Query 043638
Match_columns 198
No_of_seqs 132 out of 413
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 06:52:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043638.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043638hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00575 ZnF_PMZ plant mutat 99.3 3.7E-13 8.1E-18 76.7 2.1 28 111-138 1-28 (28)
2 PLN03097 FHY3 Protein FAR-RED 99.0 6.3E-10 1.4E-14 107.6 5.6 153 2-157 443-622 (846)
3 PF04434 SWIM: SWIM zinc finge 98.7 1.2E-08 2.7E-13 62.4 3.0 30 106-135 10-39 (40)
4 COG5431 Uncharacterized metal- 91.1 0.11 2.4E-06 38.3 1.3 59 97-157 38-103 (117)
5 COG4279 Uncharacterized conser 63.0 3.7 8E-05 35.0 1.1 24 110-136 124-147 (266)
6 PF00872 Transposase_mut: Tran 57.3 3.2 7E-05 37.2 -0.2 29 2-30 321-349 (381)
7 KOG0489 Transcription factor z 56.6 6.2 0.00013 33.6 1.4 35 23-57 179-213 (261)
8 COG4715 Uncharacterized conser 47.1 29 0.00062 33.0 4.2 38 97-136 54-96 (587)
9 KOG0487 Transcription factor A 45.7 6.3 0.00014 34.6 -0.3 35 23-57 255-289 (308)
10 PF08063 PADR1: PADR1 (NUC008) 39.9 12 0.00027 24.2 0.5 14 7-20 38-51 (55)
11 PF08788 NHR2: NHR2 domain lik 38.7 55 0.0012 22.0 3.4 26 25-50 12-42 (67)
12 KOG1466 Translation initiation 28.1 1.1E+02 0.0024 26.6 4.5 43 17-59 10-61 (313)
13 TIGR01323 nitrile_alph nitrile 23.3 37 0.0008 27.5 0.8 15 110-124 89-104 (185)
14 PF11098 Chlorosome_CsmC: Chlo 20.8 1.2E+02 0.0026 23.0 3.0 28 20-47 1-28 (139)
No 1
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=99.35 E-value=3.7e-13 Score=76.68 Aligned_cols=28 Identities=54% Similarity=0.904 Sum_probs=25.7
Q ss_pred ceeeccccccCCCCchhHHHHHHHhcCC
Q 043638 111 MTCSCRLWQLSGIPCEHACRCIHSWGDK 138 (198)
Q Consensus 111 ~tCtC~~wql~giPC~HaiAa~~~~~~~ 138 (198)
++|||++||++||||+|||||+...|++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~~ 28 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGLS 28 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCCC
Confidence 5899999999999999999999988763
No 2
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=98.97 E-value=6.3e-10 Score=107.61 Aligned_cols=153 Identities=15% Similarity=0.263 Sum_probs=87.1
Q ss_pred ccccCCCccccccccccchHHHHHHHHHhh--hCCcHHHHHHHHHHHHHHHHHHHH-Hhhhhcccc-------cCChhhh
Q 043638 2 WALFSMPQWVKSTEVTNSSSEQLRIWLSKF--LDLNVAQRYTTITRTIAEMFQRRY-LAGWEWVYD-------KITPAAR 71 (198)
Q Consensus 2 w~~s~~~~~~k~~~mt~N~aEsfN~~i~~~--R~lPI~~m~e~ir~~~~~~f~~Rr-~~a~~~~~~-------~l~p~~~ 71 (198)
||..=|..-.-.+..||..+||+|+.|++. +..+|..+++..-.-+-.+..+-- ....++... .+-..+.
T Consensus 443 WapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs 522 (846)
T PLN03097 443 WVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVS 522 (846)
T ss_pred hhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHH
Confidence 555555555556788999999999999984 445565555433222222111100 000111000 1111223
Q ss_pred hhhhhhhhhhcCCcee------ec---cCC-Ccce-EEe--CCeEEEEEcc----cceeeccccccCCCCchhHHHHHHH
Q 043638 72 QQIIQNVFQSDGWNVD------VP---SNN-AVSF-VSR--HGFVFEVNRE----LMTCSCRLWQLSGIPCEHACRCIHS 134 (198)
Q Consensus 72 ~~i~p~i~k~~~~~~~------V~---~~g-~~~f-V~~--~~~~~~VdL~----~~tCtC~~wql~giPC~HaiAa~~~ 134 (198)
+.++++|+++...++. +. ..| ...| |.+ ....|.|..+ .-+|+|++|+..||||+|||.|+..
T Consensus 523 ~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~ 602 (846)
T PLN03097 523 GVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQM 602 (846)
T ss_pred HHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhh
Confidence 4556666666544321 21 122 1257 775 3456777554 4599999999999999999999999
Q ss_pred hcCCccccccccccHHHHHHhhC
Q 043638 135 WGDKLDKHVHRLWSVDEYRSAYG 157 (198)
Q Consensus 135 ~~~~~~~~v~~~ys~~~~~~tY~ 157 (198)
.++.- |++.|-+..|.+-..
T Consensus 603 ~~v~~---IP~~YILkRWTKdAK 622 (846)
T PLN03097 603 CQLSA---IPSQYILKRWTKDAK 622 (846)
T ss_pred cCccc---Cchhhhhhhchhhhh
Confidence 98753 444444445544433
No 3
>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=98.70 E-value=1.2e-08 Score=62.43 Aligned_cols=30 Identities=33% Similarity=0.727 Sum_probs=27.6
Q ss_pred EEcccceeeccccccCCCCchhHHHHHHHh
Q 043638 106 VNRELMTCSCRLWQLSGIPCEHACRCIHSW 135 (198)
Q Consensus 106 VdL~~~tCtC~~wql~giPC~HaiAa~~~~ 135 (198)
+++...+|||+.|+..|.||.|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 778899999999999999999999998764
No 4
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=91.08 E-value=0.11 Score=38.32 Aligned_cols=59 Identities=15% Similarity=0.159 Sum_probs=38.9
Q ss_pred EEeCCeEEEEEcccceeecccccc----C-CCCchhHHHHHHHhcCCcccccccccc--HHHHHHhhC
Q 043638 97 VSRHGFVFEVNRELMTCSCRLWQL----S-GIPCEHACRCIHSWGDKLDKHVHRLWS--VDEYRSAYG 157 (198)
Q Consensus 97 V~~~~~~~~VdL~~~tCtC~~wql----~-giPC~HaiAa~~~~~~~~~~~v~~~ys--~~~~~~tY~ 157 (198)
+-+..+.|+++++ .|||..+-. - .-||.|.|+.=...-..-.++|+-||- .+-+...|+
T Consensus 38 yvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y~~d~~~Il~e~ys 103 (117)
T COG5431 38 YVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAYYVDYPDILREKYS 103 (117)
T ss_pred EEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEecccHHHHHHHHHh
Confidence 3456678998876 899987762 2 457999998755555566677766653 233444444
No 5
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=62.97 E-value=3.7 Score=34.99 Aligned_cols=24 Identities=25% Similarity=0.541 Sum_probs=19.2
Q ss_pred cceeeccccccCCCCchhHHHHHHHhc
Q 043638 110 LMTCSCRLWQLSGIPCEHACRCIHSWG 136 (198)
Q Consensus 110 ~~tCtC~~wql~giPC~HaiAa~~~~~ 136 (198)
.-.|||..|. .||.|+.|+....+
T Consensus 124 ~~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCcc---cchHHHHHHHHHHH
Confidence 3569998886 59999999987753
No 6
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=57.32 E-value=3.2 Score=37.22 Aligned_cols=29 Identities=14% Similarity=0.193 Sum_probs=24.2
Q ss_pred ccccCCCccccccccccchHHHHHHHHHh
Q 043638 2 WALFSMPQWVKSTEVTNSSSEQLRIWLSK 30 (198)
Q Consensus 2 w~~s~~~~~~k~~~mt~N~aEsfN~~i~~ 30 (198)
|+...||+--+..+-|||..|+||+.|+.
T Consensus 321 ~tf~~fP~~~~~~i~TTN~iEsln~~irr 349 (381)
T PF00872_consen 321 LTFLDFPPEHRRSIRTTNAIESLNKEIRR 349 (381)
T ss_pred cceeeecchhccccchhhhccccccchhh
Confidence 45667888777778899999999999986
No 7
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=56.61 E-value=6.2 Score=33.65 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=32.6
Q ss_pred HHHHHHHhhhCCcHHHHHHHHHHHHHHHHHHHHHh
Q 043638 23 QLRIWLSKFLDLNVAQRYTTITRTIAEMFQRRYLA 57 (198)
Q Consensus 23 sfN~~i~~~R~lPI~~m~e~ir~~~~~~f~~Rr~~ 57 (198)
.||..|...|..-|...|...=+++--||.+||.+
T Consensus 179 hfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK 213 (261)
T KOG0489|consen 179 HFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMK 213 (261)
T ss_pred ccccccchHHHHHHHhhcchhHHHHHHHHHHHHHH
Confidence 48999999999999999999999999999999975
No 8
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=47.10 E-value=29 Score=33.01 Aligned_cols=38 Identities=18% Similarity=0.400 Sum_probs=25.3
Q ss_pred EEe-CCeEEEEEcc----cceeeccccccCCCCchhHHHHHHHhc
Q 043638 97 VSR-HGFVFEVNRE----LMTCSCRLWQLSGIPCEHACRCIHSWG 136 (198)
Q Consensus 97 V~~-~~~~~~VdL~----~~tCtC~~wql~giPC~HaiAa~~~~~ 136 (198)
|.+ ....+.|.|. ..+|||.. . ..-=|.|++|++...-
T Consensus 54 V~Gs~~y~v~vtL~~~~~ss~CTCP~-~-~~gaCKH~VAvvl~~~ 96 (587)
T COG4715 54 VEGSRRYRVRVTLEGGALSSICTCPY-G-GSGACKHVVAVVLEYL 96 (587)
T ss_pred EeccceeeEEEEeecCCcCceeeCCC-C-CCcchHHHHHHHHHHh
Confidence 444 3345566663 56899987 2 2234999999988764
No 9
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=45.71 E-value=6.3 Score=34.62 Aligned_cols=35 Identities=17% Similarity=0.336 Sum_probs=30.6
Q ss_pred HHHHHHHhhhCCcHHHHHHHHHHHHHHHHHHHHHh
Q 043638 23 QLRIWLSKFLDLNVAQRYTTITRTIAEMFQRRYLA 57 (198)
Q Consensus 23 sfN~~i~~~R~lPI~~m~e~ir~~~~~~f~~Rr~~ 57 (198)
.||-.|..-|.+=|-.+|..+=+++--||++||.+
T Consensus 255 lfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK 289 (308)
T KOG0487|consen 255 LFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMK 289 (308)
T ss_pred HHHHHHhHHHHHHHHHhcccchhheeeeehhhhhH
Confidence 48888999999999899988889999999999876
No 10
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=39.92 E-value=12 Score=24.24 Aligned_cols=14 Identities=29% Similarity=0.598 Sum_probs=11.5
Q ss_pred CCccccccccccch
Q 043638 7 MPQWVKSTEVTNSS 20 (198)
Q Consensus 7 ~~~~~k~~~mt~N~ 20 (198)
+++|+||.+.|.+.
T Consensus 38 ~sewtkC~~~t~~p 51 (55)
T PF08063_consen 38 ISEWTKCTYSTKDP 51 (55)
T ss_dssp CCTTCEEEEEESS-
T ss_pred cCceeEcccCcCCC
Confidence 58999999998874
No 11
>PF08788 NHR2: NHR2 domain like; InterPro: IPR014896 Transcriptional activation and repression are required for control of cell proliferation and differentiation during embryonic development and homeostasis in the adult organism. Perturbations of these processes can lead to the development of cancer []. The Eight-Twenty-One (ETO) gene product is able to form complexes with corepressors and deacetylases, such as nuclear receptor corepressor (N-CoR), which repress transcription when recruited by transcription factors []. The ETO gene derives its name from its association with many cases of acute myelogenous leukaemia (AML), in which a reciprocal translocation, t(8;21), brings together a large portion of the ETO gene from chromosome eight and part of the AML1 gene from chromosome 21. The human ETO gene family currently comprises three major subfamilies: ETO/myeloid transforming gene on chromosome 8 (MTG8); myeloid transforming gene related protein-1 (MTGR1) and myeloid transforming gene on chromosome 16 (MTG16). ETO proteins are composed of four evolutionarily conserved domains termed nervy homology regions (NHR) 1-4. NHR1 is thought to stabilise the formation of high molecular weight complexes, but is not directly responsible for repressor activity. NHR2 and its flanking sequence comprise the core repressor domain, which mediates 50% of the wild type repressor activity. Furthermore, there is evidence that the amphipathic helical structure of NHR2 promotes the formation of ETO/AML1 homodimers []. NHR3 and NHR4 have been shown to act in concert to bind N-CoR. NHR4 contains two zinc finger motifs, which are thought to play a role in protein interactions rather than DNA binding []. This entry represents the NHR2 (Nervy homology 2) domain found in ETO proteins. It mediates oligomerisation and protein-protein interactions, forming an alpha-helical tetramer []. ; PDB: 1WQ6_A.
Probab=38.68 E-value=55 Score=22.01 Aligned_cols=26 Identities=19% Similarity=0.473 Sum_probs=20.1
Q ss_pred HHHHHhhhCCc-----HHHHHHHHHHHHHHH
Q 043638 25 RIWLSKFLDLN-----VAQRYTTITRTIAEM 50 (198)
Q Consensus 25 N~~i~~~R~lP-----I~~m~e~ir~~~~~~ 50 (198)
+.|..+.|.++ |+.|||.+++-+..+
T Consensus 12 ~~~~deWkh~~~mLnCI~~MVeKTrRsl~vL 42 (67)
T PF08788_consen 12 REWADEWKHLDHMLNCIMDMVEKTRRSLAVL 42 (67)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccHHHHhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666677665 789999999988776
No 12
>KOG1466 consensus Translation initiation factor 2B, alpha subunit (eIF-2Balpha/GCN3) [Translation, ribosomal structure and biogenesis]
Probab=28.08 E-value=1.1e+02 Score=26.61 Aligned_cols=43 Identities=23% Similarity=0.138 Sum_probs=30.7
Q ss_pred ccchHHHHHHHHHhhhCCc-----HHHHHHHHHHH----HHHHHHHHHHhhh
Q 043638 17 TNSSSEQLRIWLSKFLDLN-----VAQRYTTITRT----IAEMFQRRYLAGW 59 (198)
Q Consensus 17 t~N~aEsfN~~i~~~R~lP-----I~~m~e~ir~~----~~~~f~~Rr~~a~ 59 (198)
.-|+.|.||+|+++-.++. |-+|++.+++. ++++..+-++.+.
T Consensus 10 ~f~iie~f~~~l~eDpd~a~~vAAIraL~~vL~~s~a~Ti~el~~~l~~a~~ 61 (313)
T KOG1466|consen 10 EFSIIEYFLSFLQEDPDLAMAVAAIRALLEVLRRSQATTIAELENELKSASA 61 (313)
T ss_pred cchHHHHHHHHHhcCchhhhHHHHHHHHHHHHhhcccchHHHHHHHHHHHHH
Confidence 3478999999999977654 55778888765 6666666655443
No 13
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=23.35 E-value=37 Score=27.53 Aligned_cols=15 Identities=47% Similarity=1.225 Sum_probs=13.5
Q ss_pred cce-eeccccccCCCC
Q 043638 110 LMT-CSCRLWQLSGIP 124 (198)
Q Consensus 110 ~~t-CtC~~wql~giP 124 (198)
-+| |||--|-++|+|
T Consensus 89 VCTLCSCyP~pvLGlp 104 (185)
T TIGR01323 89 VCTLCSCYPWPVLGLP 104 (185)
T ss_pred EeccccccCchhcCCC
Confidence 477 999999999998
No 14
>PF11098 Chlorosome_CsmC: Chlorosome envelope protein C; InterPro: IPR020995 Chlorosomes are light-harvesting antennae found in green bacteria. This entry represents Chlorosome envelope protein C (CsmC) which is one of the proteins that exists in the chlorosome envelope and has been shown to exist as a homomultimer with CsmD in the chlorosome envelope []. CsmC is thought to be important in chlorosome elongation and shape [].
Probab=20.82 E-value=1.2e+02 Score=22.96 Aligned_cols=28 Identities=21% Similarity=0.349 Sum_probs=24.2
Q ss_pred hHHHHHHHHHhhhCCcHHHHHHHHHHHH
Q 043638 20 SSEQLRIWLSKFLDLNVAQRYTTITRTI 47 (198)
Q Consensus 20 ~aEsfN~~i~~~R~lPI~~m~e~ir~~~ 47 (198)
|+||+-..=+++++|+.++.+-++-+-.
T Consensus 1 MsEsYqKlRkdFKeL~ftDRltFlAE~~ 28 (139)
T PF11098_consen 1 MSESYQKLRKDFKELEFTDRLTFLAESV 28 (139)
T ss_pred CchHHHHHHHHhhhCChhHHHHHHHHHH
Confidence 5899999999999999999888886653
Done!