Query 021635
Match_columns 310
No_of_seqs 177 out of 968
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 04:30:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021635.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021635hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 5.7E-37 1.2E-41 256.9 8.8 125 72-213 1-129 (129)
2 PF13248 zf-ribbon_3: zinc-rib 65.8 3.2 6.9E-05 25.9 0.9 12 49-60 3-14 (26)
3 COG0178 UvrA Excinuclease ATPa 65.1 4.9 0.00011 44.3 2.8 73 6-78 71-150 (935)
4 PF03604 DNA_RNApol_7kD: DNA d 64.3 3.2 7E-05 27.5 0.8 14 46-59 15-28 (32)
5 PF13240 zinc_ribbon_2: zinc-r 60.5 4.6 0.0001 24.7 0.9 11 50-60 1-11 (23)
6 smart00659 RPOLCX RNA polymera 57.2 4.7 0.0001 28.4 0.7 17 45-61 16-32 (44)
7 PF10571 UPF0547: Uncharacteri 54.7 6.5 0.00014 24.8 0.9 13 47-59 13-25 (26)
8 COG1996 RPC10 DNA-directed RNA 49.1 7.1 0.00015 28.5 0.5 16 45-60 21-36 (49)
9 PRK00635 excinuclease ABC subu 38.8 15 0.00033 43.8 1.4 72 7-78 72-150 (1809)
10 COG0777 AccD Acetyl-CoA carbox 38.7 24 0.00052 34.4 2.5 45 44-90 24-69 (294)
11 PRK05654 acetyl-CoA carboxylas 38.3 23 0.0005 34.4 2.3 46 44-91 23-69 (292)
12 CHL00174 accD acetyl-CoA carbo 36.9 24 0.00052 34.5 2.2 46 44-91 34-80 (296)
13 PF14255 Cys_rich_CPXG: Cystei 35.3 16 0.00036 26.7 0.6 12 49-60 1-12 (52)
14 TIGR02098 MJ0042_CXXC MJ0042 f 35.0 17 0.00037 24.0 0.6 12 48-59 25-36 (38)
15 PF00301 Rubredoxin: Rubredoxi 34.1 13 0.00029 26.6 -0.0 27 50-79 3-29 (47)
16 PF14353 CpXC: CpXC protein 33.2 18 0.0004 30.1 0.7 13 49-61 2-14 (128)
17 PF13717 zinc_ribbon_4: zinc-r 31.8 21 0.00046 23.9 0.7 14 45-58 22-35 (36)
18 PF01096 TFIIS_C: Transcriptio 30.9 22 0.00047 24.2 0.6 9 50-58 2-10 (39)
19 PF13005 zf-IS66: zinc-finger 30.9 17 0.00036 25.1 0.0 26 49-74 3-28 (47)
20 PF08209 Sgf11: Sgf11 (transcr 30.6 21 0.00046 23.9 0.5 16 47-62 3-18 (33)
21 PF07754 DUF1610: Domain of un 30.0 23 0.0005 22.2 0.6 9 48-56 16-24 (24)
22 PF13719 zinc_ribbon_5: zinc-r 29.5 25 0.00053 23.6 0.7 16 44-59 21-36 (37)
23 PHA00626 hypothetical protein 29.2 34 0.00073 25.8 1.4 6 51-56 3-8 (59)
24 PRK00398 rpoP DNA-directed RNA 28.5 25 0.00054 24.4 0.6 16 48-63 21-36 (46)
25 PF14319 Zn_Tnp_IS91: Transpos 28.3 26 0.00056 29.1 0.8 21 39-59 51-71 (111)
26 PF09889 DUF2116: Uncharacteri 28.3 31 0.00066 26.0 1.1 14 47-60 2-15 (59)
27 PF05412 Peptidase_C33: Equine 28.0 15 0.00032 31.0 -0.8 16 49-64 64-79 (108)
28 PF07282 OrfB_Zn_ribbon: Putat 27.2 40 0.00087 24.9 1.6 16 45-60 43-58 (69)
29 PF08271 TF_Zn_Ribbon: TFIIB z 25.8 32 0.0007 23.5 0.8 17 46-62 17-33 (43)
30 TIGR00630 uvra excinuclease AB 24.9 43 0.00094 37.5 1.9 71 7-77 68-145 (924)
31 TIGR00515 accD acetyl-CoA carb 24.8 51 0.0011 31.9 2.2 46 44-91 22-68 (285)
32 PRK00349 uvrA excinuclease ABC 23.2 46 0.00099 37.4 1.7 71 7-77 72-149 (943)
33 smart00440 ZnF_C2C2 C2C2 Zinc 23.0 40 0.00086 23.1 0.8 8 50-57 2-9 (40)
34 PF08274 PhnA_Zn_Ribbon: PhnA 22.9 30 0.00066 22.6 0.2 16 44-59 15-30 (30)
35 PF14149 YhfH: YhfH-like prote 21.0 18 0.0004 24.9 -1.2 18 44-61 9-26 (37)
36 PF03119 DNA_ligase_ZBD: NAD-d 20.1 44 0.00095 21.3 0.5 12 50-61 1-12 (28)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=5.7e-37 Score=256.94 Aligned_cols=125 Identities=41% Similarity=0.703 Sum_probs=87.9
Q ss_pred CCCceeeCCChHHHHH-HHHHHHhcCcCCCCCccc-ccccccccccCccCCCCCCCCCc-ccCCceEEEEecCCCCCCCC
Q 021635 72 LPAGVKFDPTDQELLE-HLEAKVRADARKLHPLID-EFIPTLEGENGICYTHPEKLPGV-SKDGLIRHFFHRPSKAYTTG 148 (310)
Q Consensus 72 LPpGfRF~PTDeELI~-yL~~Kv~g~~~~~~Plid-~fIp~id~e~DVy~~~PweLPg~-~~dG~~~yFF~~~~kky~~G 148 (310)
|||||||+|||+|||. ||.+|+.+.. ++. .+|++ +|||.+|||+||+. ...++.||||+++.+++.+|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~-----~~~~~~i~~----~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~ 71 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEP-----LPCEDVIHD----VDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNG 71 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-H-----HCS-CHSEE------GGGS-GGGCHHHSSS-SSEEEEEEE--------
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCC-----CCcccceee----cccCccChHHhhhhccCCCceEEEEEecccccCCc
Confidence 8999999999999996 6999999964 222 55654 57999999999943 23456788899888888899
Q ss_pred CcccccccccCCCCccEEeecCCCeeEee-CCEEEEEEEEEEEEeecCCCCCCCcccEEEEEEeeC
Q 021635 149 TRKRRKVHTDEQGGETRWHKTGKTRPVFI-GGKVKGYKKILVLYTNYGKQKKPEKTNWVMHQYHLG 213 (310)
Q Consensus 149 ~RkrR~~~~~~~gG~G~Wk~tGk~k~I~~-~G~vvG~KK~LvFY~~~G~~~~g~KT~WvMhEY~L~ 213 (310)
.|++|++ ++|+||.+|+.++|.. +|.++|+||+|+||. ++.+++.+|+|+||||+|.
T Consensus 72 ~r~~R~~------~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~--~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 72 GRPNRVT------GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYS--GKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp --S-EEE------TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEE--SSTTS-EEEEEEEEEEEE-
T ss_pred ccccccc------cceEEeecccccccccccceeeeeEEEEEEEe--ccCCCCCcCCeEEEEEEeC
Confidence 9999976 4699999999999999 999999999999997 7778899999999999984
No 2
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=65.84 E-value=3.2 Score=25.87 Aligned_cols=12 Identities=42% Similarity=0.996 Sum_probs=8.5
Q ss_pred ccCCCCCCcccc
Q 021635 49 RSCPSCGHQIKC 60 (310)
Q Consensus 49 ~~~~~~~~~~~~ 60 (310)
+.||+||+.|+.
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 568888886653
No 3
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=65.12 E-value=4.9 Score=44.31 Aligned_cols=73 Identities=25% Similarity=0.403 Sum_probs=54.1
Q ss_pred CCCccceeecccCCCCCCCCCCCCCCCCCCCCcc------chhhcccccccCCCCCCcccccchh-cccCCCCCCCceee
Q 021635 6 DCSDVQTIERISSPPSSSTNNNNNNNNNTSNSSS------SAKAKNCLVRSCPSCGHQIKCNEQA-RIHDLPGLPAGVKF 78 (310)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~LPpGfRF 78 (310)
+..|+..||.+++.++.-.+.-..+.-|+|-+.. ...+.......||+|+..|+.+-.. ++.....||.|-|+
T Consensus 71 ~kPdVD~IeGLSPAIsIdQktts~NpRSTVGTvTEiydyLRLLfARvG~p~cp~~~~~i~~qt~~qivd~i~~~~~~~~~ 150 (935)
T COG0178 71 DKPDVDSIEGLSPAISIDQKTTSHNPRSTVGTVTEIYDYLRLLFARVGTPYCPNCGLPIESQTVSQIVDRILALPEGTKI 150 (935)
T ss_pred CCCCCcccCCCCcceEeecccCCCCCCCCCccchhhHHHHHHHHHccCCCCCCCCCCCccccCHHHHHHHHhccCCCcee
Confidence 4568889999999888776666666677777755 3455667778999999999986654 34566688888773
No 4
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=64.29 E-value=3.2 Score=27.51 Aligned_cols=14 Identities=43% Similarity=0.866 Sum_probs=10.2
Q ss_pred cccccCCCCCCccc
Q 021635 46 CLVRSCPSCGHQIK 59 (310)
Q Consensus 46 ~~~~~~~~~~~~~~ 59 (310)
.....||.|||+|=
T Consensus 15 ~~~irC~~CG~RIl 28 (32)
T PF03604_consen 15 GDPIRCPECGHRIL 28 (32)
T ss_dssp SSTSSBSSSS-SEE
T ss_pred CCcEECCcCCCeEE
Confidence 34579999999984
No 5
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=60.54 E-value=4.6 Score=24.72 Aligned_cols=11 Identities=45% Similarity=1.183 Sum_probs=9.3
Q ss_pred cCCCCCCcccc
Q 021635 50 SCPSCGHQIKC 60 (310)
Q Consensus 50 ~~~~~~~~~~~ 60 (310)
.||+||+.|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 49999999974
No 6
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.16 E-value=4.7 Score=28.44 Aligned_cols=17 Identities=29% Similarity=0.505 Sum_probs=13.4
Q ss_pred ccccccCCCCCCccccc
Q 021635 45 NCLVRSCPSCGHQIKCN 61 (310)
Q Consensus 45 ~~~~~~~~~~~~~~~~~ 61 (310)
......||.|||+|-..
T Consensus 16 ~~~~irC~~CG~rIlyK 32 (44)
T smart00659 16 SKDVVRCRECGYRILYK 32 (44)
T ss_pred CCCceECCCCCceEEEE
Confidence 34568999999999764
No 7
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=54.70 E-value=6.5 Score=24.84 Aligned_cols=13 Identities=31% Similarity=0.917 Sum_probs=10.2
Q ss_pred ccccCCCCCCccc
Q 021635 47 LVRSCPSCGHQIK 59 (310)
Q Consensus 47 ~~~~~~~~~~~~~ 59 (310)
..+.||.|||...
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 4578999999763
No 8
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=49.05 E-value=7.1 Score=28.45 Aligned_cols=16 Identities=31% Similarity=0.642 Sum_probs=12.5
Q ss_pred ccccccCCCCCCcccc
Q 021635 45 NCLVRSCPSCGHQIKC 60 (310)
Q Consensus 45 ~~~~~~~~~~~~~~~~ 60 (310)
.-.-..||.|||.|=.
T Consensus 21 ~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 21 ETRGIRCPYCGSRILV 36 (49)
T ss_pred ccCceeCCCCCcEEEE
Confidence 3455799999999964
No 9
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=38.78 E-value=15 Score=43.83 Aligned_cols=72 Identities=15% Similarity=0.178 Sum_probs=51.3
Q ss_pred CCccceeecccCCCCCCCCCCCCCCCCCCCCcc------chhhcccccccCCCCCCcccccchh-cccCCCCCCCceee
Q 021635 7 CSDVQTIERISSPPSSSTNNNNNNNNNTSNSSS------SAKAKNCLVRSCPSCGHQIKCNEQA-RIHDLPGLPAGVKF 78 (310)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~LPpGfRF 78 (310)
..|+..|+.++++++...+....+.-|+|-+.. ...........||.||+.|.-+... .+.....+|.|-||
T Consensus 72 kP~VD~I~gLsPaIaI~Qk~~~~npRSTVGT~TeI~dyLRLLfar~G~~~cp~cg~~i~~~t~~~i~~~i~~~p~~~~~ 150 (1809)
T PRK00635 72 DPSVEKIEGLSPTIAVKQNHFSQHSHATVGSTTELNSHLALLFSLEGQARDPVTLHPLTLYSKEKILSTIAAIPDGTQI 150 (1809)
T ss_pred CCCcceecCCCceEEEeccCCCCCCCcccchHHHHHHHHHHHHHhhCCCCCCCCCCEeecCCHHHHHHHHHhCCCCceE
Confidence 457778999998888777766677778887755 3345566778999999999765443 23444567888664
No 10
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=38.75 E-value=24 Score=34.41 Aligned_cols=45 Identities=31% Similarity=0.458 Sum_probs=36.9
Q ss_pred cccccccCCCCCCcccccchhcccCCCCCC-CceeeCCChHHHHHHHH
Q 021635 44 KNCLVRSCPSCGHQIKCNEQARIHDLPGLP-AGVKFDPTDQELLEHLE 90 (310)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LP-pGfRF~PTDeELI~yL~ 90 (310)
.+..|..||+|++.+-..|. ..++...| -|+-|.=+-.|.|..|.
T Consensus 24 ~e~lw~KCp~c~~~~y~~eL--~~n~~vcp~c~~h~ri~A~~Ri~~ll 69 (294)
T COG0777 24 PEGLWTKCPSCGEMLYRKEL--ESNLKVCPKCGHHMRISARERLEALL 69 (294)
T ss_pred CCCceeECCCccceeeHHHH--HhhhhcccccCcccccCHHHHHHHhh
Confidence 38899999999999988874 44566777 48999999999998765
No 11
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=38.27 E-value=23 Score=34.37 Aligned_cols=46 Identities=28% Similarity=0.421 Sum_probs=35.5
Q ss_pred cccccccCCCCCCcccccchhcccCCCCCCC-ceeeCCChHHHHHHHHH
Q 021635 44 KNCLVRSCPSCGHQIKCNEQARIHDLPGLPA-GVKFDPTDQELLEHLEA 91 (310)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LPp-GfRF~PTDeELI~yL~~ 91 (310)
.+..|..||+|+..|-..+. ..+..--|. |+.|.-|-.|-|+.|.-
T Consensus 23 ~~~~~~~c~~c~~~~~~~~l--~~~~~vc~~c~~h~rl~areRi~~L~D 69 (292)
T PRK05654 23 PEGLWTKCPSCGQVLYRKEL--EANLNVCPKCGHHMRISARERLDLLLD 69 (292)
T ss_pred CCCCeeECCCccchhhHHHH--HhcCCCCCCCCCCeeCCHHHHHHHHcc
Confidence 35579999999999988774 233445663 89999999999988754
No 12
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=36.90 E-value=24 Score=34.52 Aligned_cols=46 Identities=13% Similarity=0.071 Sum_probs=35.5
Q ss_pred cccccccCCCCCCcccccchhcccCCCCCC-CceeeCCChHHHHHHHHH
Q 021635 44 KNCLVRSCPSCGHQIKCNEQARIHDLPGLP-AGVKFDPTDQELLEHLEA 91 (310)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LP-pGfRF~PTDeELI~yL~~ 91 (310)
.+..|..||+|+..|...+. ..++.--| =|+-|.-|-.|-|+.|.-
T Consensus 34 p~~lw~kc~~C~~~~~~~~l--~~~~~vcp~c~~h~rltAreRI~~L~D 80 (296)
T CHL00174 34 YKHLWVQCENCYGLNYKKFL--KSKMNICEQCGYHLKMSSSDRIELLID 80 (296)
T ss_pred CCCCeeECCCccchhhHHHH--HHcCCCCCCCCCCcCCCHHHHHHHHcc
Confidence 34579999999999988774 33455566 499999999999987653
No 13
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.30 E-value=16 Score=26.74 Aligned_cols=12 Identities=42% Similarity=1.038 Sum_probs=9.9
Q ss_pred ccCCCCCCcccc
Q 021635 49 RSCPSCGHQIKC 60 (310)
Q Consensus 49 ~~~~~~~~~~~~ 60 (310)
..||.||+.|+.
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 369999999875
No 14
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=34.97 E-value=17 Score=24.00 Aligned_cols=12 Identities=33% Similarity=0.689 Sum_probs=9.8
Q ss_pred cccCCCCCCccc
Q 021635 48 VRSCPSCGHQIK 59 (310)
Q Consensus 48 ~~~~~~~~~~~~ 59 (310)
...||+|++.|.
T Consensus 25 ~v~C~~C~~~~~ 36 (38)
T TIGR02098 25 KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEE
Confidence 468999999874
No 15
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=34.10 E-value=13 Score=26.62 Aligned_cols=27 Identities=30% Similarity=0.691 Sum_probs=16.7
Q ss_pred cCCCCCCcccccchhcccCCCCCCCceeeC
Q 021635 50 SCPSCGHQIKCNEQARIHDLPGLPAGVKFD 79 (310)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~~~LPpGfRF~ 79 (310)
.|+.||+.-|-.. -....++|||..|.
T Consensus 3 ~C~~CgyvYd~~~---Gd~~~~i~pGt~F~ 29 (47)
T PF00301_consen 3 QCPVCGYVYDPEK---GDPENGIPPGTPFE 29 (47)
T ss_dssp EETTTSBEEETTT---BBGGGTB-TT--GG
T ss_pred CCCCCCEEEcCCc---CCcccCcCCCCCHH
Confidence 6999999987532 23345788888774
No 16
>PF14353 CpXC: CpXC protein
Probab=33.24 E-value=18 Score=30.08 Aligned_cols=13 Identities=38% Similarity=1.180 Sum_probs=11.0
Q ss_pred ccCCCCCCccccc
Q 021635 49 RSCPSCGHQIKCN 61 (310)
Q Consensus 49 ~~~~~~~~~~~~~ 61 (310)
.+||+|+|..+..
T Consensus 2 itCP~C~~~~~~~ 14 (128)
T PF14353_consen 2 ITCPHCGHEFEFE 14 (128)
T ss_pred cCCCCCCCeeEEE
Confidence 5899999999864
No 17
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=31.79 E-value=21 Score=23.92 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=10.0
Q ss_pred ccccccCCCCCCcc
Q 021635 45 NCLVRSCPSCGHQI 58 (310)
Q Consensus 45 ~~~~~~~~~~~~~~ 58 (310)
.-....|++|+|.+
T Consensus 22 ~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 22 KGRKVRCSKCGHVF 35 (36)
T ss_pred CCcEEECCCCCCEe
Confidence 33456899999875
No 18
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=30.89 E-value=22 Score=24.24 Aligned_cols=9 Identities=56% Similarity=1.531 Sum_probs=4.3
Q ss_pred cCCCCCCcc
Q 021635 50 SCPSCGHQI 58 (310)
Q Consensus 50 ~~~~~~~~~ 58 (310)
.||+|||.=
T Consensus 2 ~Cp~Cg~~~ 10 (39)
T PF01096_consen 2 KCPKCGHNE 10 (39)
T ss_dssp --SSS-SSE
T ss_pred CCcCCCCCe
Confidence 588888853
No 19
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=30.87 E-value=17 Score=25.07 Aligned_cols=26 Identities=31% Similarity=0.816 Sum_probs=16.3
Q ss_pred ccCCCCCCcccccchhcccCCCCCCC
Q 021635 49 RSCPSCGHQIKCNEQARIHDLPGLPA 74 (310)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~LPp 74 (310)
..||.||..+..-....+.+...|||
T Consensus 3 ~~C~~Cg~~l~~ig~~~~~q~l~~~p 28 (47)
T PF13005_consen 3 RACPDCGGELKEIGEEKVRQVLDLPP 28 (47)
T ss_pred CcCCCCCceeeECCceeeEEEEeecc
Confidence 57999999887432222345555665
No 20
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=30.58 E-value=21 Score=23.85 Aligned_cols=16 Identities=25% Similarity=0.787 Sum_probs=10.9
Q ss_pred ccccCCCCCCcccccc
Q 021635 47 LVRSCPSCGHQIKCNE 62 (310)
Q Consensus 47 ~~~~~~~~~~~~~~~~ 62 (310)
..-.||+|+..|.-+-
T Consensus 3 ~~~~C~nC~R~v~a~R 18 (33)
T PF08209_consen 3 PYVECPNCGRPVAASR 18 (33)
T ss_dssp -EEE-TTTSSEEEGGG
T ss_pred CeEECCCCcCCcchhh
Confidence 4568999999987543
No 21
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=29.99 E-value=23 Score=22.17 Aligned_cols=9 Identities=44% Similarity=1.235 Sum_probs=7.0
Q ss_pred cccCCCCCC
Q 021635 48 VRSCPSCGH 56 (310)
Q Consensus 48 ~~~~~~~~~ 56 (310)
.-.||+||.
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 458999984
No 22
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=29.48 E-value=25 Score=23.63 Aligned_cols=16 Identities=31% Similarity=0.779 Sum_probs=11.2
Q ss_pred cccccccCCCCCCccc
Q 021635 44 KNCLVRSCPSCGHQIK 59 (310)
Q Consensus 44 ~~~~~~~~~~~~~~~~ 59 (310)
.....-.||+|+|.+.
T Consensus 21 ~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 21 AGGRKVRCPKCGHVFR 36 (37)
T ss_pred cCCcEEECCCCCcEee
Confidence 3344568999998764
No 23
>PHA00626 hypothetical protein
Probab=29.15 E-value=34 Score=25.85 Aligned_cols=6 Identities=67% Similarity=2.057 Sum_probs=3.2
Q ss_pred CCCCCC
Q 021635 51 CPSCGH 56 (310)
Q Consensus 51 ~~~~~~ 56 (310)
||+||+
T Consensus 3 CP~CGS 8 (59)
T PHA00626 3 CPKCGS 8 (59)
T ss_pred CCCCCC
Confidence 555555
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.52 E-value=25 Score=24.42 Aligned_cols=16 Identities=38% Similarity=0.752 Sum_probs=12.9
Q ss_pred cccCCCCCCcccccch
Q 021635 48 VRSCPSCGHQIKCNEQ 63 (310)
Q Consensus 48 ~~~~~~~~~~~~~~~~ 63 (310)
...||.||..+...+.
T Consensus 21 ~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 21 GVRCPYCGYRILFKER 36 (46)
T ss_pred ceECCCCCCeEEEccC
Confidence 5799999999987553
No 25
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=28.32 E-value=26 Score=29.14 Aligned_cols=21 Identities=29% Similarity=0.648 Sum_probs=16.7
Q ss_pred cchhhcccccccCCCCCCccc
Q 021635 39 SSAKAKNCLVRSCPSCGHQIK 59 (310)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~ 59 (310)
......+|..|.||+|++.--
T Consensus 51 ~~~~~~SCk~R~CP~C~~~~~ 71 (111)
T PF14319_consen 51 EKIVYNSCKNRHCPSCQAKAT 71 (111)
T ss_pred eEEecCcccCcCCCCCCChHH
Confidence 346678899999999998753
No 26
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=28.26 E-value=31 Score=26.02 Aligned_cols=14 Identities=36% Similarity=0.835 Sum_probs=11.3
Q ss_pred ccccCCCCCCcccc
Q 021635 47 LVRSCPSCGHQIKC 60 (310)
Q Consensus 47 ~~~~~~~~~~~~~~ 60 (310)
+-+.||.||..|+-
T Consensus 2 ~HkHC~~CG~~Ip~ 15 (59)
T PF09889_consen 2 PHKHCPVCGKPIPP 15 (59)
T ss_pred CCCcCCcCCCcCCc
Confidence 34789999998874
No 27
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=27.97 E-value=15 Score=30.98 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=14.1
Q ss_pred ccCCCCCCcccccchh
Q 021635 49 RSCPSCGHQIKCNEQA 64 (310)
Q Consensus 49 ~~~~~~~~~~~~~~~~ 64 (310)
..||++.+.|+..+|.
T Consensus 64 ~~Cp~ArYv~~l~~qH 79 (108)
T PF05412_consen 64 GACPHARYVLKLDGQH 79 (108)
T ss_pred CCCCCCEEEEEecCce
Confidence 6899999999998764
No 28
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.23 E-value=40 Score=24.90 Aligned_cols=16 Identities=31% Similarity=0.810 Sum_probs=9.5
Q ss_pred ccccccCCCCCCcccc
Q 021635 45 NCLVRSCPSCGHQIKC 60 (310)
Q Consensus 45 ~~~~~~~~~~~~~~~~ 60 (310)
....-.||+||+.+|.
T Consensus 43 ~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMDR 58 (69)
T ss_pred ccceEEcCCCCCEECc
Confidence 3344567777776654
No 29
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=25.84 E-value=32 Score=23.53 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=11.6
Q ss_pred cccccCCCCCCcccccc
Q 021635 46 CLVRSCPSCGHQIKCNE 62 (310)
Q Consensus 46 ~~~~~~~~~~~~~~~~~ 62 (310)
.....|++||.+|+...
T Consensus 17 ~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 17 RGELVCPNCGLVLEENI 33 (43)
T ss_dssp TTEEEETTT-BBEE-TT
T ss_pred CCeEECCCCCCEeeccc
Confidence 45568999999998654
No 30
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.89 E-value=43 Score=37.52 Aligned_cols=71 Identities=23% Similarity=0.413 Sum_probs=48.8
Q ss_pred CCccceeecccCCCCCCCCCCCCCCCCCCCCcc------chhhcccccccCCCCCCcccccchhc-ccCCCCCCCcee
Q 021635 7 CSDVQTIERISSPPSSSTNNNNNNNNNTSNSSS------SAKAKNCLVRSCPSCGHQIKCNEQAR-IHDLPGLPAGVK 77 (310)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~LPpGfR 77 (310)
..++..|+.+++.++........+.-|+|.+.. ...+.......||.|+..|.....+. +.....+|.|-|
T Consensus 68 ~P~vd~i~gl~paiai~Q~~~~~n~RSTVgT~Tei~~~LrlLfar~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (924)
T TIGR00630 68 KPDVDSIEGLSPAISIDQKTTSHNPRSTVGTITEIYDYLRLLFARVGTPYCPNCGRPISSQSVSQIVDQILALPEGTR 145 (924)
T ss_pred CCCcCeEcCCCceEEEeccCCCCCCCcccchHHHHHHHHHHHHHhcCCCCCCCCCCCcccCCHHHHHHHHHhCCCCCE
Confidence 346777888888877766666667778887754 33445567789999999987655443 344456677754
No 31
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=24.76 E-value=51 Score=31.94 Aligned_cols=46 Identities=22% Similarity=0.375 Sum_probs=35.0
Q ss_pred cccccccCCCCCCcccccchhcccCCCCCC-CceeeCCChHHHHHHHHH
Q 021635 44 KNCLVRSCPSCGHQIKCNEQARIHDLPGLP-AGVKFDPTDQELLEHLEA 91 (310)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~LP-pGfRF~PTDeELI~yL~~ 91 (310)
.+..|..||+|+..|-..|. ..++.--| =|+.|.-|-.|-|+.|.-
T Consensus 22 ~~~~~~~c~~c~~~~~~~~l--~~~~~vc~~c~~h~rl~areRi~~L~D 68 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYTKEL--ERNLEVCPKCDHHMRMDARERIESLLD 68 (285)
T ss_pred CCCCeeECCCCcchhhHHHH--HhhCCCCCCCCCcCcCCHHHHHHHcee
Confidence 34579999999999988764 33445566 499999999998887653
No 32
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=23.21 E-value=46 Score=37.43 Aligned_cols=71 Identities=23% Similarity=0.393 Sum_probs=47.5
Q ss_pred CCccceeecccCCCCCCCCCCCCCCCCCCCCccc------hhhcccccccCCCCCCcccccchh-cccCCCCCCCcee
Q 021635 7 CSDVQTIERISSPPSSSTNNNNNNNNNTSNSSSS------AKAKNCLVRSCPSCGHQIKCNEQA-RIHDLPGLPAGVK 77 (310)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~LPpGfR 77 (310)
..++..|+.+++.++.....-..++-|+|.+... ..........||.|+..|...... .+.....+|.|-|
T Consensus 72 ~P~vd~i~gl~p~Iai~Q~~~~~n~RSTVgT~Tei~~~LrlLfar~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (943)
T PRK00349 72 KPDVDSIEGLSPAISIDQKTTSHNPRSTVGTVTEIYDYLRLLYARVGKPHCPNCGRPIEAQTVSQMVDRVLELPEGTR 149 (943)
T ss_pred CCCcCeEcCCCceEEEEecCCCCCCCccchhHHHHHHHHHHHHHhcCCCCCCCCCCCcccCCHHHHHHHHHhCCCCCE
Confidence 3467778888888777666655677788877543 344556678899999998765443 2344456677654
No 33
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.03 E-value=40 Score=23.10 Aligned_cols=8 Identities=50% Similarity=1.680 Sum_probs=5.7
Q ss_pred cCCCCCCc
Q 021635 50 SCPSCGHQ 57 (310)
Q Consensus 50 ~~~~~~~~ 57 (310)
.||+|||.
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 57888765
No 34
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.92 E-value=30 Score=22.64 Aligned_cols=16 Identities=31% Similarity=0.860 Sum_probs=11.4
Q ss_pred cccccccCCCCCCccc
Q 021635 44 KNCLVRSCPSCGHQIK 59 (310)
Q Consensus 44 ~~~~~~~~~~~~~~~~ 59 (310)
.+...-.||.|+|.|+
T Consensus 15 ~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 15 EDGELLVCPECGHEWN 30 (30)
T ss_dssp E-SSSEEETTTTEEE-
T ss_pred ccCCEEeCCcccccCC
Confidence 4556678999999874
No 35
>PF14149 YhfH: YhfH-like protein
Probab=21.03 E-value=18 Score=24.92 Aligned_cols=18 Identities=28% Similarity=0.719 Sum_probs=14.0
Q ss_pred cccccccCCCCCCccccc
Q 021635 44 KNCLVRSCPSCGHQIKCN 61 (310)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~ 61 (310)
..-+.+.|+.||..|+-+
T Consensus 9 rnLp~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 9 RNLPPKKCTECGKEIEEQ 26 (37)
T ss_pred HhCCCcccHHHHHHHHHH
Confidence 345778999999999743
No 36
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=20.08 E-value=44 Score=21.30 Aligned_cols=12 Identities=33% Similarity=1.077 Sum_probs=6.2
Q ss_pred cCCCCCCccccc
Q 021635 50 SCPSCGHQIKCN 61 (310)
Q Consensus 50 ~~~~~~~~~~~~ 61 (310)
.||.||..+-..
T Consensus 1 ~CP~C~s~l~~~ 12 (28)
T PF03119_consen 1 TCPVCGSKLVRE 12 (28)
T ss_dssp B-TTT--BEEE-
T ss_pred CcCCCCCEeEcC
Confidence 599999888643
Done!