Query 032553
Match_columns 138
No_of_seqs 110 out of 195
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 02:56:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4279 Uncharacterized conser 98.3 4.3E-07 9.3E-12 75.8 2.5 54 58-111 116-172 (266)
2 PF04434 SWIM: SWIM zinc finge 98.1 1.5E-06 3.3E-11 52.3 2.5 30 58-87 1-39 (40)
3 COG4715 Uncharacterized conser 96.5 0.0024 5.1E-08 58.7 3.8 46 47-92 51-100 (587)
4 COG5431 Uncharacterized metal- 94.7 0.026 5.7E-07 42.2 2.6 33 47-83 35-75 (117)
5 smart00575 ZnF_PMZ plant mutat 90.5 0.15 3.2E-06 28.8 1.1 20 67-86 2-24 (28)
6 PLN03097 FHY3 Protein FAR-RED 86.8 1.2 2.7E-05 42.9 5.3 47 47-93 556-611 (846)
7 KOG3908 Queuine-tRNA ribosyltr 24.7 51 0.0011 29.2 1.9 50 57-110 298-356 (396)
8 PHA03099 epidermal growth fact 24.3 44 0.00096 25.9 1.3 23 58-81 60-84 (139)
9 PF12662 cEGF: Complement Clr- 24.0 39 0.00084 18.6 0.7 6 67-72 3-8 (24)
10 PF12661 hEGF: Human growth fa 20.9 25 0.00055 16.6 -0.4 11 67-77 1-13 (13)
11 PF15032 DUF4529: Protein of u 20.5 48 0.001 29.7 0.9 15 64-78 25-43 (400)
No 1
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=98.27 E-value=4.3e-07 Score=75.83 Aligned_cols=54 Identities=30% Similarity=0.546 Sum_probs=44.2
Q ss_pred EEEEcCC-CCcccCCCCCCCceehhHHHHHHh-cCCCCchhhhhccCCHHH-HHHhh
Q 032553 58 YTVNLSS-NPSCTCPDRVTPCKHILFVFMRVL-GVSPDDKCLRRRTLRPCQ-LSRLL 111 (138)
Q Consensus 58 Y~V~Ig~-~psCtCpd~g~~CKHI~~VllkVL-~~p~~~~l~~Q~aL~~~E-l~~il 111 (138)
|.-++++ ...|||||+.|.||||.-|++.+- ++++|..++|++..++.| |..+|
T Consensus 116 fP~t~~dl~~dCSCPD~anPCKHi~AvyY~lae~f~~dPflif~lRG~~k~eL~a~l 172 (266)
T COG4279 116 FPFTLRDLSTDCSCPDYANPCKHIAAVYYLLAEKFDEDPFLIFKLRGRNKEELLALL 172 (266)
T ss_pred CCCchhhcccccCCCCcccchHHHHHHHHHHHHHhccCCeeeeeecCCCHHHHHHHH
Confidence 4444333 457999999999999999999985 789999999999888754 87777
No 2
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 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 the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.15 E-value=1.5e-06 Score=52.29 Aligned_cols=30 Identities=43% Similarity=0.993 Sum_probs=24.5
Q ss_pred EEEEcCC------CCcccCCC---CCCCceehhHHHHHH
Q 032553 58 YTVNLSS------NPSCTCPD---RVTPCKHILFVFMRV 87 (138)
Q Consensus 58 Y~V~Ig~------~psCtCpd---~g~~CKHI~~VllkV 87 (138)
|+|+|+. ..+||||+ .+..||||+.|++.+
T Consensus 1 y~V~i~~~~~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 1 YQVTIDDERVSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred CEEEEcCCcccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 5666653 68999998 689999999999864
No 3
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=96.55 E-value=0.0024 Score=58.67 Aligned_cols=46 Identities=28% Similarity=0.465 Sum_probs=38.5
Q ss_pred eeEEeccCCCeEEEEc-CC--CCcccCCC-CCCCceehhHHHHHHhcCCC
Q 032553 47 LFFVLGATANVYTVNL-SS--NPSCTCPD-RVTPCKHILFVFMRVLGVSP 92 (138)
Q Consensus 47 ~f~V~gstgnvY~V~I-g~--~psCtCpd-~g~~CKHI~~VllkVL~~p~ 92 (138)
.-.|.|+-+--|.|++ ++ .++||||- ...-|||+.-|++..+..|.
T Consensus 51 ~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~~~~gaCKH~VAvvl~~~~~p~ 100 (587)
T COG4715 51 RAVVEGSRRYRVRVTLEGGALSSICTCPYGGSGACKHVVAVVLEYLDDPE 100 (587)
T ss_pred EEEEeccceeeEEEEeecCCcCceeeCCCCCCcchHHHHHHHHHHhhccc
Confidence 5567788887789999 33 89999996 67899999999999998874
No 4
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=94.73 E-value=0.026 Score=42.17 Aligned_cols=33 Identities=33% Similarity=0.858 Sum_probs=23.8
Q ss_pred eeEEeccCCCeEEEEcCCCCcccCCC-------CCC-CceehhHH
Q 032553 47 LFFVLGATANVYTVNLSSNPSCTCPD-------RVT-PCKHILFV 83 (138)
Q Consensus 47 ~f~V~gstgnvY~V~Ig~~psCtCpd-------~g~-~CKHI~~V 83 (138)
.|.++|.+-+ |-+..| -||||| +|. .|+||+-+
T Consensus 35 ~fVyvG~~rd-YIl~~g---fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 35 FFVYVGKERD-YILEGG---FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred EEEEEccccc-eEEEcC---cccCHHHHhHhhhcCcccchhhhhe
Confidence 5666676544 888776 799999 343 49999753
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=90.45 E-value=0.15 Score=28.80 Aligned_cols=20 Identities=30% Similarity=0.851 Sum_probs=17.4
Q ss_pred cccCCC---CCCCceehhHHHHH
Q 032553 67 SCTCPD---RVTPCKHILFVFMR 86 (138)
Q Consensus 67 sCtCpd---~g~~CKHI~~Vllk 86 (138)
+|||.. .|-+|.|++.|+..
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~ 24 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIH 24 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHH
Confidence 799998 68999999999864
No 6
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=86.75 E-value=1.2 Score=42.92 Aligned_cols=47 Identities=23% Similarity=0.424 Sum_probs=34.3
Q ss_pred eeEEeccCC-CeEEEEcCC---CCcccCCC---CCCCceehhHHHH--HHhcCCCC
Q 032553 47 LFFVLGATA-NVYTVNLSS---NPSCTCPD---RVTPCKHILFVFM--RVLGVSPD 93 (138)
Q Consensus 47 ~f~V~gstg-nvY~V~Ig~---~psCtCpd---~g~~CKHI~~Vll--kVL~~p~~ 93 (138)
+|.|....+ ..|+|+.+. .-+|+|.- .|-+|.||+-||. .|..+|..
T Consensus 556 ~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~ 611 (846)
T PLN03097 556 TFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQ 611 (846)
T ss_pred EEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchh
Confidence 666765433 358887654 57999998 7999999999887 44666764
No 7
>KOG3908 consensus Queuine-tRNA ribosyltransferase [RNA processing and modification]
Probab=24.71 E-value=51 Score=29.16 Aligned_cols=50 Identities=16% Similarity=0.351 Sum_probs=34.2
Q ss_pred eEEEEcCC-CCcccCCCCCCCceehhHHHHHHhcCCCC--------chhhhhccCCHHHHHHh
Q 032553 57 VYTVNLSS-NPSCTCPDRVTPCKHILFVFMRVLGVSPD--------DKCLRRRTLRPCQLSRL 110 (138)
Q Consensus 57 vY~V~Ig~-~psCtCpd~g~~CKHI~~VllkVL~~p~~--------~~l~~Q~aL~~~El~~i 110 (138)
+|+-.++. .++|+||. ||-+...++.-|.-.+. +.+.||+.|..+--+.|
T Consensus 298 k~k~D~~pid~~C~C~t----C~~ytRaylh~l~~~etv~~~lltiHNi~yql~Lmr~vResI 356 (396)
T KOG3908|consen 298 KYKSDFGPIDETCGCPT----CKKYTRAYLHALVGKETVGCHLLTIHNIAYQLQLMRDVRESI 356 (396)
T ss_pred hhhhcccCCCCCCCCch----hhhHHHHHHHHHccccccceeeeehhhHHHHHHHHHHHHHHH
Confidence 57777776 78999996 88777777766543322 35789999986543333
No 8
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=24.34 E-value=44 Score=25.89 Aligned_cols=23 Identities=17% Similarity=0.587 Sum_probs=18.0
Q ss_pred EEEEcCCCCcccCCC--CCCCceehh
Q 032553 58 YTVNLSSNPSCTCPD--RVTPCKHIL 81 (138)
Q Consensus 58 Y~V~Ig~~psCtCpd--~g~~CKHI~ 81 (138)
|-+.++. +.|.|+. -|+.|-|.-
T Consensus 60 yI~dl~~-~~CrC~~GYtGeRCEh~d 84 (139)
T PHA03099 60 HARDIDG-MYCRCSHGYTGIRCQHVV 84 (139)
T ss_pred eeccCCC-ceeECCCCccccccccee
Confidence 4455544 9999999 799999974
No 9
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=24.00 E-value=39 Score=18.58 Aligned_cols=6 Identities=50% Similarity=1.824 Sum_probs=5.0
Q ss_pred cccCCC
Q 032553 67 SCTCPD 72 (138)
Q Consensus 67 sCtCpd 72 (138)
+|+|+.
T Consensus 3 ~C~C~~ 8 (24)
T PF12662_consen 3 TCSCPP 8 (24)
T ss_pred EeeCCC
Confidence 688987
No 10
>PF12661 hEGF: Human growth factor-like EGF; PDB: 2YGQ_A 2E26_A 3A7Q_A 2YGP_A 2YGO_A 1HRE_A 1HAE_A 1HAF_A 1HRF_A.
Probab=20.93 E-value=25 Score=16.58 Aligned_cols=11 Identities=36% Similarity=1.168 Sum_probs=6.1
Q ss_pred cccCCC--CCCCc
Q 032553 67 SCTCPD--RVTPC 77 (138)
Q Consensus 67 sCtCpd--~g~~C 77 (138)
+|.|+. .|..|
T Consensus 1 ~C~C~~G~~G~~C 13 (13)
T PF12661_consen 1 TCQCPPGWTGPNC 13 (13)
T ss_dssp EEEE-TTEETTTT
T ss_pred CccCcCCCcCCCC
Confidence 477877 45554
No 11
>PF15032 DUF4529: Protein of unknown function (DUF4529)
Probab=20.47 E-value=48 Score=29.71 Aligned_cols=15 Identities=40% Similarity=1.032 Sum_probs=10.8
Q ss_pred CCCcccCCC----CCCCce
Q 032553 64 SNPSCTCPD----RVTPCK 78 (138)
Q Consensus 64 ~~psCtCpd----~g~~CK 78 (138)
..++||||| +++.|-
T Consensus 25 te~t~tcpdErsEknHV~c 43 (400)
T PF15032_consen 25 TELTCTCPDERSEKNHVCC 43 (400)
T ss_pred ccccccCCcccccccceEE
Confidence 369999999 555553
Done!