Query 040161
Match_columns 366
No_of_seqs 137 out of 202
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 05:41:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040161hhsearch_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 8.1E-37 1.8E-41 235.4 4.0 61 84-144 2-62 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.4 0.032 7E-07 48.8 1.0 34 87-122 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 93.2 0.079 1.7E-06 37.8 2.5 29 86-120 17-45 (46)
4 COG3677 Transposase and inacti 92.8 0.074 1.6E-06 45.7 2.3 36 87-124 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 91.0 0.15 3.3E-06 36.0 1.8 31 87-119 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 89.1 0.42 9E-06 33.8 2.8 37 88-124 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.8 0.66 1.4E-05 32.6 2.2 35 89-123 2-39 (39)
8 PF04216 FdhE: Protein involve 84.2 0.51 1.1E-05 44.1 1.4 38 86-123 210-249 (290)
9 PF13453 zf-TFIIB: Transcripti 77.5 0.76 1.6E-05 32.0 0.1 37 89-130 1-37 (41)
10 PHA02998 RNA polymerase subuni 77.5 2.3 4.9E-05 40.0 3.1 39 86-124 142-183 (195)
11 TIGR01384 TFS_arch transcripti 76.6 3.3 7.2E-05 33.1 3.5 39 87-125 62-103 (104)
12 cd00202 ZnF_GATA Zinc finger D 74.3 2.8 6.1E-05 31.4 2.4 40 89-131 1-40 (54)
13 PF04981 NMD3: NMD3 family ; 69.9 2.3 5E-05 38.9 1.3 37 90-126 1-49 (236)
14 PRK14810 formamidopyrimidine-D 66.8 3.8 8.3E-05 38.5 2.1 31 85-120 242-272 (272)
15 TIGR01385 TFSII transcription 66.4 5.6 0.00012 38.7 3.2 38 86-123 257-297 (299)
16 smart00401 ZnF_GATA zinc finge 64.3 5.2 0.00011 29.6 1.9 40 86-128 2-41 (52)
17 PF14690 zf-ISL3: zinc-finger 63.4 3.7 7.9E-05 28.4 1.0 32 87-118 2-47 (47)
18 PRK14811 formamidopyrimidine-D 62.7 5.2 0.00011 37.7 2.1 30 86-120 234-263 (269)
19 TIGR00244 transcriptional regu 62.7 5.5 0.00012 36.0 2.1 44 89-132 2-48 (147)
20 PRK03564 formate dehydrogenase 60.1 6.1 0.00013 38.9 2.2 39 85-124 224-264 (309)
21 PRK01103 formamidopyrimidine/5 59.3 6.5 0.00014 36.8 2.1 30 86-120 244-273 (274)
22 PF06220 zf-U1: U1 zinc finger 58.7 3.9 8.5E-05 28.9 0.4 17 110-126 1-17 (38)
23 PRK10445 endonuclease VIII; Pr 58.1 7 0.00015 36.6 2.1 30 86-120 234-263 (263)
24 TIGR01562 FdhE formate dehydro 57.0 7.1 0.00015 38.3 2.0 37 86-123 223-263 (305)
25 PRK13945 formamidopyrimidine-D 56.7 7.9 0.00017 36.6 2.2 30 86-120 253-282 (282)
26 PRK00464 nrdR transcriptional 56.6 8 0.00017 34.6 2.1 45 88-132 1-48 (154)
27 PHA00626 hypothetical protein 55.4 8.3 0.00018 30.6 1.8 36 89-126 2-37 (59)
28 TIGR00577 fpg formamidopyrimid 50.3 11 0.00024 35.4 2.1 29 86-119 244-272 (272)
29 PF09526 DUF2387: Probable met 46.7 15 0.00033 29.3 2.1 32 87-121 8-39 (71)
30 PRK00432 30S ribosomal protein 46.5 11 0.00023 28.2 1.1 27 86-120 19-45 (50)
31 KOG1819 FYVE finger-containing 46.2 7.7 0.00017 41.9 0.4 16 110-125 915-930 (990)
32 KOG2906 RNA polymerase III sub 43.5 22 0.00047 31.0 2.7 41 83-123 61-104 (105)
33 COG0266 Nei Formamidopyrimidin 39.6 19 0.00041 35.1 2.0 30 86-120 244-273 (273)
34 PF14599 zinc_ribbon_6: Zinc-r 36.0 15 0.00032 28.7 0.5 15 85-99 46-60 (61)
35 TIGR03655 anti_R_Lar restricti 34.8 34 0.00074 25.0 2.2 32 88-120 2-34 (53)
36 PF01807 zf-CHC2: CHC2 zinc fi 33.8 28 0.0006 28.2 1.8 30 87-120 33-62 (97)
37 PF14354 Lar_restr_allev: Rest 33.8 38 0.00082 24.6 2.3 35 86-120 2-37 (61)
38 PF07282 OrfB_Zn_ribbon: Putat 33.5 25 0.00053 26.1 1.3 32 86-124 27-58 (69)
39 COG1327 Predicted transcriptio 32.0 28 0.00061 32.0 1.7 43 89-131 2-47 (156)
40 KOG1899 LAR transmembrane tyro 30.1 2.3E+02 0.005 31.8 8.2 31 294-324 486-517 (861)
41 PF06827 zf-FPG_IleRS: Zinc fi 30.1 25 0.00055 22.9 0.8 27 88-119 2-28 (30)
42 COG4260 Membrane protease subu 30.0 30 0.00065 35.0 1.6 36 83-120 302-342 (345)
43 PF08273 Prim_Zn_Ribbon: Zinc- 28.6 41 0.00089 24.4 1.7 32 87-120 3-34 (40)
44 COG1997 RPL43A Ribosomal prote 28.6 32 0.0007 29.2 1.4 45 83-134 31-75 (89)
45 smart00661 RPOL9 RNA polymeras 24.3 52 0.0011 23.0 1.6 33 89-126 2-34 (52)
46 TIGR02443 conserved hypothetic 24.3 57 0.0012 25.9 1.9 30 87-119 9-38 (59)
47 KOG0170 E3 ubiquitin protein l 24.1 24 0.00052 38.0 -0.2 19 259-278 273-291 (621)
48 PF08274 PhnA_Zn_Ribbon: PhnA 22.7 40 0.00087 23.3 0.7 28 88-123 3-30 (30)
49 PF06044 DRP: Dam-replacing fa 22.6 34 0.00075 33.5 0.5 33 87-123 31-64 (254)
50 COG5175 MOT2 Transcriptional r 22.5 13 0.00028 38.4 -2.4 36 98-136 41-76 (480)
51 TIGR00686 phnA alkylphosphonat 22.1 63 0.0014 28.3 2.0 31 88-126 3-33 (109)
52 TIGR00595 priA primosomal prot 21.8 65 0.0014 33.0 2.3 33 85-118 220-259 (505)
53 PRK10220 hypothetical protein; 20.5 74 0.0016 28.0 2.1 32 87-126 3-34 (111)
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=8.1e-37 Score=235.43 Aligned_cols=61 Identities=80% Similarity=1.580 Sum_probs=59.3
Q ss_pred CCCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccccCCCCcccCCCCC
Q 040161 84 NNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSS 144 (366)
Q Consensus 84 ~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNVPVGGG~RKnK~ss 144 (366)
+++.++||||+|.||||||||||++.||||||++|+||||+||+|||||||||+||+|+++
T Consensus 2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~ 62 (63)
T PF02701_consen 2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSS 62 (63)
T ss_pred CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCC
Confidence 5688999999999999999999999999999999999999999999999999999999987
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=93.41 E-value=0.032 Score=48.79 Aligned_cols=34 Identities=24% Similarity=0.728 Sum_probs=27.3
Q ss_pred CcCCCCCCCCCceeeeecCc--CCCCCccccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNY--NLTQPRHFCKTCRRYW 122 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNy--n~~QPRhfCksCrRYW 122 (366)
...||||.|.+|+.. +.| +.++.-|+|++|+.=+
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 589999999999964 566 4457779999998644
No 3
>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=93.20 E-value=0.079 Score=37.77 Aligned_cols=29 Identities=34% Similarity=0.825 Sum_probs=23.3
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
++..||+|.+. ++..+.+ +.+|.|++|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 34779999998 6666665 78999999986
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.77 E-value=0.074 Score=45.65 Aligned_cols=36 Identities=33% Similarity=0.653 Sum_probs=28.5
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCccccccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTK 124 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~ 124 (366)
...||+|.+.+ +-=+.-+.....||.|++|++-|+.
T Consensus 30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred cCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 47899999999 3335555555999999999999874
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=91.02 E-value=0.15 Score=35.98 Aligned_cols=31 Identities=35% Similarity=0.790 Sum_probs=21.6
Q ss_pred CcCCCCCCCCCceeeeecCcCCC-CCcccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLT-QPRHFCKTCR 119 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~-QPRhfCksCr 119 (366)
.+.||||.+.+. -|=|-.+.. ..||+|++|+
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 368999999872 123444333 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.10 E-value=0.42 Score=33.83 Aligned_cols=37 Identities=22% Similarity=0.697 Sum_probs=27.9
Q ss_pred cCCCCCCCCCceeeeecCcCCCCC---ccccccccccccc
Q 040161 88 LRCPRCDSSNTKFCYYNNYNLTQP---RHFCKTCRRYWTK 124 (366)
Q Consensus 88 ~~CPRC~S~nTKFcYYNNyn~~QP---RhfCksCrRYWT~ 124 (366)
.+||+|...+.-|-..+-.....| -|.|.+|...|..
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 379999977777666655655555 4999999999963
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=85.76 E-value=0.66 Score=32.61 Aligned_cols=35 Identities=23% Similarity=0.738 Sum_probs=24.0
Q ss_pred CCCCCCCCCceeeeecCcCCCCCc---ccccccccccc
Q 040161 89 RCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWT 123 (366)
Q Consensus 89 ~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT 123 (366)
+||+|...+..|--.+......|- |.|.+|..-|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 799999988766555555555443 99999999995
No 8
>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=84.22 E-value=0.51 Score=44.10 Aligned_cols=38 Identities=21% Similarity=0.647 Sum_probs=18.8
Q ss_pred CCcCCCCCCCCC-ceeeeecCcCCC-CCcccccccccccc
Q 040161 86 QNLRCPRCDSSN-TKFCYYNNYNLT-QPRHFCKTCRRYWT 123 (366)
Q Consensus 86 e~~~CPRC~S~n-TKFcYYNNyn~~-QPRhfCksCrRYWT 123 (366)
....||.|...+ .++-||..-... .--+.|+.|+.|+-
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 467899999854 567777433333 33499999999983
No 9
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=77.51 E-value=0.76 Score=32.05 Aligned_cols=37 Identities=24% Similarity=0.646 Sum_probs=27.0
Q ss_pred CCCCCCCCCceeeeecCcCCCCCcccccccccccccCccccc
Q 040161 89 RCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRN 130 (366)
Q Consensus 89 ~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRN 130 (366)
+||+|...=...-+ ..-+-+.|.+|.-.|=..|.+..
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 69999985444433 23566889999999988776654
No 10
>PHA02998 RNA polymerase subunit; Provisional
Probab=77.48 E-value=2.3 Score=40.05 Aligned_cols=39 Identities=28% Similarity=0.653 Sum_probs=33.5
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCc---cccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWTK 124 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT~ 124 (366)
...+||+|...+.-|--.|-++...|- |.|..|..-|.-
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 568999999999998888888887775 899999999963
No 11
>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=76.62 E-value=3.3 Score=33.13 Aligned_cols=39 Identities=18% Similarity=0.620 Sum_probs=28.3
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCc---ccccccccccccC
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWTKG 125 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT~G 125 (366)
...||+|...+.-|-..+-.+...|- |.|..|+-.|+.+
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 47999998777666555544443333 9999999999875
No 12
>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=74.30 E-value=2.8 Score=31.43 Aligned_cols=40 Identities=25% Similarity=0.717 Sum_probs=28.6
Q ss_pred CCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccc
Q 040161 89 RCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNV 131 (366)
Q Consensus 89 ~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNV 131 (366)
.|-.|...+|..=.-.. .....+|-+|.-||.+.|..|-+
T Consensus 1 ~C~~C~~~~Tp~WR~g~---~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 1 ACSNCGTTTTPLWRRGP---SGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCCcccccCC---CCcchHHHHHHHHHHhcCCCCCc
Confidence 37778887775322222 46779999999999999965554
No 13
>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=69.91 E-value=2.3 Score=38.93 Aligned_cols=37 Identities=30% Similarity=0.842 Sum_probs=24.4
Q ss_pred CCCCCCCCce-------eeeecCcCCCC-----CcccccccccccccCc
Q 040161 90 CPRCDSSNTK-------FCYYNNYNLTQ-----PRHFCKTCRRYWTKGG 126 (366)
Q Consensus 90 CPRC~S~nTK-------FcYYNNyn~~Q-----PRhfCksCrRYWT~GG 126 (366)
||+|...... =||...+.+.. --.+|+.|.||+..|.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 6666654433 26666666543 2379999999998843
No 14
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=66.81 E-value=3.8 Score=38.54 Aligned_cols=31 Identities=16% Similarity=0.591 Sum_probs=22.9
Q ss_pred CCCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
.+..+||||...=.|.-+= .+.-|||..|++
T Consensus 242 R~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 242 RTGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 3567999999866665442 266699999985
No 15
>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=66.35 E-value=5.6 Score=38.73 Aligned_cols=38 Identities=16% Similarity=0.582 Sum_probs=28.0
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCc---ccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWT 123 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT 123 (366)
....||+|...+..|-..+......|- |.|..|...|.
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 358999999777776555555555553 78999999994
No 16
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=64.33 E-value=5.2 Score=29.63 Aligned_cols=40 Identities=23% Similarity=0.612 Sum_probs=29.4
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGAL 128 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtL 128 (366)
....|--|...+|..=.- ...-++.+|-+|.-||.+.|.+
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 357899999888864322 2223379999999999998886
No 17
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=63.39 E-value=3.7 Score=28.38 Aligned_cols=32 Identities=31% Similarity=0.687 Sum_probs=19.2
Q ss_pred CcCCCCCCCCCcee-eeecCc-------------CCCCCccccccc
Q 040161 87 NLRCPRCDSSNTKF-CYYNNY-------------NLTQPRHFCKTC 118 (366)
Q Consensus 87 ~~~CPRC~S~nTKF-cYYNNy-------------n~~QPRhfCksC 118 (366)
...||.|.+..-+. -++... .+..+|++|++|
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 46799999876221 111111 344778888887
No 18
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=62.69 E-value=5.2 Score=37.68 Aligned_cols=30 Identities=30% Similarity=0.801 Sum_probs=22.4
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
+..+||||...=.|.-+ . .+.-|||..|++
T Consensus 234 ~g~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVV-G----GRGTHFCPQCQP 263 (269)
T ss_pred CcCCCCcCCCeeEEEEE-C----CCCcEECCCCcC
Confidence 45789999987666433 2 266799999996
No 19
>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=62.65 E-value=5.5 Score=36.00 Aligned_cols=44 Identities=23% Similarity=0.423 Sum_probs=32.3
Q ss_pred CCCCCCCCCceeeee---cCcCCCCCcccccccccccccCccccccc
Q 040161 89 RCPRCDSSNTKFCYY---NNYNLTQPRHFCKTCRRYWTKGGALRNVP 132 (366)
Q Consensus 89 ~CPRC~S~nTKFcYY---NNyn~~QPRhfCksCrRYWT~GGtLRNVP 132 (366)
+||.|...+||+-== ..-+.-+-|..|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998643 34445567899999999998654444333
No 20
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=60.09 E-value=6.1 Score=38.92 Aligned_cols=39 Identities=21% Similarity=0.520 Sum_probs=25.8
Q ss_pred CCCcCCCCCCCCCceeeeecCcC--CCCCccccccccccccc
Q 040161 85 NQNLRCPRCDSSNTKFCYYNNYN--LTQPRHFCKTCRRYWTK 124 (366)
Q Consensus 85 ~e~~~CPRC~S~nTKFcYYNNyn--~~QPRhfCksCrRYWT~ 124 (366)
-....||.|... .|.-||.--. ..---+.|.+|++|+--
T Consensus 224 ~~R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 224 VVRVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred ccCccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 356789999974 4666764222 22233899999999853
No 21
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=59.26 E-value=6.5 Score=36.82 Aligned_cols=30 Identities=23% Similarity=0.648 Sum_probs=22.1
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
+..+||||...=.|.- ++ .+.-|||..|++
T Consensus 244 ~g~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIK-QG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEE-EC----CCCcEECcCCCC
Confidence 4678999998765543 33 266799999986
No 22
>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=58.71 E-value=3.9 Score=28.92 Aligned_cols=17 Identities=35% Similarity=1.017 Sum_probs=7.1
Q ss_pred CCcccccccccccccCc
Q 040161 110 QPRHFCKTCRRYWTKGG 126 (366)
Q Consensus 110 QPRhfCksCrRYWT~GG 126 (366)
+|||||.=|..|.+..-
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 68999999999997654
No 23
>PRK10445 endonuclease VIII; Provisional
Probab=58.07 E-value=7 Score=36.65 Aligned_cols=30 Identities=23% Similarity=0.629 Sum_probs=22.5
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
...+||||...=.|.-+ . .+.-|||..|++
T Consensus 234 ~g~~Cp~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 263 (263)
T PRK10445 234 DGEACERCGGIIEKTTL-S----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCEeEEEEE-C----CCCcEECCCCcC
Confidence 46789999987666554 2 366799999985
No 24
>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=57.02 E-value=7.1 Score=38.32 Aligned_cols=37 Identities=19% Similarity=0.608 Sum_probs=25.1
Q ss_pred CCcCCCCCCCCCceeeeecCcC----CCCCcccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYN----LTQPRHFCKTCRRYWT 123 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn----~~QPRhfCksCrRYWT 123 (366)
...+||.|.+.+ +.-||.-.. ..---..|.+|++|+-
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 467899999864 566665432 1122378999999974
No 25
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=56.66 E-value=7.9 Score=36.59 Aligned_cols=30 Identities=17% Similarity=0.637 Sum_probs=22.4
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
+..+||||...=.|.-+= .+--|||..|++
T Consensus 253 ~g~pC~~Cg~~I~~~~~~-----gR~t~~CP~CQ~ 282 (282)
T PRK13945 253 TGKPCRKCGTPIERIKLA-----GRSTHWCPNCQK 282 (282)
T ss_pred CcCCCCcCCCeeEEEEEC-----CCccEECCCCcC
Confidence 457999999877665442 266699999985
No 26
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=56.65 E-value=8 Score=34.59 Aligned_cols=45 Identities=27% Similarity=0.524 Sum_probs=31.9
Q ss_pred cCCCCCCCCCceee---eecCcCCCCCcccccccccccccCccccccc
Q 040161 88 LRCPRCDSSNTKFC---YYNNYNLTQPRHFCKTCRRYWTKGGALRNVP 132 (366)
Q Consensus 88 ~~CPRC~S~nTKFc---YYNNyn~~QPRhfCksCrRYWT~GGtLRNVP 132 (366)
.+||-|.+..|++- |+-.-+.-.-||-|++|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999887764 4545555666799999998887655544443
No 27
>PHA00626 hypothetical protein
Probab=55.39 E-value=8.3 Score=30.63 Aligned_cols=36 Identities=22% Similarity=0.295 Sum_probs=24.3
Q ss_pred CCCCCCCCCceeeeecCcCCCCCcccccccccccccCc
Q 040161 89 RCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGG 126 (366)
Q Consensus 89 ~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GG 126 (366)
.||+|.|.+--=|-.= ....-||.|++|.=++|+..
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 6999999754322110 11246899999999999864
No 28
>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=50.29 E-value=11 Score=35.41 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=21.7
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCcccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCR 119 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCr 119 (366)
+..+||||...=.|.-+ . .+.-|||..|+
T Consensus 244 ~g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ 272 (272)
T TIGR00577 244 KGEPCRRCGTPIEKIKV-G----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCCeeEEEEE-C----CCCCEECCCCC
Confidence 46799999987666443 3 26679999996
No 29
>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=46.75 E-value=15 Score=29.28 Aligned_cols=32 Identities=22% Similarity=0.461 Sum_probs=25.5
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCcccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRY 121 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRY 121 (366)
+..||+|.+.++=..|..|. ..-.-|-.|.-.
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~---ve~vECV~CGy~ 39 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENG---VEYVECVECGYT 39 (71)
T ss_pred CccCCCCcCccEEEEEEeCC---ceEEEecCCCCe
Confidence 57899999999888888776 556778888643
No 30
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.49 E-value=11 Score=28.19 Aligned_cols=27 Identities=37% Similarity=0.737 Sum_probs=19.8
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
....||+|.+. |..-.. .|+.|..|..
T Consensus 19 ~~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 35689999873 555443 6999999974
No 31
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=46.15 E-value=7.7 Score=41.90 Aligned_cols=16 Identities=25% Similarity=0.742 Sum_probs=13.2
Q ss_pred CCcccccccccccccC
Q 040161 110 QPRHFCKTCRRYWTKG 125 (366)
Q Consensus 110 QPRhfCksCrRYWT~G 125 (366)
+-||.|++|.+.|-+-
T Consensus 915 rrrhhcrncggifcg~ 930 (990)
T KOG1819|consen 915 RRRHHCRNCGGIFCGK 930 (990)
T ss_pred HHhhhhcccCceeecc
Confidence 7899999998877543
No 32
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=43.53 E-value=22 Score=30.99 Aligned_cols=41 Identities=20% Similarity=0.568 Sum_probs=34.6
Q ss_pred CCCCCcCCCCCCCCCceeeeecCcCCCCCc---ccccccccccc
Q 040161 83 GNNQNLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWT 123 (366)
Q Consensus 83 ~~~e~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT 123 (366)
..+-...||+|...+--|--++-.+..-|- |.|-.|+--|-
T Consensus 61 v~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 61 VDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 445568999999999999888888888776 99999999884
No 33
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=39.64 E-value=19 Score=35.14 Aligned_cols=30 Identities=20% Similarity=0.574 Sum_probs=22.0
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
+..+|+||.+.=.|.-. -.+..|||..|++
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 67899999996555322 2367799999985
No 34
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=36.04 E-value=15 Score=28.75 Aligned_cols=15 Identities=33% Similarity=0.665 Sum_probs=6.5
Q ss_pred CCCcCCCCCCCCCce
Q 040161 85 NQNLRCPRCDSSNTK 99 (366)
Q Consensus 85 ~e~~~CPRC~S~nTK 99 (366)
--+.+|+.|.|.||+
T Consensus 46 ~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 46 FLGHKCSHCGSYNTR 60 (61)
T ss_dssp TT----TTTS---EE
T ss_pred HhhhcCCCCCCcccC
Confidence 357899999999997
No 35
>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=34.75 E-value=34 Score=25.01 Aligned_cols=32 Identities=25% Similarity=0.520 Sum_probs=19.6
Q ss_pred cCCCCCCCCCceeeeecCcCCCCCccc-cccccc
Q 040161 88 LRCPRCDSSNTKFCYYNNYNLTQPRHF-CKTCRR 120 (366)
Q Consensus 88 ~~CPRC~S~nTKFcYYNNyn~~QPRhf-CksCrR 120 (366)
.+||.|.+..-.|=+ ...+....+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997765532 12333344454 887764
No 36
>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=33.85 E-value=28 Score=28.16 Aligned_cols=30 Identities=23% Similarity=0.469 Sum_probs=17.0
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
...||.|+..+..|..+.+- -++.|-+|.+
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp EE--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EEECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 46799999887787777543 3899999985
No 37
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=33.83 E-value=38 Score=24.60 Aligned_cols=35 Identities=17% Similarity=0.364 Sum_probs=20.2
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCC-Cccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQ-PRHFCKTCRR 120 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~Q-PRhfCksCrR 120 (366)
+..+||.|.+....+.+........ -.-+|..|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5678999966655554432221111 3455888865
No 38
>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=33.47 E-value=25 Score=26.11 Aligned_cols=32 Identities=25% Similarity=0.545 Sum_probs=25.0
Q ss_pred CCcCCCCCCCCCceeeeecCcCCCCCccccccccccccc
Q 040161 86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTK 124 (366)
Q Consensus 86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~ 124 (366)
.-..||.|.....+ .+.+-.+.|..|...+.+
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 34569999998877 666777999999877654
No 39
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=31.98 E-value=28 Score=32.01 Aligned_cols=43 Identities=23% Similarity=0.356 Sum_probs=30.1
Q ss_pred CCCCCCCCCceeeeec---CcCCCCCcccccccccccccCcccccc
Q 040161 89 RCPRCDSSNTKFCYYN---NYNLTQPRHFCKTCRRYWTKGGALRNV 131 (366)
Q Consensus 89 ~CPRC~S~nTKFcYYN---Nyn~~QPRhfCksCrRYWT~GGtLRNV 131 (366)
.||.|.+.+||+-==- .-+.-+-|.-|.+|..-+|-==++--+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 6999999999985321 223446678999999888855444333
No 40
>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]
Probab=30.09 E-value=2.3e+02 Score=31.81 Aligned_cols=31 Identities=19% Similarity=0.502 Sum_probs=24.3
Q ss_pred eccchhHHHHHHHhhccccc-ccccCCCCceE
Q 040161 294 EVQNSGVQELYQRFKSSTNN-YYADHLASPVV 324 (366)
Q Consensus 294 e~~nsgiqelyqr~~sstn~-y~~d~~~~~~~ 324 (366)
|-...||..+|-|||.|... ||.|..+-+-|
T Consensus 486 er~~rglrnifgKlrRSqS~~f~~ddqs~peF 517 (861)
T KOG1899|consen 486 ERTRRGLRNIFGKLRRSQSQEFTADDQSEPEF 517 (861)
T ss_pred ccchhHHHHHHHHhhhcccCCcCcccccchhh
Confidence 56689999999999988854 88887774444
No 41
>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=30.07 E-value=25 Score=22.90 Aligned_cols=27 Identities=22% Similarity=0.607 Sum_probs=14.7
Q ss_pred cCCCCCCCCCceeeeecCcCCCCCcccccccc
Q 040161 88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCR 119 (366)
Q Consensus 88 ~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCr 119 (366)
.+||||...-.++-..+ +.-+||..|+
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 57999998877665421 3347788775
No 42
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=29.97 E-value=30 Score=35.05 Aligned_cols=36 Identities=28% Similarity=0.672 Sum_probs=22.6
Q ss_pred CCCCCcCCCCCCCCCceeeeecCcCCC-----CCccccccccc
Q 040161 83 GNNQNLRCPRCDSSNTKFCYYNNYNLT-----QPRHFCKTCRR 120 (366)
Q Consensus 83 ~~~e~~~CPRC~S~nTKFcYYNNyn~~-----QPRhfCksCrR 120 (366)
.+...-.||||...| ||.-----.. -..-||+.|..
T Consensus 302 ~pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cgq 342 (345)
T COG4260 302 APAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECGQ 342 (345)
T ss_pred CCcccCcchhccccc--cccccCcccccCCccchhhhChhhcC
Confidence 455678999999887 7753331111 23578888853
No 43
>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=28.60 E-value=41 Score=24.41 Aligned_cols=32 Identities=19% Similarity=0.606 Sum_probs=18.5
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR 120 (366)
+.+||-|.. ..+|..|-+. .-+-..+|+.|..
T Consensus 3 h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 468999988 5688866654 3347899999943
No 44
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.60 E-value=32 Score=29.20 Aligned_cols=45 Identities=20% Similarity=0.474 Sum_probs=32.6
Q ss_pred CCCCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccccCC
Q 040161 83 GNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIG 134 (366)
Q Consensus 83 ~~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNVPVG 134 (366)
+..+...||-|.....| -..---..|+.|..-|+.|+-....|.|
T Consensus 31 ~~~~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 31 QQRAKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred HHhcCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 44567899999998555 1122337899999999999986655544
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.34 E-value=52 Score=23.02 Aligned_cols=33 Identities=18% Similarity=0.438 Sum_probs=20.5
Q ss_pred CCCCCCCCCceeeeecCcCCCCCcccccccccccccCc
Q 040161 89 RCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGG 126 (366)
Q Consensus 89 ~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GG 126 (366)
-||.|.. ..|..... ...|+.|..|...+-...
T Consensus 2 FCp~Cg~----~l~~~~~~-~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGN----MLIPKEGK-EKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCC----ccccccCC-CCCEEECCcCCCeEECCC
Confidence 5899977 33333222 124899999997665543
No 46
>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=24.26 E-value=57 Score=25.90 Aligned_cols=30 Identities=23% Similarity=0.473 Sum_probs=22.8
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCcccccccc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCR 119 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCr 119 (366)
+..||+|...++=..|..|.- .-.-|-.|.
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred cccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 578999999999988866653 445677774
No 47
>KOG0170 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.14 E-value=24 Score=38.02 Aligned_cols=19 Identities=37% Similarity=0.756 Sum_probs=16.6
Q ss_pred ccccccccCCcccccccccc
Q 040161 259 NPLSQQLQVPSQLGLWKNNQ 278 (366)
Q Consensus 259 d~~~q~~~~ps~lglwrnnq 278 (366)
--|++.+|-+| ||+||||.
T Consensus 273 tlVSk~fq~~s-LgmWR~~s 291 (621)
T KOG0170|consen 273 TLVSKEFQRAS-LGMWRCNS 291 (621)
T ss_pred HHHHHHHhhcc-ccccccCc
Confidence 35799999999 99999983
No 48
>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=22.68 E-value=40 Score=23.27 Aligned_cols=28 Identities=29% Similarity=0.666 Sum_probs=14.7
Q ss_pred cCCCCCCCCCceeeeecCcCCCCCcccccccccccc
Q 040161 88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWT 123 (366)
Q Consensus 88 ~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT 123 (366)
.+||.|.|..+= ...--+.|..|..=|.
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 479999998775 4566789999988774
No 49
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=22.62 E-value=34 Score=33.53 Aligned_cols=33 Identities=30% Similarity=0.772 Sum_probs=12.5
Q ss_pred CcCCCCCCCC-CceeeeecCcCCCCCcccccccccccc
Q 040161 87 NLRCPRCDSS-NTKFCYYNNYNLTQPRHFCKTCRRYWT 123 (366)
Q Consensus 87 ~~~CPRC~S~-nTKFcYYNNyn~~QPRhfCksCrRYWT 123 (366)
...||+|.+. =.+| ..|.+-.-++|..|..-+-
T Consensus 31 n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred CCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 4579999997 4554 3345556799999987654
No 50
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=22.47 E-value=13 Score=38.45 Aligned_cols=36 Identities=28% Similarity=0.557 Sum_probs=24.8
Q ss_pred ceeeeecCcCCCCCcccccccccccccCcccccccCCCC
Q 040161 98 TKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGG 136 (366)
Q Consensus 98 TKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNVPVGGG 136 (366)
-+|||-|=..- ---.|.+|||.++.-- .|-||+..-
T Consensus 41 c~fc~~~irq~--lngrcpacrr~y~den-v~~~~~s~e 76 (480)
T COG5175 41 CQFCYNNIRQN--LNGRCPACRRKYDDEN-VRYVTLSPE 76 (480)
T ss_pred HHHHHHHHHhh--ccCCChHhhhhccccc-eeEEecCHH
Confidence 46787653322 3467999999999764 577887653
No 51
>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=22.05 E-value=63 Score=28.30 Aligned_cols=31 Identities=26% Similarity=0.687 Sum_probs=24.6
Q ss_pred cCCCCCCCCCceeeeecCcCCCCCcccccccccccccCc
Q 040161 88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGG 126 (366)
Q Consensus 88 ~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GG 126 (366)
..||.|.|..|- - .+.-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY---~-----dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY---H-----DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE---e-----cCCeeECccccccccccc
Confidence 579999997653 2 355699999999998875
No 52
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.85 E-value=65 Score=33.01 Aligned_cols=33 Identities=33% Similarity=0.764 Sum_probs=21.0
Q ss_pred CCCcCCCCCCC-------CCceeeeecCcCCCCCccccccc
Q 040161 85 NQNLRCPRCDS-------SNTKFCYYNNYNLTQPRHFCKTC 118 (366)
Q Consensus 85 ~e~~~CPRC~S-------~nTKFcYYNNyn~~QPRhfCksC 118 (366)
+....||+|+. .+.=.|-|=.|...-| ..|..|
T Consensus 220 g~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~-~~Cp~C 259 (505)
T TIGR00595 220 GYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIP-KTCPQC 259 (505)
T ss_pred cCccCCCCCCCceEEecCCCeEEcCCCcCcCCCC-CCCCCC
Confidence 35567999984 3444566666665555 467777
No 53
>PRK10220 hypothetical protein; Provisional
Probab=20.55 E-value=74 Score=28.01 Aligned_cols=32 Identities=25% Similarity=0.626 Sum_probs=25.0
Q ss_pred CcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCc
Q 040161 87 NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGG 126 (366)
Q Consensus 87 ~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GG 126 (366)
...||.|.|..|- ..+..+.|..|.-=|....
T Consensus 3 lP~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 3 LPHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 3689999997653 2356799999999998764
Done!