Query 047290
Match_columns 172
No_of_seqs 129 out of 201
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 09:37:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047290.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047290hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02701 zf-Dof: Dof domain, z 100.0 5.7E-39 1.2E-43 227.5 3.9 62 43-104 1-62 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.0 0.036 7.8E-07 44.1 0.6 34 47-82 105-140 (146)
3 COG3677 Transposase and inacti 93.0 0.071 1.5E-06 41.6 2.2 35 48-84 31-65 (129)
4 PF12760 Zn_Tnp_IS1595: Transp 92.4 0.11 2.4E-06 33.6 2.2 27 48-80 19-45 (46)
5 PF03811 Zn_Tnp_IS1: InsA N-te 92.0 0.094 2E-06 33.6 1.5 31 47-79 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 91.3 0.22 4.7E-06 32.0 2.6 37 48-84 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 89.9 0.27 5.8E-06 31.3 2.1 36 48-83 1-39 (39)
8 TIGR01384 TFS_arch transcripti 83.3 1.7 3.7E-05 31.5 3.5 42 44-85 59-103 (104)
9 PF13453 zf-TFIIB: Transcripti 82.3 0.39 8.5E-06 30.3 -0.1 37 49-90 1-37 (41)
10 PHA02998 RNA polymerase subuni 80.1 1.9 4E-05 37.1 3.1 39 46-84 142-183 (195)
11 cd00202 ZnF_GATA Zinc finger D 77.0 2.1 4.6E-05 29.1 2.1 41 49-92 1-41 (54)
12 PF14690 zf-ISL3: zinc-finger 70.3 2.2 4.8E-05 26.6 0.9 32 47-78 2-47 (47)
13 TIGR01385 TFSII transcription 68.7 5 0.00011 35.5 3.0 41 43-83 254-297 (299)
14 PRK14810 formamidopyrimidine-D 67.6 3.6 7.9E-05 35.1 1.9 30 46-80 243-272 (272)
15 smart00401 ZnF_GATA zinc finge 66.1 4.8 0.0001 26.9 1.9 40 46-88 2-41 (52)
16 PRK14811 formamidopyrimidine-D 64.8 4.6 9.9E-05 34.5 2.0 29 47-80 235-263 (269)
17 TIGR00244 transcriptional regu 63.3 5.7 0.00012 32.6 2.2 44 49-92 2-48 (147)
18 PF04216 FdhE: Protein involve 62.8 3.4 7.3E-05 35.1 0.8 38 46-83 210-249 (290)
19 PF09526 DUF2387: Probable met 61.7 5.9 0.00013 28.6 1.8 31 47-80 8-38 (71)
20 PRK01103 formamidopyrimidine/5 61.2 5.8 0.00013 33.7 2.0 30 46-80 244-273 (274)
21 PF04981 NMD3: NMD3 family ; 61.1 4.4 9.5E-05 33.7 1.2 13 73-85 36-48 (236)
22 PRK10445 endonuclease VIII; Pr 58.8 6.7 0.00015 33.3 2.0 30 46-80 234-263 (263)
23 PRK13945 formamidopyrimidine-D 57.8 7.5 0.00016 33.3 2.1 29 47-80 254-282 (282)
24 TIGR00577 fpg formamidopyrimid 55.1 8.6 0.00019 32.8 2.0 28 47-79 245-272 (272)
25 PF06220 zf-U1: U1 zinc finger 54.9 5.2 0.00011 25.6 0.5 17 70-86 1-17 (38)
26 TIGR01562 FdhE formate dehydro 54.2 9.7 0.00021 34.0 2.2 37 46-83 223-263 (305)
27 PF14354 Lar_restr_allev: Rest 53.7 11 0.00024 24.7 2.0 35 46-80 2-37 (61)
28 PHA00626 hypothetical protein 52.3 9.9 0.00021 27.4 1.6 36 49-86 2-37 (59)
29 PRK00432 30S ribosomal protein 50.4 8.7 0.00019 25.9 1.1 26 47-80 20-45 (50)
30 PRK00464 nrdR transcriptional 50.1 11 0.00025 30.5 1.9 45 48-92 1-48 (154)
31 PRK03564 formate dehydrogenase 48.6 14 0.00031 33.1 2.4 38 46-84 225-264 (309)
32 PF14599 zinc_ribbon_6: Zinc-r 45.2 9 0.0002 27.1 0.5 17 43-59 44-60 (61)
33 TIGR03655 anti_R_Lar restricti 43.9 21 0.00045 23.6 2.1 32 48-80 2-34 (53)
34 KOG2906 RNA polymerase III sub 41.4 22 0.00048 28.1 2.2 39 45-83 63-104 (105)
35 PF06827 zf-FPG_IleRS: Zinc fi 40.9 12 0.00027 21.9 0.6 27 48-79 2-28 (30)
36 PF08273 Prim_Zn_Ribbon: Zinc- 40.7 16 0.00035 23.9 1.1 33 46-80 2-34 (40)
37 COG0266 Nei Formamidopyrimidin 39.9 19 0.00042 31.9 1.9 30 46-80 244-273 (273)
38 TIGR02443 conserved hypothetic 39.2 24 0.00052 25.3 1.9 31 46-79 8-38 (59)
39 COG1327 Predicted transcriptio 34.1 26 0.00056 29.3 1.7 44 49-92 2-48 (156)
40 PF15242 FAM53: Family of FAM5 33.5 20 0.00043 32.7 0.9 24 140-170 136-159 (314)
41 PRK09710 lar restriction allev 30.8 40 0.00086 24.5 2.0 34 44-81 3-36 (64)
42 PLN02779 haloacid dehalogenase 29.7 14 0.0003 31.1 -0.6 12 131-142 44-55 (286)
43 COG1997 RPL43A Ribosomal prote 29.1 32 0.0007 26.5 1.3 42 46-94 34-75 (89)
44 PF07282 OrfB_Zn_ribbon: Putat 28.2 34 0.00073 22.9 1.2 32 46-84 27-58 (69)
45 PF08274 PhnA_Zn_Ribbon: PhnA 25.1 34 0.00073 21.3 0.7 28 48-83 3-30 (30)
46 PF01783 Ribosomal_L32p: Ribos 24.8 64 0.0014 21.8 2.0 27 40-79 20-46 (56)
47 PF10122 Mu-like_Com: Mu-like 24.3 32 0.0007 24.0 0.5 13 46-58 23-35 (51)
48 TIGR00686 phnA alkylphosphonat 24.1 50 0.0011 26.2 1.6 31 48-86 3-33 (109)
49 PF01807 zf-CHC2: CHC2 zinc fi 23.8 47 0.001 24.2 1.3 31 46-80 32-62 (97)
50 smart00778 Prim_Zn_Ribbon Zinc 22.6 68 0.0015 20.7 1.8 31 46-79 2-32 (37)
51 PF07383 DUF1496: Protein of u 22.5 63 0.0014 22.7 1.7 14 57-70 11-24 (56)
52 PRK14892 putative transcriptio 22.5 80 0.0017 24.1 2.4 35 45-83 19-53 (99)
53 PRK10220 hypothetical protein; 22.3 58 0.0013 26.0 1.6 31 48-86 4-34 (111)
54 PF09723 Zn-ribbon_8: Zinc rib 22.1 61 0.0013 20.6 1.5 14 45-58 24-37 (42)
55 COG4260 Membrane protease subu 21.3 50 0.0011 30.6 1.3 19 42-62 301-319 (345)
56 smart00661 RPOL9 RNA polymeras 21.3 61 0.0013 20.4 1.3 32 49-85 2-33 (52)
57 PF05129 Elf1: Transcription e 21.1 58 0.0013 23.7 1.3 41 42-83 17-57 (81)
58 TIGR00100 hypA hydrogenase nic 20.7 67 0.0015 24.3 1.7 13 47-59 86-98 (115)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=5.7e-39 Score=227.52 Aligned_cols=62 Identities=65% Similarity=1.393 Sum_probs=60.2
Q ss_pred CCCCcccCCCCCCCCceeeEeccccCCCCCccccccccccccCcccccccCCCCccCCCCCC
Q 047290 43 RPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVGAGRRKTKPPG 104 (172)
Q Consensus 43 ~p~~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GGtLRnVPVGgG~RKnK~s~ 104 (172)
+|++.++||||+|++|||||||||+++||||||++|+||||+||+|||||||||+||+|+++
T Consensus 1 ~~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~ 62 (63)
T PF02701_consen 1 KPEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSS 62 (63)
T ss_pred CCccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCC
Confidence 48899999999999999999999999999999999999999999999999999999999975
No 2
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=93.01 E-value=0.036 Score=44.14 Aligned_cols=34 Identities=24% Similarity=0.661 Sum_probs=27.1
Q ss_pred cccCCCCCCCCceeeEeccc--cCCCCCcccccccccc
Q 047290 47 IIPCPRCKSMETKFCYFNNY--NVNQPRHFCKGCQRYW 82 (172)
Q Consensus 47 ~~~CPRC~S~~TKFcYyNNy--n~~QPRhfCksCrRYW 82 (172)
...||+|.|.+|+.. +.+ +.+..-|.|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 589999999999965 455 4567779999998644
No 3
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.00 E-value=0.071 Score=41.62 Aligned_cols=35 Identities=31% Similarity=0.668 Sum_probs=28.2
Q ss_pred ccCCCCCCCCceeeEeccccCCCCCcccccccccccc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTA 84 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~ 84 (172)
..||+|.+.+ +-=++-+.....||.|++|.+-|+.
T Consensus 31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 6799999999 3444555555999999999999874
No 4
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=92.44 E-value=0.11 Score=33.56 Aligned_cols=27 Identities=33% Similarity=0.803 Sum_probs=21.7
Q ss_pred ccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
..||+|.+. +...+.+ ..++.|++|++
T Consensus 19 ~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 669999998 6555555 78899999985
No 5
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=92.02 E-value=0.094 Score=33.56 Aligned_cols=31 Identities=35% Similarity=0.687 Sum_probs=21.9
Q ss_pred cccCCCCCCCCceeeEeccccCC-CCCccccccc
Q 047290 47 IIPCPRCKSMETKFCYFNNYNVN-QPRHFCKGCQ 79 (172)
Q Consensus 47 ~~~CPRC~S~~TKFcYyNNyn~~-QPRhfCksCr 79 (172)
.+.||+|.|.+. -|=|-.+.+ ..||.|++|+
T Consensus 5 ~v~CP~C~s~~~--v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEG--VKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCc--ceeCCCCCCCCEeEecCcCC
Confidence 478999999872 123444433 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=91.30 E-value=0.22 Score=31.95 Aligned_cols=37 Identities=27% Similarity=0.805 Sum_probs=29.1
Q ss_pred ccCCCCCCCCceeeEeccccCCCC---Ccccccccccccc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQP---RHFCKGCQRYWTA 84 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QP---RhfCksCrRYWT~ 84 (172)
.+||.|...+.-|-..+-.+...| -|.|.+|..-|..
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 379999988887777666666666 3999999999963
No 7
>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=89.90 E-value=0.27 Score=31.31 Aligned_cols=36 Identities=28% Similarity=0.756 Sum_probs=25.2
Q ss_pred ccCCCCCCCCceeeEeccccCCCCC---ccccccccccc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWT 83 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT 83 (172)
.+||.|.+.+.-|--.+......|- |.|.+|..-|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 3799999988776666666655554 89999999885
No 8
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=83.29 E-value=1.7 Score=31.49 Aligned_cols=42 Identities=21% Similarity=0.643 Sum_probs=31.2
Q ss_pred CCCcccCCCCCCCCceeeEeccccCCCCC---ccccccccccccC
Q 047290 44 PDKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWTAG 85 (172)
Q Consensus 44 p~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT~G 85 (172)
|--...||.|.+.+.-|-..+-.+...|- |.|.+|.-.|+.+
T Consensus 59 ~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 59 PTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred CcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 44458999999877776666655544443 9999999999865
No 9
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=82.29 E-value=0.39 Score=30.32 Aligned_cols=37 Identities=24% Similarity=0.600 Sum_probs=27.1
Q ss_pred cCCCCCCCCceeeEeccccCCCCCccccccccccccCccccc
Q 047290 49 PCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRN 90 (172)
Q Consensus 49 ~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GGtLRn 90 (172)
+||+|...=...-+ ..-+-+.|.+|.-.|=..+.+..
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence 59999985554444 23466889999999988877654
No 10
>PHA02998 RNA polymerase subunit; Provisional
Probab=80.07 E-value=1.9 Score=37.05 Aligned_cols=39 Identities=28% Similarity=0.700 Sum_probs=34.3
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCC---cccccccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWTA 84 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT~ 84 (172)
...+||+|...++-|--.|-.+-..|- |.|..|..-|.-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 568999999999999999999888875 899999999863
No 11
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=77.04 E-value=2.1 Score=29.05 Aligned_cols=41 Identities=22% Similarity=0.625 Sum_probs=29.1
Q ss_pred cCCCCCCCCceeeEeccccCCCCCccccccccccccCccccccc
Q 047290 49 PCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVP 92 (172)
Q Consensus 49 ~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GGtLRnVP 92 (172)
.|-.|...+|..=.-. ...+..+|-+|.-||...|..|.+-
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~~ 41 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPLS 41 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCcc
Confidence 3677887777533222 2467789999999999999766554
No 12
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=70.34 E-value=2.2 Score=26.62 Aligned_cols=32 Identities=28% Similarity=0.554 Sum_probs=19.2
Q ss_pred cccCCCCCCCCcee-eEeccc-------------cCCCCCcccccc
Q 047290 47 IIPCPRCKSMETKF-CYFNNY-------------NVNQPRHFCKGC 78 (172)
Q Consensus 47 ~~~CPRC~S~~TKF-cYyNNy-------------n~~QPRhfCksC 78 (172)
...||.|.+..... -++... .+..+|++|++|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 45799999877221 111110 356778888887
No 13
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=68.66 E-value=5 Score=35.48 Aligned_cols=41 Identities=17% Similarity=0.610 Sum_probs=31.3
Q ss_pred CCCCcccCCCCCCCCceeeEeccccCCCCC---ccccccccccc
Q 047290 43 RPDKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWT 83 (172)
Q Consensus 43 ~p~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT 83 (172)
.+....+||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 344568999999888887666666666664 78999999984
No 14
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=67.63 E-value=3.6 Score=35.08 Aligned_cols=30 Identities=27% Similarity=0.666 Sum_probs=22.4
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
+..+||+|...=.+.-+= .+.-|||..||+
T Consensus 243 ~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 357999999776665442 366799999985
No 15
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=66.11 E-value=4.8 Score=26.94 Aligned_cols=40 Identities=23% Similarity=0.526 Sum_probs=29.5
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCccccccccccccCccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGAL 88 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GGtL 88 (172)
....|--|.+.+|..=.- ...-++.+|-+|.-||...|.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~---g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRR---GPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCcccc---CCCCCCcEeecccHHHHHcCCC
Confidence 356899999888853322 2333369999999999998886
No 16
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=64.84 E-value=4.6 Score=34.51 Aligned_cols=29 Identities=38% Similarity=0.757 Sum_probs=21.9
Q ss_pred cccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 47 IIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 47 ~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
..+||+|...=.+.-+= .+.-|||..||+
T Consensus 235 g~pC~~Cg~~I~~~~~~-----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVG-----GRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEEC-----CCCcEECCCCcC
Confidence 46899999876664442 367799999995
No 17
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=63.32 E-value=5.7 Score=32.60 Aligned_cols=44 Identities=20% Similarity=0.372 Sum_probs=32.4
Q ss_pred cCCCCCCCCceeeEe---ccccCCCCCccccccccccccCccccccc
Q 047290 49 PCPRCKSMETKFCYF---NNYNVNQPRHFCKGCQRYWTAGGALRNVP 92 (172)
Q Consensus 49 ~CPRC~S~~TKFcYy---NNyn~~QPRhfCksCrRYWT~GGtLRnVP 92 (172)
.||-|...+||+-=- .+-+.-+-|..|.+|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998643 33344566799999999888655544444
No 18
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=62.75 E-value=3.4 Score=35.11 Aligned_cols=38 Identities=24% Similarity=0.565 Sum_probs=18.1
Q ss_pred CcccCCCCCCCCce-eeEeccccCC-CCCccccccccccc
Q 047290 46 KIIPCPRCKSMETK-FCYFNNYNVN-QPRHFCKGCQRYWT 83 (172)
Q Consensus 46 ~~~~CPRC~S~~TK-FcYyNNyn~~-QPRhfCksCrRYWT 83 (172)
....||.|.+.+.. +-||..-... .--+.|.+|+.|+-
T Consensus 210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp -TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 45689999877654 5565333333 33389999999983
No 19
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=61.65 E-value=5.9 Score=28.60 Aligned_cols=31 Identities=26% Similarity=0.501 Sum_probs=24.5
Q ss_pred cccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 47 IIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 47 ~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
+..||+|.+++|=..|..|. ..-..|-+|.=
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~---ve~vECV~CGy 38 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENG---VEYVECVECGY 38 (71)
T ss_pred CccCCCCcCccEEEEEEeCC---ceEEEecCCCC
Confidence 57899999999888887776 55567888853
No 20
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=61.21 E-value=5.8 Score=33.69 Aligned_cols=30 Identities=30% Similarity=0.661 Sum_probs=21.9
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
...+||+|...=.+.-+ + .+.-|||..||+
T Consensus 244 ~g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQ-G----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEEE-C----CCCcEECcCCCC
Confidence 35689999977655333 3 366799999986
No 21
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=61.14 E-value=4.4 Score=33.68 Aligned_cols=13 Identities=38% Similarity=0.984 Sum_probs=11.7
Q ss_pred ccccccccccccC
Q 047290 73 HFCKGCQRYWTAG 85 (172)
Q Consensus 73 hfCksCrRYWT~G 85 (172)
..|+.|.+|+..|
T Consensus 36 ~~C~~Cg~~~~~~ 48 (236)
T PF04981_consen 36 TICPKCGRYRIGG 48 (236)
T ss_pred eECCCCCCEECCC
Confidence 7899999999984
No 22
>PRK10445 endonuclease VIII; Provisional
Probab=58.82 E-value=6.7 Score=33.33 Aligned_cols=30 Identities=30% Similarity=0.668 Sum_probs=22.3
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
...+||+|...=.+.-+= .+.-|||..||.
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~-----gR~t~~CP~CQ~ 263 (263)
T PRK10445 234 DGEACERCGGIIEKTTLS-----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCEeEEEEEC-----CCCcEECCCCcC
Confidence 357899998877665552 366799999984
No 23
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=57.75 E-value=7.5 Score=33.31 Aligned_cols=29 Identities=24% Similarity=0.684 Sum_probs=21.8
Q ss_pred cccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 47 IIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 47 ~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
..+||+|...=.+.-+= .+.-|||..||+
T Consensus 254 g~pC~~Cg~~I~~~~~~-----gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKLA-----GRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEEC-----CCccEECCCCcC
Confidence 46999999877665542 266699999984
No 24
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.07 E-value=8.6 Score=32.76 Aligned_cols=28 Identities=36% Similarity=0.718 Sum_probs=21.1
Q ss_pred cccCCCCCCCCceeeEeccccCCCCCccccccc
Q 047290 47 IIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQ 79 (172)
Q Consensus 47 ~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCr 79 (172)
..+||+|...=.+.-+ + .+.-|||..||
T Consensus 245 g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKV-G----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEE-C----CCCCEECCCCC
Confidence 5699999987766443 3 36679999997
No 25
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=54.91 E-value=5.2 Score=25.57 Aligned_cols=17 Identities=35% Similarity=0.925 Sum_probs=7.2
Q ss_pred CCCccccccccccccCc
Q 047290 70 QPRHFCKGCQRYWTAGG 86 (172)
Q Consensus 70 QPRhfCksCrRYWT~GG 86 (172)
+|||+|.=|..|.|..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 26
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=54.20 E-value=9.7 Score=33.99 Aligned_cols=37 Identities=19% Similarity=0.533 Sum_probs=22.2
Q ss_pred CcccCCCCCCCCceeeEecccc---CC-CCCccccccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYN---VN-QPRHFCKGCQRYWT 83 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn---~~-QPRhfCksCrRYWT 83 (172)
....||.|.+.+ +.-|+.-.. .. ---..|.+|+.|+-
T Consensus 223 ~R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 223 VRVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred cCccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 456788888764 455654332 11 12267888888874
No 27
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=53.69 E-value=11 Score=24.72 Aligned_cols=35 Identities=20% Similarity=0.460 Sum_probs=20.1
Q ss_pred CcccCCCCCCCCceeeEeccccCCC-CCcccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQ-PRHFCKGCQR 80 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~Q-PRhfCksCrR 80 (172)
+..+||.|.+....+.+........ -.-.|.+|.-
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5789999966665555433222111 2345888865
No 28
>PHA00626 hypothetical protein
Probab=52.32 E-value=9.9 Score=27.41 Aligned_cols=36 Identities=17% Similarity=0.201 Sum_probs=23.9
Q ss_pred cCCCCCCCCceeeEeccccCCCCCccccccccccccCc
Q 047290 49 PCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGG 86 (172)
Q Consensus 49 ~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GG 86 (172)
.||.|.|.+--=|-.= +...-||.|++|.=.+|+..
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhh
Confidence 5999999754321110 11135799999999998764
No 29
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=50.44 E-value=8.7 Score=25.87 Aligned_cols=26 Identities=35% Similarity=0.558 Sum_probs=18.6
Q ss_pred cccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 47 IIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 47 ~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
..-||+|.+. |..-.+ .|+.|..|..
T Consensus 20 ~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 3479999873 555443 6899999964
No 30
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=50.13 E-value=11 Score=30.49 Aligned_cols=45 Identities=24% Similarity=0.450 Sum_probs=32.8
Q ss_pred ccCCCCCCCCceee---EeccccCCCCCccccccccccccCccccccc
Q 047290 48 IPCPRCKSMETKFC---YFNNYNVNQPRHFCKGCQRYWTAGGALRNVP 92 (172)
Q Consensus 48 ~~CPRC~S~~TKFc---YyNNyn~~QPRhfCksCrRYWT~GGtLRnVP 92 (172)
..||-|.+..|.+- |+-.-|.-.-|+-|.+|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999998764 4444444555699999999888766655555
No 31
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=48.63 E-value=14 Score=33.11 Aligned_cols=38 Identities=18% Similarity=0.459 Sum_probs=22.5
Q ss_pred CcccCCCCCCCCceeeEeccccC--CCCCcccccccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNV--NQPRHFCKGCQRYWTA 84 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~--~QPRhfCksCrRYWT~ 84 (172)
....||.|.+. .+.-|+.--.. .---..|.+|+.|+--
T Consensus 225 ~R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 225 VRVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred cCccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 35678888874 35556532221 1222788888888743
No 32
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=45.21 E-value=9 Score=27.06 Aligned_cols=17 Identities=24% Similarity=0.253 Sum_probs=6.7
Q ss_pred CCCCcccCCCCCCCCce
Q 047290 43 RPDKIIPCPRCKSMETK 59 (172)
Q Consensus 43 ~p~~~~~CPRC~S~~TK 59 (172)
----.++|+.|.|.||+
T Consensus 44 fH~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 44 FHFLGHKCSHCGSYNTR 60 (61)
T ss_dssp --TT----TTTS---EE
T ss_pred eeHhhhcCCCCCCcccC
Confidence 34557899999999997
No 33
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=43.88 E-value=21 Score=23.56 Aligned_cols=32 Identities=22% Similarity=0.545 Sum_probs=19.0
Q ss_pred ccCCCCCCCCceeeEeccccCCCCCcc-cccccc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPRHF-CKGCQR 80 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPRhf-CksCrR 80 (172)
.+||.|.+..-.|-+ ...+..-..++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 689999997765542 12233334444 777754
No 34
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=41.45 E-value=22 Score=28.13 Aligned_cols=39 Identities=21% Similarity=0.582 Sum_probs=33.3
Q ss_pred CCcccCCCCCCCCceeeEeccccCCCCC---ccccccccccc
Q 047290 45 DKIIPCPRCKSMETKFCYFNNYNVNQPR---HFCKGCQRYWT 83 (172)
Q Consensus 45 ~~~~~CPRC~S~~TKFcYyNNyn~~QPR---hfCksCrRYWT 83 (172)
.-...||+|...+.-|--+|-.+..-|- |.|-+|.--|-
T Consensus 63 ~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 63 QTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 3457899999999999999888888886 89999998884
No 35
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=40.91 E-value=12 Score=21.94 Aligned_cols=27 Identities=26% Similarity=0.594 Sum_probs=14.1
Q ss_pred ccCCCCCCCCceeeEeccccCCCCCccccccc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQ 79 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCr 79 (172)
.+||||...-.++-..+ +.-+||..|+
T Consensus 2 ~~C~rC~~~~~~~~~~~-----r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING-----RSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETT-----EEEEE-TTTC
T ss_pred CcCccCCCcceEeEecC-----CCCeECcCCc
Confidence 57999988877665522 2236777765
No 36
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=40.71 E-value=16 Score=23.91 Aligned_cols=33 Identities=27% Similarity=0.748 Sum_probs=18.9
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
...+||-|.+ ..+|..|-+.. .+-..+|..|..
T Consensus 2 ~h~pCP~CGG-~DrFri~~d~~-~~G~~~C~~C~~ 34 (40)
T PF08273_consen 2 KHGPCPICGG-KDRFRIFDDKD-GRGTWICRQCGG 34 (40)
T ss_dssp EEE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCCcC-ccccccCcCcc-cCCCEECCCCCC
Confidence 3568999988 56888666543 337789999943
No 37
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=39.87 E-value=19 Score=31.90 Aligned_cols=30 Identities=27% Similarity=0.575 Sum_probs=23.0
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
+..+|++|.+.=.|.-. ..+..|||..||+
T Consensus 244 ~GepC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 56799999998766432 3467799999985
No 38
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=39.20 E-value=24 Score=25.28 Aligned_cols=31 Identities=23% Similarity=0.375 Sum_probs=22.5
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQ 79 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCr 79 (172)
-+..||+|.+++|=..|.-|.. .-..|-.|.
T Consensus 8 AGA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred ccccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 3578999999999988855543 345676664
No 39
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=34.11 E-value=26 Score=29.30 Aligned_cols=44 Identities=25% Similarity=0.330 Sum_probs=30.3
Q ss_pred cCCCCCCCCceeeEecc---ccCCCCCccccccccccccCccccccc
Q 047290 49 PCPRCKSMETKFCYFNN---YNVNQPRHFCKGCQRYWTAGGALRNVP 92 (172)
Q Consensus 49 ~CPRC~S~~TKFcYyNN---yn~~QPRhfCksCrRYWT~GGtLRnVP 92 (172)
.||.|.+.+||+-==-. -+.-+-|.-|.+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 69999999999863221 233345689999998888554444443
No 40
>PF15242 FAM53: Family of FAM53
Probab=33.50 E-value=20 Score=32.67 Aligned_cols=24 Identities=42% Similarity=0.825 Sum_probs=18.7
Q ss_pred ccchhhhhhcCCCCcccccccceeecCCCCC
Q 047290 140 EDWHPAAAAHGYGGFQNAFPVKRRRSNSGGQ 170 (172)
Q Consensus 140 ~~~~~a~~~h~~g~f~~~fp~kr~r~~s~~q 170 (172)
--|++ +|=+..-|||+|||+|||-
T Consensus 136 s~WRP-------~gSKVWTpV~kRrC~SGGs 159 (314)
T PF15242_consen 136 SPWRP-------QGSKVWTPVEKRRCHSGGS 159 (314)
T ss_pred CcccC-------CCCcccceecccccCCCCc
Confidence 35887 4456677999999999984
No 41
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=30.78 E-value=40 Score=24.50 Aligned_cols=34 Identities=29% Similarity=0.684 Sum_probs=24.0
Q ss_pred CCCcccCCCCCCCCceeeEeccccCCCCCccccccccc
Q 047290 44 PDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRY 81 (172)
Q Consensus 44 p~~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRY 81 (172)
-|...+||.|.-..-.+---++|- +..|..|..-
T Consensus 3 ~d~lKPCPFCG~~~~~v~~~~g~~----~v~C~~CgA~ 36 (64)
T PRK09710 3 YDNVKPCPFCGCPSVTVKAISGYY----RAKCNGCESR 36 (64)
T ss_pred cccccCCCCCCCceeEEEecCceE----EEEcCCCCcC
Confidence 367889999988776665433332 4679999874
No 42
>PLN02779 haloacid dehalogenase-like hydrolase family protein
Probab=29.67 E-value=14 Score=31.12 Aligned_cols=12 Identities=50% Similarity=0.722 Sum_probs=9.7
Q ss_pred ccccccchhccc
Q 047290 131 QFDLEGVFVEDW 142 (172)
Q Consensus 131 ~~~l~~~~~~~~ 142 (172)
-||+||++++.+
T Consensus 44 IFDlDGTLvDS~ 55 (286)
T PLN02779 44 LFDCDGVLVETE 55 (286)
T ss_pred EEeCceeEEccc
Confidence 488898888777
No 43
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=29.11 E-value=32 Score=26.48 Aligned_cols=42 Identities=21% Similarity=0.457 Sum_probs=30.5
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCccccccccccccCcccccccCC
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGGALRNVPVG 94 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GGtLRnVPVG 94 (172)
....||.|.+...| -..----.|..|..-|+.|+-....|.|
T Consensus 34 ~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 34 AKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred cCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 34689999998555 1122237899999999999987766654
No 44
>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=28.24 E-value=34 Score=22.87 Aligned_cols=32 Identities=22% Similarity=0.421 Sum_probs=23.6
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCcccccccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTA 84 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~ 84 (172)
....||.|.....+ +..+-.+.|..|.-.+..
T Consensus 27 TSq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 34569999988877 666667889998766543
No 45
>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=25.15 E-value=34 Score=21.28 Aligned_cols=28 Identities=29% Similarity=0.596 Sum_probs=13.8
Q ss_pred ccCCCCCCCCceeeEeccccCCCCCccccccccccc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWT 83 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT 83 (172)
-+||-|.|..|= ...--+.|..|..=|.
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 369999998774 5566688888877663
No 46
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=24.79 E-value=64 Score=21.81 Aligned_cols=27 Identities=30% Similarity=0.848 Sum_probs=19.9
Q ss_pred cCCCCCCcccCCCCCCCCceeeEeccccCCCCCccccccc
Q 047290 40 VDKRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQ 79 (172)
Q Consensus 40 ~~~~p~~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCr 79 (172)
.+..| +...||-|.. +.+|.+.|.+|.
T Consensus 20 ~l~~~-~l~~c~~cg~------------~~~~H~vc~~cG 46 (56)
T PF01783_consen 20 KLKAP-NLVKCPNCGE------------PKLPHRVCPSCG 46 (56)
T ss_dssp S--TT-SEEESSSSSS------------EESTTSBCTTTB
T ss_pred ccccc-ceeeeccCCC------------EecccEeeCCCC
Confidence 44556 8899999985 238899999996
No 47
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=24.30 E-value=32 Score=24.04 Aligned_cols=13 Identities=46% Similarity=1.068 Sum_probs=10.6
Q ss_pred CcccCCCCCCCCc
Q 047290 46 KIIPCPRCKSMET 58 (172)
Q Consensus 46 ~~~~CPRC~S~~T 58 (172)
-...||||...|.
T Consensus 23 leIKCpRC~tiN~ 35 (51)
T PF10122_consen 23 LEIKCPRCKTINH 35 (51)
T ss_pred EEEECCCCCccce
Confidence 4578999998875
No 48
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=24.12 E-value=50 Score=26.18 Aligned_cols=31 Identities=29% Similarity=0.730 Sum_probs=24.7
Q ss_pred ccCCCCCCCCceeeEeccccCCCCCccccccccccccCc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGG 86 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GG 86 (172)
.+||.|.|..|- ..+.-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY--------~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY--------HDGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE--------ecCCeeECccccccccccc
Confidence 479999998663 2355699999999999876
No 49
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=23.76 E-value=47 Score=24.21 Aligned_cols=31 Identities=26% Similarity=0.452 Sum_probs=17.2
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCcccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQR 80 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrR 80 (172)
-...||-|+..+..|..+.+.+ ++.|-+|..
T Consensus 32 ~~~~CPfH~d~~pS~~i~~~k~----~~~Cf~Cg~ 62 (97)
T PF01807_consen 32 YRCLCPFHDDKTPSFSINPDKN----RFKCFGCGK 62 (97)
T ss_dssp EEE--SSS--SS--EEEETTTT----EEEETTT--
T ss_pred EEEECcCCCCCCCceEEECCCC----eEEECCCCC
Confidence 3577999998777777665433 799999984
No 50
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=22.58 E-value=68 Score=20.68 Aligned_cols=31 Identities=29% Similarity=0.800 Sum_probs=20.5
Q ss_pred CcccCCCCCCCCceeeEeccccCCCCCccccccc
Q 047290 46 KIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQ 79 (172)
Q Consensus 46 ~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCr 79 (172)
+..+||-|.+ ..+|= |++... .-..+|..|.
T Consensus 2 ~~~pCP~CGG-~DrFr-~~d~~g-~G~~~C~~Cg 32 (37)
T smart00778 2 RHGPCPNCGG-SDRFR-FDDKDG-RGTWFCSVCG 32 (37)
T ss_pred CccCCCCCCC-ccccc-cccCCC-CcCEEeCCCC
Confidence 3579999988 45677 554322 2557888883
No 51
>PF07383 DUF1496: Protein of unknown function (DUF1496); InterPro: IPR009971 This family consists of several bacterial proteins of around 90 residues in length. Members of this family seem to be found exclusively in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown.
Probab=22.52 E-value=63 Score=22.68 Aligned_cols=14 Identities=14% Similarity=0.724 Sum_probs=10.1
Q ss_pred CceeeEeccccCCC
Q 047290 57 ETKFCYFNNYNVNQ 70 (172)
Q Consensus 57 ~TKFcYyNNyn~~Q 70 (172)
..|+|||+|-+-+.
T Consensus 11 ~~r~C~Yqdq~YSe 24 (56)
T PF07383_consen 11 QQRCCYYQDQAYSE 24 (56)
T ss_pred cceEEEEcCCccCC
Confidence 34999999865443
No 52
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.49 E-value=80 Score=24.15 Aligned_cols=35 Identities=29% Similarity=0.560 Sum_probs=25.0
Q ss_pred CCcccCCCCCCCCceeeEeccccCCCCCccccccccccc
Q 047290 45 DKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWT 83 (172)
Q Consensus 45 ~~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT 83 (172)
.....||.|.+. +--+=... ..+.+.|..|.-|..
T Consensus 19 pt~f~CP~Cge~-~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 19 PKIFECPRCGKV-SISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred CcEeECCCCCCe-EeeeecCC---CcceEECCCCCCccC
Confidence 478899999953 33333433 578899999998843
No 53
>PRK10220 hypothetical protein; Provisional
Probab=22.31 E-value=58 Score=25.97 Aligned_cols=31 Identities=26% Similarity=0.626 Sum_probs=24.8
Q ss_pred ccCCCCCCCCceeeEeccccCCCCCccccccccccccCc
Q 047290 48 IPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAGG 86 (172)
Q Consensus 48 ~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~GG 86 (172)
.+||.|.|..|- ..+.-+.|..|.-=|+...
T Consensus 4 P~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 579999998663 2355699999999999875
No 54
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.07 E-value=61 Score=20.58 Aligned_cols=14 Identities=50% Similarity=1.151 Sum_probs=11.1
Q ss_pred CCcccCCCCCCCCc
Q 047290 45 DKIIPCPRCKSMET 58 (172)
Q Consensus 45 ~~~~~CPRC~S~~T 58 (172)
+....||.|.+.+.
T Consensus 24 ~~~~~CP~Cg~~~~ 37 (42)
T PF09723_consen 24 DDPVPCPECGSTEV 37 (42)
T ss_pred CCCCcCCCCCCCce
Confidence 56789999999544
No 55
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=21.32 E-value=50 Score=30.61 Aligned_cols=19 Identities=37% Similarity=1.069 Sum_probs=14.6
Q ss_pred CCCCCcccCCCCCCCCceeeE
Q 047290 42 KRPDKIIPCPRCKSMETKFCY 62 (172)
Q Consensus 42 ~~p~~~~~CPRC~S~~TKFcY 62 (172)
..|...-+||||...| ||.
T Consensus 301 a~pa~t~~~~r~~k~n--fc~ 319 (345)
T COG4260 301 AAPAATWPCARCAKLN--FCL 319 (345)
T ss_pred cCCcccCcchhccccc--ccc
Confidence 3467778999999888 654
No 56
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.29 E-value=61 Score=20.36 Aligned_cols=32 Identities=22% Similarity=0.476 Sum_probs=17.7
Q ss_pred cCCCCCCCCceeeEeccccCCCCCccccccccccccC
Q 047290 49 PCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWTAG 85 (172)
Q Consensus 49 ~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT~G 85 (172)
-||.|.++ .|..... ...++.|..|.-.+-..
T Consensus 2 FCp~Cg~~----l~~~~~~-~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNM----LIPKEGK-EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCc----cccccCC-CCCEEECCcCCCeEECC
Confidence 47888762 2333221 11478888888654433
No 57
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=21.07 E-value=58 Score=23.73 Aligned_cols=41 Identities=15% Similarity=0.335 Sum_probs=21.2
Q ss_pred CCCCCcccCCCCCCCCceeeEeccccCCCCCccccccccccc
Q 047290 42 KRPDKIIPCPRCKSMETKFCYFNNYNVNQPRHFCKGCQRYWT 83 (172)
Q Consensus 42 ~~p~~~~~CPRC~S~~TKFcYyNNyn~~QPRhfCksCrRYWT 83 (172)
.+.+..-.||.|+..++=-|=...- ......-|..|.-.|.
T Consensus 17 ~~l~~~F~CPfC~~~~sV~v~idkk-~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 17 PKLPKVFDCPFCNHEKSVSVKIDKK-EGIGILSCRVCGESFQ 57 (81)
T ss_dssp ---SS----TTT--SS-EEEEEETT-TTEEEEEESSS--EEE
T ss_pred CCCCceEcCCcCCCCCeEEEEEEcc-CCEEEEEecCCCCeEE
Confidence 3457889999999888877777443 5566788999966554
No 58
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.67 E-value=67 Score=24.34 Aligned_cols=13 Identities=23% Similarity=0.928 Sum_probs=6.4
Q ss_pred cccCCCCCCCCce
Q 047290 47 IIPCPRCKSMETK 59 (172)
Q Consensus 47 ~~~CPRC~S~~TK 59 (172)
...||.|.|.+.+
T Consensus 86 ~~~CP~Cgs~~~~ 98 (115)
T TIGR00100 86 LYRCPKCHGIMLQ 98 (115)
T ss_pred CccCcCCcCCCcE
Confidence 3445555555443
Done!