptrd~~~dr~~c~I~S~~~ssd~~~~p~d~la~vgq~~i~~ke~~~~g~~~l~aa 94 (477)
T KOG3541|consen 15 CGTRCKQTVGQKSSGSRDADKCHLVPTRDRRPDRRRCYIFSNLSSSDSFSAPHDLLAEVGQSGIDSKEALAGGGAGLQAA 94 (477)
T ss_pred cCcccccccccccccccccchhhcCCccccCCccceeecccccccccccCCcHHHHHHHHhcccCchhhhcCCCcchhhh
Confidence 4566777899999999999999999999999999 99999999999999999999999999999887776665557888
Q ss_pred hhhhh---hhhhh
Q psy3929 107 IRKYK---YNLKF 116 (120)
Q Consensus 107 ~~~~~---~ki~q 116 (120)
+..+. |..+|
T Consensus 95 ~~~~f~l~a~~hq 107 (477)
T KOG3541|consen 95 QGGIFSLDAGHHQ 107 (477)
T ss_pred hhhhhccCChHHH
Confidence 88877 77777
No 2
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=99.18 E-value=2.4e-11 Score=84.49 Aligned_cols=55 Identities=33% Similarity=0.525 Sum_probs=50.3
Q ss_pred cCCCCCcCHHHHHHHHccCCCCCccHHHHHHHHhhccCccChHHHHHHHHHHHHHH
Q psy3929 37 EGHLVSGTLDALIQHIVPTIDYYPDRAYLFAFLLSSRLFIKPHELLGRVIALCDVQ 92 (120)
Q Consensus 37 dg~lvSGsLeaLI~hLvPT~dyypD~syiFaFLLssRLFI~PhELL~kv~q~C~~q 92 (120)
+|.+.+||+++||+||+++.++ +|.+|+.+||++.|.|++|++|+.++++.+...
T Consensus 2 ~~~i~~gtl~~Li~~L~~~~~~-~d~~f~~~Flltyr~F~tp~~ll~~L~~rf~~~ 56 (127)
T smart00229 2 GGLIKGGTLEKLIEHLTEAFDK-ADPFFVETFLLTYRSFITTQELLQLLLYRYNAI 56 (127)
T ss_pred CCeeeeecHHHHHHHHcCCCcC-CCHHHHHHHHHHhhhhCCHHHHHHHHHHHhCCC
Confidence 5788999999999999998664 789999999999999999999999999988753
No 3
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=99.08 E-value=6e-11 Score=80.26 Aligned_cols=50 Identities=32% Similarity=0.603 Sum_probs=42.7
Q ss_pred CCCcCHHHHHHHHccCCCCCccHHHHHHHHhhccCccChHHHHHHHHHHHH
Q psy3929 40 LVSGTLDALIQHIVPTIDYYPDRAYLFAFLLSSRLFIKPHELLGRVIALCD 90 (120)
Q Consensus 40 lvSGsLeaLI~hLvPT~dyypD~syiFaFLLssRLFI~PhELL~kv~q~C~ 90 (120)
+++|||++||++|++..+.. |..|+.+||++.|.|++|.|||.++.+.|+
T Consensus 2 I~~gtl~~Li~~L~~~~~~~-d~~f~~~FllTyr~F~tp~~Ll~~L~~ry~ 51 (104)
T PF00618_consen 2 IKAGTLEKLIERLTSSFNSD-DEEFVDTFLLTYRSFTTPEELLDKLIQRYN 51 (104)
T ss_dssp EEEE-HHHHHHHHCHC-SS--HHHHHHHHHHHHHHCS-HHHHHHHHHHHHT
T ss_pred eeeeCHHHHHHHHhcccccC-CHHHHHHHHHHhHhhCCHHHHHHHHHHHhc
Confidence 57999999999999985544 669999999999999999999999999996
No 4
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=98.73 E-value=2e-08 Score=68.39 Aligned_cols=49 Identities=41% Similarity=0.739 Sum_probs=45.0
Q ss_pred CHHHHHHHHccCCCCCccHHHHHHHHhhccCccChHHHHHHHHHHHHHHh
Q psy3929 44 TLDALIQHIVPTIDYYPDRAYLFAFLLSSRLFIKPHELLGRVIALCDVQQ 93 (120)
Q Consensus 44 sLeaLI~hLvPT~dyypD~syiFaFLLssRLFI~PhELL~kv~q~C~~qq 93 (120)
|+++||++|+++.+ .+|.+|+.+||++.|.|++|.+||+++.+.+....
T Consensus 1 tl~~Li~~L~~~~~-~~d~~f~~~FllTyrsF~s~~~ll~~L~~rf~~~~ 49 (122)
T cd06224 1 TLEALIEHLTSTFD-MPDPSFVSTFLLTYRSFTTPTELLEKLIERYEIAP 49 (122)
T ss_pred CHHHHHHHHcCCCc-cccHHHHHHHHHHhhhhCCHHHHHHHHHHHhCCCC
Confidence 68999999999877 68999999999999999999999999999998643
No 5
>KOG3541|consensus
Probab=97.90 E-value=1.1e-05 Score=71.27 Aligned_cols=60 Identities=32% Similarity=0.388 Sum_probs=57.5
Q ss_pred cCCcceeeecCCCCCcCHHHHHHHHccCCCCCccHHHHHHHHhhccCccChHHHHHHHHH
Q psy3929 28 RRSWALVYREGHLVSGTLDALIQHIVPTIDYYPDRAYLFAFLLSSRLFIKPHELLGRVIA 87 (120)
Q Consensus 28 ~~~~~LvY~dg~lvSGsLeaLI~hLvPT~dyypD~syiFaFLLssRLFI~PhELL~kv~q 87 (120)
.++++++|++|.+++|+|+++++-|+|.-....|.++.|+|+.+.|+|+.|||.|.++++
T Consensus 179 ~~~~~a~~q~~i~~~kpl~a~~~~ll~~c~dal~laqqlt~Ie~~rls~i~~EelvqiL~ 238 (477)
T KOG3541|consen 179 LGSGGAMYQNGIIVSKPLAALIETLLPKCVDALDLAQQLTHIESCRLSLIPHEELVQILD 238 (477)
T ss_pred hcCCcccccccccccCCchHHHhhhhhccccHHHHHHHHHHHHHHHHhccCHHHHHHHHh
Confidence 468999999999999999999999999999999999999999999999999999999986
No 6
>KOG3629|consensus
Probab=96.36 E-value=0.012 Score=54.41 Aligned_cols=54 Identities=22% Similarity=0.322 Sum_probs=49.3
Q ss_pred cCCCCCcCHHHHHHHHccCCCCCccHHHHHHHHhhccCccChHHHHHHHHHHHHH
Q psy3929 37 EGHLVSGTLDALIQHIVPTIDYYPDRAYLFAFLLSSRLFIKPHELLGRVIALCDV 91 (120)
Q Consensus 37 dg~lvSGsLeaLI~hLvPT~dyypD~syiFaFLLssRLFI~PhELL~kv~q~C~~ 91 (120)
...+.+||||+|++||+- .+...|.+|+-.||.+.|-|.+..++|.-+++.-..
T Consensus 64 ~r~ikAGTlE~LVe~Ll~-~~~~~D~~~~svFlaTyR~Ftst~~vL~llldRye~ 117 (728)
T KOG3629|consen 64 ERLIKAGTLERLVECLLG-SDDMMDSRHFSVFLATYRSFTSTAIVLDLLLDRYEL 117 (728)
T ss_pred hhhhhcchHHHHHHHHhc-CCCCcchhHHHHHHHHhhcccccHHHHHHHHHHHHh
Confidence 467889999999999998 777999999999999999999999999999987664
No 7
>KOG3542|consensus
Probab=84.90 E-value=0.82 Score=44.29 Aligned_cols=47 Identities=30% Similarity=0.568 Sum_probs=40.0
Q ss_pred CCCcCHHHHHHHHccCCCCCccHHHHHHHHhhccCccC-hHHHHHHHHH
Q psy3929 40 LVSGTLDALIQHIVPTIDYYPDRAYLFAFLLSSRLFIK-PHELLGRVIA 87 (120)
Q Consensus 40 lvSGsLeaLI~hLvPT~dyypD~syiFaFLLssRLFI~-PhELL~kv~q 87 (120)
++.|+-|.||-|||--++ -.|-+||=.|||+.|.|++ |-+.-.|+..
T Consensus 424 vIKgtperLimHLveEhs-~VDPtyieDFLLTYRtFl~sP~~vg~KLle 471 (1283)
T KOG3542|consen 424 VIKGTPERLIMHLVEEHS-NVDPTYIEDFLLTYRTFLRSPTTVGEKLLE 471 (1283)
T ss_pred EEecChHHHHHHHHhhcc-cCCchHHHHHHHHHHHHhcChHHHHHHHHH
Confidence 468999999999999988 7899999999999999996 6666556554
No 8
>KOG2378|consensus
Probab=58.79 E-value=13 Score=34.43 Aligned_cols=54 Identities=19% Similarity=0.364 Sum_probs=43.6
Q ss_pred CCCCcCHHHHHHHHccCCCC----CccHHHHHHHHhhccCccChHHHHHHHHHHHHHH
Q psy3929 39 HLVSGTLDALIQHIVPTIDY----YPDRAYLFAFLLSSRLFIKPHELLGRVIALCDVQ 92 (120)
Q Consensus 39 ~lvSGsLeaLI~hLvPT~dy----ypD~syiFaFLLssRLFI~PhELL~kv~q~C~~q 92 (120)
..+||+-|-.++||+-|+-. ++-.+|+=.|+|+.+.|++-..|-+-+...-+.+
T Consensus 69 tVmsGtpEKILE~lLe~~lda~~dd~tdt~l~DFilth~vFMp~~~lC~aL~~hy~~~ 126 (573)
T KOG2378|consen 69 TVMSGTPEKILEHLLETRLDALGDDITDTFLEDFILTHDVFMPDNQLCNALLSHYHAT 126 (573)
T ss_pred EEecCCHHHHHHHHHhhchhhhccchHHHHHHHHHHHhhhccCcHHHHHHHHHHhccC
Confidence 46999999999999977422 4556799999999999999988877777666643
No 9
>PF04520 Senescence_reg: Senescence regulator; InterPro: IPR007608 This family contains several uncharacterised proteins.
Probab=42.56 E-value=13 Score=28.52 Aligned_cols=13 Identities=38% Similarity=0.741 Sum_probs=11.3
Q ss_pred ccCccChHHHHHH
Q psy3929 72 SRLFIKPHELLGR 84 (120)
Q Consensus 72 sRLFI~PhELL~k 84 (120)
..-+++||||+++
T Consensus 104 ~~~~vPPHe~~ar 116 (152)
T PF04520_consen 104 GGEMVPPHELVAR 116 (152)
T ss_pred CccccCcHHHHhh
Confidence 4569999999999
No 10
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=26.26 E-value=89 Score=26.30 Aligned_cols=37 Identities=27% Similarity=0.501 Sum_probs=32.0
Q ss_pred ccHHHHHHHHhhccCccCh----HHHHHHHHHHHHHHhhhc
Q psy3929 60 PDRAYLFAFLLSSRLFIKP----HELLGRVIALCDVQQKLT 96 (120)
Q Consensus 60 pD~syiFaFLLssRLFI~P----hELL~kv~q~C~~qq~~~ 96 (120)
.-|+.||.+|-+=...++| |.|..++.+.|..|.+..
T Consensus 61 V~RelLFkYLa~kgv~v~p~s~K~~LI~~~l~~W~~~~~~~ 101 (262)
T PF15008_consen 61 VKRELLFKYLASKGVIVPPDSEKADLIQRVLQYWSSQLQQS 101 (262)
T ss_pred ccHHHHHHHHHHcCCCCCCCccHHHHHHHHHHHHhcccccc
Confidence 4578999999999999999 789999999998876653
No 11
>KOG1752|consensus
Probab=23.86 E-value=76 Score=22.82 Aligned_cols=48 Identities=19% Similarity=0.385 Sum_probs=29.0
Q ss_pred hhHHHHhccccchHHHHHHHHhhhhcCCcceeeecCCCCCcCHHHHHHH
Q psy3929 3 TPYIIRLVKEEEDEEENERKRRRRRRRSWALVYREGHLVSGTLDALIQH 51 (120)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LvY~dg~lvSGsLeaLI~h 51 (120)
.|.++.|-+.++..|-...-.+--....-+-+|.+|+.+ |..+.|+..
T Consensus 40 ~~~vvELD~~~~g~eiq~~l~~~tg~~tvP~vFI~Gk~i-GG~~dl~~l 87 (104)
T KOG1752|consen 40 NPKVVELDEDEDGSEIQKALKKLTGQRTVPNVFIGGKFI-GGASDLMAL 87 (104)
T ss_pred CCEEEEccCCCCcHHHHHHHHHhcCCCCCCEEEECCEEE-cCHHHHHHH
Confidence 456666666554433322222223334678899999999 777777654
Done!