Query 043493
Match_columns 254
No_of_seqs 156 out of 215
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:38:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043493hhsearch_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 1.5E-37 3.2E-42 230.7 4.3 62 24-85 1-62 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 94.5 0.021 4.6E-07 48.1 1.8 35 28-64 105-141 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 94.0 0.047 1E-06 37.4 2.5 29 27-61 17-45 (46)
4 COG3677 Transposase and inacti 93.4 0.054 1.2E-06 44.7 2.2 36 28-65 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 92.7 0.071 1.5E-06 36.0 1.7 31 28-60 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 91.5 0.21 4.5E-06 33.9 2.8 37 29-65 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 88.7 0.39 8.4E-06 32.3 2.3 35 30-64 2-39 (39)
8 PF04216 FdhE: Protein involve 84.1 0.53 1.1E-05 42.4 1.4 37 28-64 211-249 (290)
9 PHA02998 RNA polymerase subuni 83.1 1.2 2.6E-05 40.2 3.2 39 27-65 142-183 (195)
10 TIGR01384 TFS_arch transcripti 81.7 1.9 4.1E-05 33.2 3.5 39 28-66 62-103 (104)
11 PF13453 zf-TFIIB: Transcripti 81.5 0.46 1E-05 31.8 -0.0 38 30-72 1-38 (41)
12 cd00202 ZnF_GATA Zinc finger D 80.5 1.6 3.5E-05 31.4 2.5 41 30-73 1-41 (54)
13 PF14690 zf-ISL3: zinc-finger 70.6 2 4.4E-05 28.5 0.8 32 28-59 2-47 (47)
14 TIGR01385 TFSII transcription 69.0 4 8.7E-05 38.2 2.7 40 25-64 255-297 (299)
15 TIGR00244 transcriptional regu 68.4 3.7 7.9E-05 35.6 2.1 44 30-73 2-48 (147)
16 smart00401 ZnF_GATA zinc finge 66.6 4.3 9.2E-05 28.8 1.8 40 27-69 2-41 (52)
17 PRK14811 formamidopyrimidine-D 66.2 4 8.7E-05 37.0 2.0 30 28-62 235-264 (269)
18 PF04981 NMD3: NMD3 family ; 64.9 3.3 7.2E-05 36.5 1.2 25 42-66 19-48 (236)
19 PF06220 zf-U1: U1 zinc finger 64.2 2.8 6.2E-05 28.3 0.5 17 51-67 1-17 (38)
20 TIGR01562 FdhE formate dehydro 64.1 4.8 0.0001 38.0 2.2 36 28-64 224-263 (305)
21 PRK00464 nrdR transcriptional 63.7 5 0.00011 34.5 2.0 45 29-73 1-48 (154)
22 PHA00626 hypothetical protein 63.5 5 0.00011 30.5 1.7 36 30-67 2-37 (59)
23 PRK03564 formate dehydrogenase 59.1 6.5 0.00014 37.3 2.1 37 28-65 226-264 (309)
24 PF09526 DUF2387: Probable met 56.7 8.4 0.00018 29.4 2.0 31 28-61 8-38 (71)
25 PF05129 Elf1: Transcription e 53.0 8 0.00017 29.9 1.3 42 22-64 16-57 (81)
26 KOG2906 RNA polymerase III sub 48.0 16 0.00034 30.5 2.4 38 27-64 64-104 (105)
27 PRK00432 30S ribosomal protein 46.3 10 0.00023 27.0 1.0 26 28-61 20-45 (50)
28 PRK14892 putative transcriptio 45.4 20 0.00044 29.0 2.6 39 22-64 15-53 (99)
29 COG1327 Predicted transcriptio 43.0 15 0.00032 32.4 1.6 43 30-72 2-47 (156)
30 PF08273 Prim_Zn_Ribbon: Zinc- 42.7 15 0.00033 25.4 1.3 32 28-61 3-34 (40)
31 TIGR03655 anti_R_Lar restricti 39.0 27 0.00058 24.5 2.1 33 29-62 2-35 (53)
32 PF14599 zinc_ribbon_6: Zinc-r 38.5 13 0.00028 27.8 0.5 13 28-40 48-60 (61)
33 PF14354 Lar_restr_allev: Rest 37.7 30 0.00064 24.1 2.2 35 27-61 2-37 (61)
34 PF06827 zf-FPG_IleRS: Zinc fi 37.6 16 0.00035 22.7 0.8 28 29-61 2-29 (30)
35 PF10111 Glyco_tranf_2_2: Glyc 37.6 13 0.00028 32.7 0.5 26 165-192 179-204 (281)
36 COG4888 Uncharacterized Zn rib 37.5 26 0.00055 29.2 2.1 42 22-64 16-57 (104)
37 COG4260 Membrane protease subu 35.0 20 0.00044 34.8 1.4 37 23-61 301-342 (345)
38 KOG1819 FYVE finger-containing 33.5 21 0.00047 37.4 1.3 32 25-65 898-929 (990)
39 PF07282 OrfB_Zn_ribbon: Putat 33.2 24 0.00053 25.1 1.2 32 27-65 27-58 (69)
40 PF01807 zf-CHC2: CHC2 zinc fi 33.0 31 0.00067 26.8 1.9 31 28-62 33-63 (97)
41 TIGR02443 conserved hypothetic 31.7 36 0.00079 25.7 2.0 30 28-60 9-38 (59)
42 PF08274 PhnA_Zn_Ribbon: PhnA 30.6 24 0.00053 23.2 0.8 28 29-64 3-30 (30)
43 KOG2691 RNA polymerase II subu 29.5 42 0.00091 28.3 2.2 41 23-65 68-113 (113)
44 smart00778 Prim_Zn_Ribbon Zinc 28.0 49 0.0011 22.6 1.9 31 27-60 2-32 (37)
45 PF14654 Epiglycanin_C: Mucin, 26.6 52 0.0011 27.5 2.2 30 172-202 61-94 (106)
46 PRK10220 hypothetical protein; 24.3 49 0.0011 27.8 1.7 31 29-67 4-34 (111)
47 TIGR00686 phnA alkylphosphonat 24.3 45 0.00098 27.9 1.5 31 29-67 3-33 (109)
48 smart00661 RPOL9 RNA polymeras 23.8 52 0.0011 22.0 1.5 32 30-66 2-33 (52)
49 PF05876 Terminase_GpA: Phage 23.5 53 0.0011 32.9 2.0 44 28-72 200-248 (557)
50 PF01873 eIF-5_eIF-2B: Domain 23.5 75 0.0016 26.4 2.6 29 29-61 94-122 (125)
51 COG1594 RPB9 DNA-directed RNA 23.0 84 0.0018 25.6 2.8 38 28-65 72-112 (113)
52 PF03966 Trm112p: Trm112p-like 23.0 41 0.00088 24.5 0.9 17 47-63 47-63 (68)
53 COG1997 RPL43A Ribosomal prote 22.0 55 0.0012 26.6 1.5 43 26-75 33-75 (89)
54 PRK12286 rpmF 50S ribosomal pr 20.9 75 0.0016 23.3 1.9 28 23-62 22-49 (57)
55 PF07383 DUF1496: Protein of u 20.9 71 0.0015 23.8 1.8 14 39-52 12-25 (56)
56 smart00451 ZnF_U1 U1-like zinc 20.1 45 0.00098 20.5 0.5 16 52-67 2-17 (35)
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=1.5e-37 Score=230.70 Aligned_cols=62 Identities=77% Similarity=1.527 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCcCCCceeeeeccCCCCCCcccchhcccccccCcccccccCCCccCCCCCCC
Q 043493 24 KVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVGGGTRKNSKRT 85 (254)
Q Consensus 24 ~e~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnVPVGGG~RKn~krs 85 (254)
++++.++||||+|+||||||||||+++||||||++|+||||+||+|||||||||+||+++++
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 36789999999999999999999999999999999999999999999999999999995443
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=94.47 E-value=0.021 Score=48.09 Aligned_cols=35 Identities=26% Similarity=0.684 Sum_probs=27.9
Q ss_pred CCCCCCCcCCCceeeeeccC--CCCCCcccchhcccccc
Q 043493 28 SLPCPRCESTSTKFCYYNNY--NLSQPRHFCKSCRRYWT 64 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy--~~~QPR~fCk~CrRYWT 64 (254)
..+||||.|.+|+.. +.| +.++.-|.|++|+.=|.
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf~ 141 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPFE 141 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcHh
Confidence 579999999999964 555 45677899999997543
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=94.01 E-value=0.047 Score=37.38 Aligned_cols=29 Identities=38% Similarity=0.855 Sum_probs=23.1
Q ss_pred CCCCCCCCcCCCceeeeeccCCCCCCcccchhccc
Q 043493 27 ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRR 61 (254)
Q Consensus 27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 61 (254)
+...||+|.+. +...+.+ +.+|.|++|++
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 34679999998 6655655 78999999986
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.38 E-value=0.054 Score=44.74 Aligned_cols=36 Identities=31% Similarity=0.631 Sum_probs=28.4
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCcccchhccccccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQ 65 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~ 65 (254)
...||+|.+.+ +-=+.-+.....||.|++|++-|+.
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 46899999999 3334555555999999999999874
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=92.74 E-value=0.071 Score=36.02 Aligned_cols=31 Identities=42% Similarity=0.760 Sum_probs=21.8
Q ss_pred CCCCCCCcCCCceeeeeccCCCC-CCcccchhcc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLS-QPRHFCKSCR 60 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCk~Cr 60 (254)
.+.||+|.+++.- |=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence 4689999998721 23444443 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=91.49 E-value=0.21 Score=33.92 Aligned_cols=37 Identities=24% Similarity=0.768 Sum_probs=28.9
Q ss_pred CCCCCCcCCCceeeeeccCCCCCC---cccchhccccccc
Q 043493 29 LPCPRCESTSTKFCYYNNYNLSQP---RHFCKSCRRYWTQ 65 (254)
Q Consensus 29 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRYWT~ 65 (254)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
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 379999988877766666666666 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=88.74 E-value=0.39 Score=32.34 Aligned_cols=35 Identities=23% Similarity=0.696 Sum_probs=24.7
Q ss_pred CCCCCcCCCceeeeeccCCCCCCc---ccchhcccccc
Q 043493 30 PCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWT 64 (254)
Q Consensus 30 ~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT 64 (254)
+||.|...+.-|--.+......|- |.|.+|..-|+
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 799999988776655666555553 99999999885
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=84.14 E-value=0.53 Score=42.45 Aligned_cols=37 Identities=27% Similarity=0.632 Sum_probs=18.4
Q ss_pred CCCCCCCcCCC-ceeeeeccCCCCCC-cccchhcccccc
Q 043493 28 SLPCPRCESTS-TKFCYYNNYNLSQP-RHFCKSCRRYWT 64 (254)
Q Consensus 28 ~~~CPRC~S~n-TKFcYyNNy~~~QP-R~fCk~CrRYWT 64 (254)
...||.|..++ .++-||..-....- -+.|.+|+.|+-
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 45899998854 56777743333333 399999999983
No 9
>PHA02998 RNA polymerase subunit; Provisional
Probab=83.10 E-value=1.2 Score=40.19 Aligned_cols=39 Identities=26% Similarity=0.686 Sum_probs=34.1
Q ss_pred CCCCCCCCcCCCceeeeeccCCCCCCc---ccchhccccccc
Q 043493 27 ESLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWTQ 65 (254)
Q Consensus 27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~ 65 (254)
...+||+|...++-|--.|-++-..|- |.|..|..-|.-
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 568999999999999888888888885 899999999963
No 10
>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=81.71 E-value=1.9 Score=33.19 Aligned_cols=39 Identities=18% Similarity=0.603 Sum_probs=29.3
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCc---ccchhcccccccC
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWTQG 66 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~G 66 (254)
..+||+|...+.-|-..+-.+-..|- |.|..|.-.|+..
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 57999998777766655555544443 9999999999864
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=81.51 E-value=0.46 Score=31.78 Aligned_cols=38 Identities=26% Similarity=0.635 Sum_probs=27.5
Q ss_pred CCCCCcCCCceeeeeccCCCCCCcccchhcccccccCcccccc
Q 043493 30 PCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNI 72 (254)
Q Consensus 30 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnV 72 (254)
+||+|...=...-+ ..-+-+.|.+|.-.|=..+.|..+
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~~ 38 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEKL 38 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHHH
Confidence 69999985444433 235668899999999888776543
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=80.55 E-value=1.6 Score=31.37 Aligned_cols=41 Identities=27% Similarity=0.723 Sum_probs=29.5
Q ss_pred CCCCCcCCCceeeeeccCCCCCCcccchhcccccccCccccccc
Q 043493 30 PCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIP 73 (254)
Q Consensus 30 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnVP 73 (254)
.|-.|...+|..=.-.. .....+|-+|.-||.+.+..|.+-
T Consensus 1 ~C~~C~~~~Tp~WR~g~---~~~~~LCNaCgl~~~k~~~~rp~~ 41 (54)
T cd00202 1 ACSNCGTTTTPLWRRGP---SGGSTLCNACGLYWKKHGVMRPLS 41 (54)
T ss_pred CCCCCCCCCCcccccCC---CCcchHHHHHHHHHHhcCCCCCcc
Confidence 37788887775332222 467899999999999999665543
No 13
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=70.59 E-value=2 Score=28.49 Aligned_cols=32 Identities=31% Similarity=0.647 Sum_probs=19.4
Q ss_pred CCCCCCCcCCCcee-eeeccC-------------CCCCCcccchhc
Q 043493 28 SLPCPRCESTSTKF-CYYNNY-------------NLSQPRHFCKSC 59 (254)
Q Consensus 28 ~~~CPRC~S~nTKF-cYyNNy-------------~~~QPR~fCk~C 59 (254)
+..||.|.+..-+. -++... .+..+|++|++|
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 45799999876221 111111 346788888887
No 14
>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=69.02 E-value=4 Score=38.24 Aligned_cols=40 Identities=20% Similarity=0.634 Sum_probs=30.4
Q ss_pred CCCCCCCCCCcCCCceeeeeccCCCCCCc---ccchhcccccc
Q 043493 25 VTESLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWT 64 (254)
Q Consensus 25 e~~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT 64 (254)
+....+||+|...+..|-..|..+-..|- |.|..|...|.
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 34568999999888777666666655564 78999999884
No 15
>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=68.43 E-value=3.7 Score=35.62 Aligned_cols=44 Identities=20% Similarity=0.397 Sum_probs=32.3
Q ss_pred CCCCCcCCCceeeee---ccCCCCCCcccchhcccccccCccccccc
Q 043493 30 PCPRCESTSTKFCYY---NNYNLSQPRHFCKSCRRYWTQGGTLRNIP 73 (254)
Q Consensus 30 ~CPRC~S~nTKFcYy---NNy~~~QPR~fCk~CrRYWT~GGtLRnVP 73 (254)
.||.|...+||+-== ..-+.-+-|..|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998643 44455667899999999888544443333
No 16
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=66.55 E-value=4.3 Score=28.81 Aligned_cols=40 Identities=25% Similarity=0.595 Sum_probs=29.5
Q ss_pred CCCCCCCCcCCCceeeeeccCCCCCCcccchhcccccccCccc
Q 043493 27 ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTL 69 (254)
Q Consensus 27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtL 69 (254)
....|-.|...+|..=.- ...-++.+|.+|.-||.+.+.+
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 356899999888864322 2223379999999999998886
No 17
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=66.23 E-value=4 Score=37.03 Aligned_cols=30 Identities=33% Similarity=0.844 Sum_probs=22.4
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCcccchhcccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRY 62 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRY 62 (254)
..+||||...-.|.-+= .+.-|||..||+-
T Consensus 235 g~pC~~Cg~~I~~~~~~-----gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVG-----GRGTHFCPQCQPL 264 (269)
T ss_pred cCCCCcCCCeeEEEEEC-----CCCcEECCCCcCC
Confidence 45899999877665442 3667999999963
No 18
>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=64.88 E-value=3.3 Score=36.55 Aligned_cols=25 Identities=28% Similarity=0.880 Sum_probs=17.8
Q ss_pred eeeccCCCCC-----CcccchhcccccccC
Q 043493 42 CYYNNYNLSQ-----PRHFCKSCRRYWTQG 66 (254)
Q Consensus 42 cYyNNy~~~Q-----PR~fCk~CrRYWT~G 66 (254)
||...+.+.. --.+|+.|.||+..|
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~ 48 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGG 48 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCC
Confidence 5666665533 237899999999884
No 19
>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=64.18 E-value=2.8 Score=28.33 Aligned_cols=17 Identities=35% Similarity=1.028 Sum_probs=7.1
Q ss_pred CCcccchhcccccccCc
Q 043493 51 QPRHFCKSCRRYWTQGG 67 (254)
Q Consensus 51 QPR~fCk~CrRYWT~GG 67 (254)
+|||||.=|..|.+..-
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 20
>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=64.10 E-value=4.8 Score=37.97 Aligned_cols=36 Identities=22% Similarity=0.608 Sum_probs=23.7
Q ss_pred CCCCCCCcCCCceeeeeccCC---CCC-Ccccchhcccccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYN---LSQ-PRHFCKSCRRYWT 64 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~---~~Q-PR~fCk~CrRYWT 64 (254)
...||.|.+.+ +.-||.-.. ... --..|.+|+.|+-
T Consensus 224 R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 224 RVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 34899999864 566665432 111 2268999999974
No 21
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=63.72 E-value=5 Score=34.45 Aligned_cols=45 Identities=22% Similarity=0.456 Sum_probs=33.5
Q ss_pred CCCCCCcCCCceee---eeccCCCCCCcccchhcccccccCccccccc
Q 043493 29 LPCPRCESTSTKFC---YYNNYNLSQPRHFCKSCRRYWTQGGTLRNIP 73 (254)
Q Consensus 29 ~~CPRC~S~nTKFc---YyNNy~~~QPR~fCk~CrRYWT~GGtLRnVP 73 (254)
..||.|.+..|++- |+-.-++-.-||.|++|.+-++.==++-..+
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 5555555666799999999988765555554
No 22
>PHA00626 hypothetical protein
Probab=63.49 E-value=5 Score=30.45 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=24.0
Q ss_pred CCCCCcCCCceeeeeccCCCCCCcccchhcccccccCc
Q 043493 30 PCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGG 67 (254)
Q Consensus 30 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GG 67 (254)
.||+|.|.+--=|=.= ....-||.|++|.=.+|+..
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 6999999754311110 11245799999999999864
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=59.07 E-value=6.5 Score=37.30 Aligned_cols=37 Identities=22% Similarity=0.545 Sum_probs=24.0
Q ss_pred CCCCCCCcCCCceeeeeccCCC--CCCcccchhccccccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNL--SQPRHFCKSCRRYWTQ 65 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~--~QPR~fCk~CrRYWT~ 65 (254)
...||.|... .|.-||.--.. .---+.|.+|++|+--
T Consensus 226 R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 226 RVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 3489999874 46667642221 2223899999999854
No 24
>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=56.74 E-value=8.4 Score=29.43 Aligned_cols=31 Identities=23% Similarity=0.501 Sum_probs=25.4
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCcccchhccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRR 61 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 61 (254)
+..||+|.+.+|-..|..|. ..-..|-.|.-
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 56899999999888888776 66678999964
No 25
>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=52.96 E-value=8 Score=29.90 Aligned_cols=42 Identities=17% Similarity=0.395 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCCCcCCCceeeeeccCCCCCCcccchhcccccc
Q 043493 22 PPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWT 64 (254)
Q Consensus 22 p~~e~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT 64 (254)
.++-+..-.||.|+..++=-|=+..- ......-|..|.-.+.
T Consensus 16 ~~~l~~~F~CPfC~~~~sV~v~idkk-~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 16 KPKLPKVFDCPFCNHEKSVSVKIDKK-EGIGILSCRVCGESFQ 57 (81)
T ss_dssp ----SS----TTT--SS-EEEEEETT-TTEEEEEESSS--EEE
T ss_pred CCCCCceEcCCcCCCCCeEEEEEEcc-CCEEEEEecCCCCeEE
Confidence 44455778999999888877766433 5566788999976664
No 26
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=47.98 E-value=16 Score=30.51 Aligned_cols=38 Identities=21% Similarity=0.601 Sum_probs=33.0
Q ss_pred CCCCCCCCcCCCceeeeeccCCCCCCc---ccchhcccccc
Q 043493 27 ESLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWT 64 (254)
Q Consensus 27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT 64 (254)
-...||+|...+--|--+|-.+..-|- |.|-.|.--|-
T Consensus 64 t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 64 TEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred ccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 456899999999999888888888886 99999999884
No 27
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.26 E-value=10 Score=26.99 Aligned_cols=26 Identities=35% Similarity=0.671 Sum_probs=19.0
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCcccchhccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRR 61 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 61 (254)
..-||+|.+. |..-.. .|+.|..|..
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 4589999873 554443 6999999974
No 28
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=45.39 E-value=20 Score=28.99 Aligned_cols=39 Identities=23% Similarity=0.508 Sum_probs=26.7
Q ss_pred CCCCCCCCCCCCCcCCCceeeeeccCCCCCCcccchhcccccc
Q 043493 22 PPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWT 64 (254)
Q Consensus 22 p~~e~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT 64 (254)
.++.+....||.|.+. +--|=+.. ..+.+.|..|.-|..
T Consensus 15 k~klpt~f~CP~Cge~-~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 15 KPKLPKIFECPRCGKV-SISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred ccCCCcEeECCCCCCe-EeeeecCC---CcceEECCCCCCccC
Confidence 3444577899999952 33233333 478999999999954
No 29
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=42.96 E-value=15 Score=32.44 Aligned_cols=43 Identities=23% Similarity=0.301 Sum_probs=30.0
Q ss_pred CCCCCcCCCceeeeec---cCCCCCCcccchhcccccccCcccccc
Q 043493 30 PCPRCESTSTKFCYYN---NYNLSQPRHFCKSCRRYWTQGGTLRNI 72 (254)
Q Consensus 30 ~CPRC~S~nTKFcYyN---Ny~~~QPR~fCk~CrRYWT~GGtLRnV 72 (254)
.||.|.+.+||+.==- .-+.-+-|.-|.+|..-||-==++--+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 6999999999985322 223455678999999888854443333
No 30
>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=42.68 E-value=15 Score=25.42 Aligned_cols=32 Identities=22% Similarity=0.680 Sum_probs=18.7
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCcccchhccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRR 61 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 61 (254)
+.+||-|.. ..+|..|-+. .-+-..+|..|..
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 568999988 5688866654 2347799999943
No 31
>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=39.03 E-value=27 Score=24.47 Aligned_cols=33 Identities=24% Similarity=0.535 Sum_probs=20.1
Q ss_pred CCCCCCcCCCceeeeeccCCCCCCccc-chhcccc
Q 043493 29 LPCPRCESTSTKFCYYNNYNLSQPRHF-CKSCRRY 62 (254)
Q Consensus 29 ~~CPRC~S~nTKFcYyNNy~~~QPR~f-Ck~CrRY 62 (254)
.+||.|.+..-.|-+ ...+....+++ |..|...
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCCC
Confidence 589999997665542 12333344454 8888643
No 32
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=38.50 E-value=13 Score=27.83 Aligned_cols=13 Identities=31% Similarity=0.705 Sum_probs=5.6
Q ss_pred CCCCCCCcCCCce
Q 043493 28 SLPCPRCESTSTK 40 (254)
Q Consensus 28 ~~~CPRC~S~nTK 40 (254)
.++|+.|.|.||+
T Consensus 48 g~KC~~C~SYNT~ 60 (61)
T PF14599_consen 48 GHKCSHCGSYNTR 60 (61)
T ss_dssp ----TTTS---EE
T ss_pred hhcCCCCCCcccC
Confidence 4589999999997
No 33
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=37.73 E-value=30 Score=24.14 Aligned_cols=35 Identities=23% Similarity=0.461 Sum_probs=20.0
Q ss_pred CCCCCCCCcCCCceeeeeccCCCCC-Ccccchhccc
Q 043493 27 ESLPCPRCESTSTKFCYYNNYNLSQ-PRHFCKSCRR 61 (254)
Q Consensus 27 ~~~~CPRC~S~nTKFcYyNNy~~~Q-PR~fCk~CrR 61 (254)
+-.+||.|-+....+.+........ -.-+|.+|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5678999965555554432222111 3445888866
No 34
>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=37.65 E-value=16 Score=22.74 Aligned_cols=28 Identities=21% Similarity=0.601 Sum_probs=15.2
Q ss_pred CCCCCCcCCCceeeeeccCCCCCCcccchhccc
Q 043493 29 LPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRR 61 (254)
Q Consensus 29 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 61 (254)
.+||||...-.++-..+ +.-+||..|+.
T Consensus 2 ~~C~rC~~~~~~~~~~~-----r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING-----RSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETT-----EEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecC-----CCCeECcCCcC
Confidence 57999998877765422 23378887763
No 35
>PF10111 Glyco_tranf_2_2: Glycosyltransferase like family 2; InterPro: IPR019290 This conserved domain is found in a set of prokaryotic proteins including putative glucosyltransferases, which are involved in bacterial capsule biosynthesis [, ].
Probab=37.61 E-value=13 Score=32.74 Aligned_cols=26 Identities=35% Similarity=0.933 Sum_probs=19.8
Q ss_pred cccccCCccccCcccCCchhhhhccccc
Q 043493 165 NFLGLGGFHNHGYGIGSGLEELELGFGT 192 (254)
Q Consensus 165 gf~~lggf~~~G~GlG~G~~d~~~gfg~ 192 (254)
=|+.+||| +..+ .|+|+||.++++=+
T Consensus 179 ~f~~iGGf-DE~f-~G~G~ED~D~~~RL 204 (281)
T PF10111_consen 179 DFLEIGGF-DERF-RGWGYEDIDFGYRL 204 (281)
T ss_pred HHHHhCCC-Cccc-cCCCcchHHHHHHH
Confidence 48999999 5555 58899999777544
No 36
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=37.46 E-value=26 Score=29.24 Aligned_cols=42 Identities=19% Similarity=0.566 Sum_probs=28.9
Q ss_pred CCCCCCCCCCCCCcCCCceeeeeccCCCCCCcccchhcccccc
Q 043493 22 PPKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWT 64 (254)
Q Consensus 22 p~~e~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT 64 (254)
|++-+..-.||||..-+---|... .+....-.-|+.|..++.
T Consensus 16 ~~~L~k~FtCp~Cghe~vs~ctvk-k~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 16 PQVLPKTFTCPRCGHEKVSSCTVK-KTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CccCCceEecCccCCeeeeEEEEE-ecCceeEEEcccCcceEE
Confidence 444567889999999888877743 233344467999987653
No 37
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=35.01 E-value=20 Score=34.81 Aligned_cols=37 Identities=24% Similarity=0.707 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCCcCCCceeeeeccCCC-----CCCcccchhccc
Q 043493 23 PKVTESLPCPRCESTSTKFCYYNNYNL-----SQPRHFCKSCRR 61 (254)
Q Consensus 23 ~~e~~~~~CPRC~S~nTKFcYyNNy~~-----~QPR~fCk~CrR 61 (254)
..+...-+||||...| ||.-----. +-..-||+.|..
T Consensus 301 a~pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cgq 342 (345)
T COG4260 301 AAPAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECGQ 342 (345)
T ss_pred cCCcccCcchhccccc--cccccCcccccCCccchhhhChhhcC
Confidence 3345677999999988 765322111 123477888754
No 38
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=33.50 E-value=21 Score=37.37 Aligned_cols=32 Identities=22% Similarity=0.622 Sum_probs=20.9
Q ss_pred CCCCCCCCCCcCCCceeeeeccCCCCCCcccchhccccccc
Q 043493 25 VTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQ 65 (254)
Q Consensus 25 e~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~ 65 (254)
.+...+|-.|...-+-| +-||-|++|.+.|-.
T Consensus 898 d~~a~~cmacq~pf~af---------rrrhhcrncggifcg 929 (990)
T KOG1819|consen 898 DEDAEQCMACQMPFNAF---------RRRHHCRNCGGIFCG 929 (990)
T ss_pred CCcchhhhhccCcHHHH---------HHhhhhcccCceeec
Confidence 33445566665543333 789999999887753
No 39
>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=33.18 E-value=24 Score=25.07 Aligned_cols=32 Identities=28% Similarity=0.520 Sum_probs=25.3
Q ss_pred CCCCCCCCcCCCceeeeeccCCCCCCcccchhccccccc
Q 043493 27 ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQ 65 (254)
Q Consensus 27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~ 65 (254)
.-..||.|.....+ .+.+-.+.|..|...+.+
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 45679999998877 666777999999876654
No 40
>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=32.98 E-value=31 Score=26.75 Aligned_cols=31 Identities=23% Similarity=0.460 Sum_probs=17.2
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCcccchhcccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRY 62 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRY 62 (254)
...||-|+..+..|..+.+.+ ++.|-+|.+.
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k~----~~~Cf~Cg~~ 63 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDKN----RFKCFGCGKG 63 (97)
T ss_dssp EE--SSS--SS--EEEETTTT----EEEETTT--E
T ss_pred EEECcCCCCCCCceEEECCCC----eEEECCCCCC
Confidence 457999998877777765443 7999999853
No 41
>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=31.75 E-value=36 Score=25.73 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=23.1
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCcccchhcc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCR 60 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 60 (254)
...||+|...+|=..|..|.- .-..|-.|.
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 568999999999988866653 446787774
No 42
>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=30.64 E-value=24 Score=23.16 Aligned_cols=28 Identities=29% Similarity=0.616 Sum_probs=14.7
Q ss_pred CCCCCCcCCCceeeeeccCCCCCCcccchhcccccc
Q 043493 29 LPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWT 64 (254)
Q Consensus 29 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT 64 (254)
-+||.|.|..|= ...--+.|..|..=|.
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 379999998774 5567789999987774
No 43
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=29.53 E-value=42 Score=28.34 Aligned_cols=41 Identities=24% Similarity=0.537 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCCcCCCceeeeeccCCCCC-----Ccccchhccccccc
Q 043493 23 PKVTESLPCPRCESTSTKFCYYNNYNLSQ-----PRHFCKSCRRYWTQ 65 (254)
Q Consensus 23 ~~e~~~~~CPRC~S~nTKFcYyNNy~~~Q-----PR~fCk~CrRYWT~ 65 (254)
.|.-+-..||+|...+.-| ||-.+... .-|.|-+|.--||.
T Consensus 68 LPrts~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 68 LPRTSDKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred cCccccccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 4444778999999887654 55432211 11899999999985
No 44
>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=28.04 E-value=49 Score=22.62 Aligned_cols=31 Identities=29% Similarity=0.815 Sum_probs=20.8
Q ss_pred CCCCCCCCcCCCceeeeeccCCCCCCcccchhcc
Q 043493 27 ESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCR 60 (254)
Q Consensus 27 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 60 (254)
.+.+||.|.+ +.+|- |.+..- .-.++|..|.
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 4679999988 45676 444222 3558899884
No 45
>PF14654 Epiglycanin_C: Mucin, catalytic, TM and cytoplasmic tail region
Probab=26.63 E-value=52 Score=27.52 Aligned_cols=30 Identities=33% Similarity=0.533 Sum_probs=17.5
Q ss_pred ccccCcccCCchhhhhcccccccc----ccCCCCc
Q 043493 172 FHNHGYGIGSGLEELELGFGTARS----WDIPGTG 202 (254)
Q Consensus 172 f~~~G~GlG~G~~d~~~gfg~gr~----W~fpg~~ 202 (254)
+||||||.++|=. .+++++.+-+ |.=|.-.
T Consensus 61 g~n~glG~~pGG~-~~~~~~~~~s~~~~wr~p~s~ 94 (106)
T PF14654_consen 61 GPNHGLGWGPGGN-HGVPHGPGWSPSWFWRRPVSS 94 (106)
T ss_pred CccccccCCCCCC-ccCCCCCCcCcchhhcCCccc
Confidence 3688888887722 2236665555 5556543
No 46
>PRK10220 hypothetical protein; Provisional
Probab=24.28 E-value=49 Score=27.83 Aligned_cols=31 Identities=26% Similarity=0.651 Sum_probs=24.3
Q ss_pred CCCCCCcCCCceeeeeccCCCCCCcccchhcccccccCc
Q 043493 29 LPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGG 67 (254)
Q Consensus 29 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GG 67 (254)
.+||.|.|..|- ..+..+.|..|.-=|+..-
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 589999997662 2356799999999998764
No 47
>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=24.27 E-value=45 Score=27.94 Aligned_cols=31 Identities=32% Similarity=0.774 Sum_probs=24.4
Q ss_pred CCCCCCcCCCceeeeeccCCCCCCcccchhcccccccCc
Q 043493 29 LPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGG 67 (254)
Q Consensus 29 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GG 67 (254)
.+||.|.|..|- - .+.-+.|..|.-=|....
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 479999997663 2 355699999999998775
No 48
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.79 E-value=52 Score=22.04 Aligned_cols=32 Identities=19% Similarity=0.452 Sum_probs=19.1
Q ss_pred CCCCCcCCCceeeeeccCCCCCCcccchhcccccccC
Q 043493 30 PCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQG 66 (254)
Q Consensus 30 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~G 66 (254)
-||.|.+ ..|..... ...|+.|..|...+-..
T Consensus 2 FCp~Cg~----~l~~~~~~-~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGN----MLIPKEGK-EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCC----ccccccCC-CCCEEECCcCCCeEECC
Confidence 5888876 33333221 12488999998665443
No 49
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=23.52 E-value=53 Score=32.95 Aligned_cols=44 Identities=18% Similarity=0.456 Sum_probs=30.0
Q ss_pred CCCCCCCcCCCc----eeeeeccC-CCCCCcccchhcccccccCcccccc
Q 043493 28 SLPCPRCESTST----KFCYYNNY-NLSQPRHFCKSCRRYWTQGGTLRNI 72 (254)
Q Consensus 28 ~~~CPRC~S~nT----KFcYyNNy-~~~QPR~fCk~CrRYWT~GGtLRnV 72 (254)
.++||+|..... .|-| ++- .....+|.|..|..-|++.-..+.+
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w-~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~ 248 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKW-DKGEAPETARYVCPHCGCEIEEHDKRRMV 248 (557)
T ss_pred EccCCCCCCCccccccceee-cCCCCccceEEECCCCcCCCCHHHHhhcc
Confidence 569999987543 1223 322 5567789999999999986554433
No 50
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=23.48 E-value=75 Score=26.42 Aligned_cols=29 Identities=28% Similarity=0.470 Sum_probs=20.7
Q ss_pred CCCCCCcCCCceeeeeccCCCCCCcccchhccc
Q 043493 29 LPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRR 61 (254)
Q Consensus 29 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 61 (254)
+.||-|.+.+|.+--- -..--..|++|..
T Consensus 94 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE----GRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEE----TTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEc----CCEEEEEecccCC
Confidence 6899999999997544 1223367888853
No 51
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.98 E-value=84 Score=25.61 Aligned_cols=38 Identities=18% Similarity=0.606 Sum_probs=26.1
Q ss_pred CCCCCCCcCCCceeeeeccCCCCCCc---ccchhccccccc
Q 043493 28 SLPCPRCESTSTKFCYYNNYNLSQPR---HFCKSCRRYWTQ 65 (254)
Q Consensus 28 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~ 65 (254)
-..||+|...+--|-..|...-.-|- |.|..|.--|+.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 45799999877665444444333332 899999999964
No 52
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=22.96 E-value=41 Score=24.50 Aligned_cols=17 Identities=18% Similarity=0.567 Sum_probs=12.5
Q ss_pred CCCCCCcccchhccccc
Q 043493 47 YNLSQPRHFCKSCRRYW 63 (254)
Q Consensus 47 y~~~QPR~fCk~CrRYW 63 (254)
+..-.-...|..|+|.+
T Consensus 47 ~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGELICPECGREY 63 (68)
T ss_dssp EETTTTEEEETTTTEEE
T ss_pred ccccCCEEEcCCCCCEE
Confidence 45666778899998865
No 53
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.97 E-value=55 Score=26.62 Aligned_cols=43 Identities=23% Similarity=0.510 Sum_probs=31.2
Q ss_pred CCCCCCCCCcCCCceeeeeccCCCCCCcccchhcccccccCcccccccCC
Q 043493 26 TESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRYWTQGGTLRNIPVG 75 (254)
Q Consensus 26 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnVPVG 75 (254)
.+...||.|.+...| -...---.|+.|..-|+.|.-....|.|
T Consensus 33 ~~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 33 RAKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred hcCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 356689999998554 1223347899999999999887666554
No 54
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.93 E-value=75 Score=23.32 Aligned_cols=28 Identities=32% Similarity=0.796 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCcCCCceeeeeccCCCCCCcccchhcccc
Q 043493 23 PKVTESLPCPRCESTSTKFCYYNNYNLSQPRHFCKSCRRY 62 (254)
Q Consensus 23 ~~e~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRY 62 (254)
...+....||.|.+.. +|-+.|..|.-|
T Consensus 22 l~~~~l~~C~~CG~~~------------~~H~vC~~CG~Y 49 (57)
T PRK12286 22 LKAPGLVECPNCGEPK------------LPHRVCPSCGYY 49 (57)
T ss_pred ccCCcceECCCCCCcc------------CCeEECCCCCcC
Confidence 4455677899998643 778889999855
No 55
>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=20.92 E-value=71 Score=23.76 Aligned_cols=14 Identities=29% Similarity=0.766 Sum_probs=10.4
Q ss_pred ceeeeeccCCCCCC
Q 043493 39 TKFCYYNNYNLSQP 52 (254)
Q Consensus 39 TKFcYyNNy~~~QP 52 (254)
.|+|||+|..-+.-
T Consensus 12 ~r~C~Yqdq~YSeG 25 (56)
T PF07383_consen 12 QRCCYYQDQAYSEG 25 (56)
T ss_pred ceEEEEcCCccCCC
Confidence 49999998765543
No 56
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=20.06 E-value=45 Score=20.45 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=12.7
Q ss_pred CcccchhcccccccCc
Q 043493 52 PRHFCKSCRRYWTQGG 67 (254)
Q Consensus 52 PR~fCk~CrRYWT~GG 67 (254)
++|+|.-|..+++.-.
T Consensus 2 ~~~~C~~C~~~~~~~~ 17 (35)
T smart00451 2 GGFYCKLCNVTFTDEI 17 (35)
T ss_pred cCeEccccCCccCCHH
Confidence 5799999999887433
Done!