Query psy10364
Match_columns 129
No_of_seqs 60 out of 62
Neff 2.2
Searched_HMMs 46136
Date Fri Aug 16 16:00:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10364.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10364hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2494|consensus 99.7 6.6E-19 1.4E-23 149.2 4.0 59 11-71 70-131 (331)
2 KOG2494|consensus 99.3 1.3E-12 2.8E-17 111.2 2.0 82 10-114 229-310 (331)
3 PF00642 zf-CCCH: Zinc finger 93.1 0.026 5.7E-07 31.8 0.0 22 13-36 4-27 (27)
4 smart00356 ZnF_C3H1 zinc finge 89.0 0.24 5.1E-06 26.3 1.2 23 13-36 5-27 (27)
5 PF10650 zf-C3H1: Putative zin 55.5 5.6 0.00012 22.8 0.7 19 14-34 2-21 (23)
6 PF14608 zf-CCCH_2: Zinc finge 49.8 9.1 0.0002 20.3 0.9 11 23-35 8-19 (19)
7 KOG4709|consensus 46.9 7.3 0.00016 32.6 0.3 16 112-127 30-45 (217)
8 COG5175 MOT2 Transcriptional r 44.4 9.9 0.00021 34.6 0.8 30 10-41 200-230 (480)
9 KOG4791|consensus 42.4 8.4 0.00018 36.3 0.0 37 2-40 22-58 (667)
10 KOG1492|consensus 19.6 46 0.001 29.2 0.6 19 14-34 263-281 (377)
No 1
>KOG2494|consensus
Probab=99.75 E-value=6.6e-19 Score=149.16 Aligned_cols=59 Identities=53% Similarity=0.831 Sum_probs=50.8
Q ss_pred ccceeehhhcccccCCCCCceecCCChhhHHHHHhhhhhhhHHHH---HHHHhcCCCCCCCCcc
Q psy10364 11 TLNYGTFWILGRCNREKPPCKYFHPPQHLKDQLLINGRNHLALKN---ALLQQMGLTPGQPMVP 71 (129)
Q Consensus 11 ~~~~c~d~iKGRC~RekppCKYfHPP~HLk~qL~ingrnh~a~kn---a~aqqm~~~Pg~pm~~ 71 (129)
-.++|+||+||||+||+ |||+|||+|||+||+||||+++++|+ |.++|+...||+||..
T Consensus 70 ~v~aC~Ds~kgrCsR~n--CkylHpp~hlkdql~ingrn~l~lq~~~aA~~~q~~~~~g~Pi~~ 131 (331)
T KOG2494|consen 70 RVIACFDSQKGRCSREN--CKYLHPPQHLKDQLKINGRNNLILQKTAAAMLAQQMQGPGTPICS 131 (331)
T ss_pred eEEEEeccccCccCccc--ceecCCChhhhhhhhhcccccHHHHHHHHhhhcccccCCCccccc
Confidence 36789999999999999 99999999999999999999999988 4444444448887776
No 2
>KOG2494|consensus
Probab=99.27 E-value=1.3e-12 Score=111.17 Aligned_cols=82 Identities=26% Similarity=0.438 Sum_probs=62.0
Q ss_pred cccceeehhhcccccCCCCCceecCCChhhHHHHHhhhhhhhHHHHHHHHhcCCCCCCCCccCCccceecccCCCCcccc
Q psy10364 10 STLNYGTFWILGRCNREKPPCKYFHPPQHLKDQLLINGRNHLALKNALLQQMGLTPGQPMVPGQIPAVVSAAFYPHWILF 89 (129)
Q Consensus 10 ~~~~~c~d~iKGRC~RekppCKYfHPP~HLk~qL~ingrnh~a~kna~aqqm~~~Pg~pm~~gq~Pa~v~~a~~Ph~~L~ 89 (129)
.+.+.|++|++|||++|+ |||||+|.|++. +++..+++.+. .+++ ||. +-.+++ ..-
T Consensus 229 ~t~~~~~~~t~~~~~~en--~~~~~~~~h~~~--~~~aa~~~~~~-~l~a-----pga-l~~pkr------------~Al 285 (331)
T KOG2494|consen 229 NTVEVCLRYTKGRCETEN--CKYFHAPAHDQA--SAKAAQPRPNS-SLAA-----PGA-LPPPKR------------PAL 285 (331)
T ss_pred Ccchhccccccceechhc--ccccCchHHHHH--HHHHhhhccch-hhcC-----Ccc-CCCCCC------------CCC
Confidence 356789999999999999 999999999996 45666666555 2222 332 113332 345
Q ss_pred cCCCcccceeehhhhhhhhhhhhhh
Q psy10364 90 PTDDVASAIWRISCLKNLKSFESRN 114 (129)
Q Consensus 90 P~~n~aS~~~~~svlh~~~~~~~~~ 114 (129)
||+||+|++|||+|+||+|+|.+-+
T Consensus 286 eK~ngasavfnp~v~~~qQa~~~~q 310 (331)
T KOG2494|consen 286 PKTNGASAAFNPTVAQWQQAFPGLQ 310 (331)
T ss_pred CccCccchhcccchhhccccCchhh
Confidence 7999999999999999999998754
No 3
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=93.12 E-value=0.026 Score=31.79 Aligned_cols=22 Identities=27% Similarity=0.759 Sum_probs=16.0
Q ss_pred ceeehhhc-ccccC-CCCCceecCCC
Q psy10364 13 NYGTFWIL-GRCNR-EKPPCKYFHPP 36 (129)
Q Consensus 13 ~~c~d~iK-GRC~R-ekppCKYfHPP 36 (129)
..|.+|++ |.|.+ ++ |+|.|++
T Consensus 4 ~~C~~f~~~g~C~~G~~--C~f~H~~ 27 (27)
T PF00642_consen 4 KLCRFFMRTGTCPFGDK--CRFAHGE 27 (27)
T ss_dssp SB-HHHHHTS--TTGGG--SSSBSSG
T ss_pred ccChhhccCCccCCCCC--cCccCCC
Confidence 46888999 99999 66 9999985
No 4
>smart00356 ZnF_C3H1 zinc finger.
Probab=89.05 E-value=0.24 Score=26.31 Aligned_cols=23 Identities=30% Similarity=0.674 Sum_probs=19.1
Q ss_pred ceeehhhcccccCCCCCceecCCC
Q psy10364 13 NYGTFWILGRCNREKPPCKYFHPP 36 (129)
Q Consensus 13 ~~c~d~iKGRC~RekppCKYfHPP 36 (129)
.+|-+|..|.|.+.. -|+|.|.+
T Consensus 5 ~~C~~~~~g~C~~g~-~C~~~H~~ 27 (27)
T smart00356 5 ELCKFFKRGYCPYGD-RCKFAHPL 27 (27)
T ss_pred CcCcCccCCCCCCCC-CcCCCCcC
Confidence 478899999999864 59999974
No 5
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=55.50 E-value=5.6 Score=22.83 Aligned_cols=19 Identities=26% Similarity=0.723 Sum_probs=15.5
Q ss_pred eeehhhcc-cccCCCCCceecC
Q psy10364 14 YGTFWILG-RCNREKPPCKYFH 34 (129)
Q Consensus 14 ~c~d~iKG-RC~RekppCKYfH 34 (129)
+|..-+.| .|+.+. |.|-|
T Consensus 2 lC~yEl~Gg~Cnd~~--C~~QH 21 (23)
T PF10650_consen 2 LCPYELTGGVCNDPD--CEFQH 21 (23)
T ss_pred CCccccCCCeeCCCC--CCccc
Confidence 46666777 999999 99977
No 6
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=49.80 E-value=9.1 Score=20.26 Aligned_cols=11 Identities=36% Similarity=1.183 Sum_probs=9.3
Q ss_pred ccCC-CCCceecCC
Q psy10364 23 CNRE-KPPCKYFHP 35 (129)
Q Consensus 23 C~Re-kppCKYfHP 35 (129)
|..- + |.|.||
T Consensus 8 C~~~~~--C~f~HP 19 (19)
T PF14608_consen 8 CTNGDN--CPFSHP 19 (19)
T ss_pred CCCCCc--CccCCc
Confidence 7766 7 999998
No 7
>KOG4709|consensus
Probab=46.95 E-value=7.3 Score=32.59 Aligned_cols=16 Identities=56% Similarity=0.885 Sum_probs=13.4
Q ss_pred hhhHHHHhhhhhcccc
Q psy10364 112 SRNKEERKEELTGYHK 127 (129)
Q Consensus 112 ~~~~~~~~~~~~~~~~ 127 (129)
|-.+|.|++-||||||
T Consensus 30 sFDeekrkdylTGFHK 45 (217)
T KOG4709|consen 30 SFDEEKRKDYLTGFHK 45 (217)
T ss_pred eecHHHHHHHHHHHHH
Confidence 3468899999999997
No 8
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=44.44 E-value=9.9 Score=34.62 Aligned_cols=30 Identities=33% Similarity=0.644 Sum_probs=22.6
Q ss_pred cccceeehhhcc-cccCCCCCceecCCChhhHH
Q psy10364 10 STLNYGTFWILG-RCNREKPPCKYFHPPQHLKD 41 (129)
Q Consensus 10 ~~~~~c~d~iKG-RC~RekppCKYfHPP~HLk~ 41 (129)
.+--||.+||++ .|-.-. |+|||-|--=++
T Consensus 200 GTTKYCtsYLRn~~CpNp~--CMyLHEpg~e~D 230 (480)
T COG5175 200 GTTKYCTSYLRNAVCPNPD--CMYLHEPGPEKD 230 (480)
T ss_pred CchHHHHHHHcCCCCCCCC--eeeecCCCcccc
Confidence 355689999997 576655 999999965444
No 9
>KOG4791|consensus
Probab=42.42 E-value=8.4 Score=36.33 Aligned_cols=37 Identities=35% Similarity=0.627 Sum_probs=31.4
Q ss_pred cccccccccccceeehhhcccccCCCCCceecCCChhhH
Q psy10364 2 FRASTYYLSTLNYGTFWILGRCNREKPPCKYFHPPQHLK 40 (129)
Q Consensus 2 ~~~~~~~~~~~~~c~d~iKGRC~RekppCKYfHPP~HLk 40 (129)
||+----|.++++|.-|+-++|-|+. |.|=|-=.|++
T Consensus 22 ~rh~E~al~n~t~C~~w~~~~~C~k~--C~YRHSe~~~k 58 (667)
T KOG4791|consen 22 FRHCEAALGNETVCTLWQEGRCCRKV--CRYRHSEIDKK 58 (667)
T ss_pred chhhHHHhcCcchhhhhhhcCccccc--ccchhhHHhhh
Confidence 44444567889999999999999998 99999999988
No 10
>KOG1492|consensus
Probab=19.60 E-value=46 Score=29.20 Aligned_cols=19 Identities=37% Similarity=1.128 Sum_probs=12.2
Q ss_pred eeehhhcccccCCCCCceecC
Q psy10364 14 YGTFWILGRCNREKPPCKYFH 34 (129)
Q Consensus 14 ~c~d~iKGRC~RekppCKYfH 34 (129)
.|--||-|.|+.-+ |+|+|
T Consensus 263 acryfllgkcnnpn--cryvh 281 (377)
T KOG1492|consen 263 ACRYFLLGKCNNPN--CRYVH 281 (377)
T ss_pred hhhhhhhccCCCCC--ceEEE
Confidence 45556666666555 88876
Done!