Query psy16807
Match_columns 220
No_of_seqs 136 out of 1239
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 22:36:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16807.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16807hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08719 ribonuclease H; Revie 98.7 8E-09 1.7E-13 81.7 3.2 30 33-62 117-146 (147)
2 PF00075 RNase_H: RNase H; In 98.7 8.2E-09 1.8E-13 78.9 1.6 30 32-61 101-131 (132)
3 PRK00203 rnhA ribonuclease H; 98.6 1.2E-08 2.7E-13 80.6 2.2 31 34-64 113-143 (150)
4 PRK06548 ribonuclease H; Provi 98.6 3.1E-08 6.6E-13 79.4 2.4 32 34-65 113-144 (161)
5 COG0328 RnhA Ribonuclease HI [ 98.3 3.6E-07 7.7E-12 72.5 2.3 30 35-64 117-146 (154)
6 cd06222 RnaseH RNase H (RNase 97.9 8.5E-06 1.8E-10 59.9 2.9 30 32-61 101-130 (130)
7 KOG3752|consensus 97.8 1.2E-05 2.6E-10 71.5 2.6 32 32-63 334-365 (371)
8 PF13966 zf-RVT: zinc-binding 97.2 0.0002 4.2E-09 51.2 2.1 42 146-187 39-83 (86)
9 PRK13907 rnhA ribonuclease H; 91.4 0.11 2.4E-06 39.3 1.6 25 34-62 102-126 (128)
10 PRK07708 hypothetical protein; 84.2 0.85 1.8E-05 38.4 2.6 28 33-64 182-209 (219)
11 PRK07238 bifunctional RNase H/ 79.1 1.3 2.8E-05 39.9 2.0 26 34-63 107-132 (372)
12 PF13456 RVT_3: Reverse transc 78.9 1.2 2.6E-05 30.5 1.5 26 33-62 61-86 (87)
13 PF05741 zf-nanos: Nanos RNA b 58.9 5 0.00011 26.3 0.9 21 164-185 34-54 (55)
14 PF00098 zf-CCHC: Zinc knuckle 50.8 13 0.00029 18.4 1.5 17 165-185 2-18 (18)
15 COG0296 GlgB 1,4-alpha-glucan 45.1 20 0.00044 34.9 3.0 32 24-55 216-249 (628)
16 PF08274 PhnA_Zn_Ribbon: PhnA 43.9 8.4 0.00018 22.0 0.2 21 164-184 3-23 (30)
17 KOG1930|consensus 38.1 32 0.00068 31.8 3.0 63 121-184 207-281 (483)
18 PF13917 zf-CCHC_3: Zinc knuck 36.9 23 0.0005 21.8 1.4 19 163-185 4-22 (42)
19 PF09905 DUF2132: Uncharacteri 36.1 31 0.00068 23.2 2.0 17 203-220 36-52 (64)
20 PF14169 YdjO: Cold-inducible 35.7 24 0.00053 23.4 1.4 15 158-172 34-48 (59)
21 KOG1994|consensus 33.5 17 0.00036 30.9 0.4 23 164-186 240-262 (268)
22 TIGR03847 conserved hypothetic 33.0 32 0.00069 27.9 2.0 24 160-186 153-176 (177)
23 PF12760 Zn_Tnp_IS1595: Transp 32.3 31 0.00067 21.2 1.5 18 154-171 9-26 (46)
24 PF10580 Neuromodulin_N: Gap j 30.2 60 0.0013 18.5 2.2 24 41-64 5-28 (32)
25 PF09538 FYDLN_acid: Protein o 29.9 37 0.00081 25.3 1.8 20 156-177 20-39 (108)
26 PRK12380 hydrogenase nickel in 29.1 25 0.00055 26.2 0.8 23 163-186 70-92 (113)
27 PRK03681 hypA hydrogenase nick 28.9 26 0.00057 26.2 0.8 24 163-186 70-93 (114)
28 PRK09710 lar restriction allev 28.1 33 0.00071 23.2 1.1 19 161-179 4-22 (64)
29 TIGR00100 hypA hydrogenase nic 27.9 28 0.00061 26.1 0.8 23 163-186 70-92 (115)
30 COG2093 DNA-directed RNA polym 26.3 41 0.00089 22.6 1.3 19 158-177 13-31 (64)
31 PRK03824 hypA hydrogenase nick 26.1 32 0.00068 26.6 0.8 7 165-171 72-78 (135)
32 PF13395 HNH_4: HNH endonuclea 25.9 30 0.00065 22.1 0.6 15 166-180 1-24 (54)
33 PF10892 DUF2688: Protein of u 25.6 26 0.00057 23.0 0.3 29 163-194 10-38 (60)
34 PF13696 zf-CCHC_2: Zinc knuck 24.8 33 0.00072 19.9 0.6 18 164-185 9-26 (32)
35 PF07282 OrfB_Zn_ribbon: Putat 24.6 47 0.001 22.0 1.4 24 162-185 27-51 (69)
36 COG4744 Uncharacterized conser 23.1 47 0.001 25.0 1.2 12 37-52 108-119 (121)
37 PF09237 GAGA: GAGA factor; I 23.0 38 0.00082 21.9 0.6 26 158-193 19-44 (54)
38 PF03119 DNA_ligase_ZBD: NAD-d 22.5 33 0.00073 19.0 0.3 21 165-185 1-22 (28)
39 COG0333 RpmF Ribosomal protein 21.8 54 0.0012 21.6 1.2 31 157-188 21-51 (57)
40 TIGR00686 phnA alkylphosphonat 21.6 52 0.0011 24.6 1.2 22 163-186 2-25 (109)
41 COG2888 Predicted Zn-ribbon RN 20.7 64 0.0014 21.5 1.3 26 162-187 8-34 (61)
42 PF09723 Zn-ribbon_8: Zinc rib 20.4 67 0.0015 19.4 1.4 15 157-171 20-34 (42)
43 KOG4602|consensus 20.4 53 0.0011 28.4 1.2 23 163-186 268-290 (318)
No 1
>PRK08719 ribonuclease H; Reviewed
Probab=98.72 E-value=8e-09 Score=81.66 Aligned_cols=30 Identities=27% Similarity=0.306 Sum_probs=27.8
Q ss_pred CceEEEEEeccCCCCCcchhhhHHhhcccc
Q psy16807 33 WTVVSFLWIPSHVGIRENNLVDEAARNSNE 62 (220)
Q Consensus 33 ~~~V~l~WVPgH~GI~GNE~AD~~AK~A~~ 62 (220)
...|+|.|||||+|++|||.||++|++|+.
T Consensus 117 ~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 117 RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 457999999999999999999999999875
No 2
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=98.66 E-value=8.2e-09 Score=78.86 Aligned_cols=30 Identities=30% Similarity=0.599 Sum_probs=27.7
Q ss_pred CCceEEEEEeccCCCC-CcchhhhHHhhccc
Q psy16807 32 YWTVVSFLWIPSHVGI-RENNLVDEAARNSN 61 (220)
Q Consensus 32 ~~~~V~l~WVPgH~GI-~GNE~AD~~AK~A~ 61 (220)
.+..|.|.|||||+|+ .|||.||++||+|+
T Consensus 101 ~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 101 RGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 3679999999999999 69999999999986
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.64 E-value=1.2e-08 Score=80.61 Aligned_cols=31 Identities=32% Similarity=0.579 Sum_probs=28.9
Q ss_pred ceEEEEEeccCCCCCcchhhhHHhhccccCC
Q psy16807 34 TVVSFLWIPSHVGIRENNLVDEAARNSNEAP 64 (220)
Q Consensus 34 ~~V~l~WVPgH~GI~GNE~AD~~AK~A~~~~ 64 (220)
..|.|.|||||+|++|||.||++||+|+...
T Consensus 113 ~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 113 HQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred CceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 6899999999999999999999999998764
No 4
>PRK06548 ribonuclease H; Provisional
Probab=98.56 E-value=3.1e-08 Score=79.42 Aligned_cols=32 Identities=22% Similarity=0.364 Sum_probs=28.9
Q ss_pred ceEEEEEeccCCCCCcchhhhHHhhccccCCC
Q psy16807 34 TVVSFLWIPSHVGIRENNLVDEAARNSNEAPL 65 (220)
Q Consensus 34 ~~V~l~WVPgH~GI~GNE~AD~~AK~A~~~~~ 65 (220)
..|+|.|||||+|++|||.||+||++|+....
T Consensus 113 ~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~ 144 (161)
T PRK06548 113 RNIRMSWVNAHTGHPLNEAADSLARQAANNFS 144 (161)
T ss_pred CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence 47999999999999999999999999986543
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.29 E-value=3.6e-07 Score=72.52 Aligned_cols=30 Identities=33% Similarity=0.592 Sum_probs=28.7
Q ss_pred eEEEEEeccCCCCCcchhhhHHhhccccCC
Q psy16807 35 VVSFLWIPSHVGIRENNLVDEAARNSNEAP 64 (220)
Q Consensus 35 ~V~l~WVPgH~GI~GNE~AD~~AK~A~~~~ 64 (220)
.|.+.|||||.|.++||.||++|+.|+...
T Consensus 117 ~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 117 LVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred eEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 899999999999999999999999998865
No 6
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=97.90 E-value=8.5e-06 Score=59.93 Aligned_cols=30 Identities=33% Similarity=0.674 Sum_probs=27.5
Q ss_pred CCceEEEEEeccCCCCCcchhhhHHhhccc
Q psy16807 32 YWTVVSFLWIPSHVGIRENNLVDEAARNSN 61 (220)
Q Consensus 32 ~~~~V~l~WVPgH~GI~GNE~AD~~AK~A~ 61 (220)
....+.|.|||+|+|+.+|+.||.+||+|.
T Consensus 101 ~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 101 RFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred CCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 456899999999999999999999999873
No 7
>KOG3752|consensus
Probab=97.80 E-value=1.2e-05 Score=71.47 Aligned_cols=32 Identities=25% Similarity=0.301 Sum_probs=29.1
Q ss_pred CCceEEEEEeccCCCCCcchhhhHHhhccccC
Q psy16807 32 YWTVVSFLWIPSHVGIRENNLVDEAARNSNEA 63 (220)
Q Consensus 32 ~~~~V~l~WVPgH~GI~GNE~AD~~AK~A~~~ 63 (220)
.+.+|++.|||||.||.|||+||.+|++++..
T Consensus 334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 334 SNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred ccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 45899999999999999999999999998653
No 8
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=97.22 E-value=0.0002 Score=51.22 Aligned_cols=42 Identities=29% Similarity=0.412 Sum_probs=32.5
Q ss_pred cccccccc---hhhhhccCCCCCcccCCCcccccccccccccCcH
Q psy16807 146 RIGHCLAT---HQYLLERQNPPACHLCNEVPITIKHWLLECPRLN 187 (220)
Q Consensus 146 RTGH~~~~---~l~r~~~~~~p~C~~Cg~~~et~~HiL~~Cp~~~ 187 (220)
+.-|.++. -+.+.+...++.|+.||.+.||++|+|++||...
T Consensus 39 ~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 39 RALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred eeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 34445542 3666777788999999988999999999999753
No 9
>PRK13907 rnhA ribonuclease H; Provisional
Probab=91.38 E-value=0.11 Score=39.31 Aligned_cols=25 Identities=36% Similarity=0.594 Sum_probs=21.6
Q ss_pred ceEEEEEeccCCCCCcchhhhHHhhcccc
Q psy16807 34 TVVSFLWIPSHVGIRENNLVDEAARNSNE 62 (220)
Q Consensus 34 ~~V~l~WVPgH~GI~GNE~AD~~AK~A~~ 62 (220)
..+.|.|||. ++|+.||.+|++|..
T Consensus 102 ~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 102 DLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred CceEEEEcCc----hhchhHHHHHHHHHh
Confidence 3677899999 499999999999875
No 10
>PRK07708 hypothetical protein; Validated
Probab=84.25 E-value=0.85 Score=38.36 Aligned_cols=28 Identities=18% Similarity=0.128 Sum_probs=22.6
Q ss_pred CceEEEEEeccCCCCCcchhhhHHhhccccCC
Q psy16807 33 WTVVSFLWIPSHVGIRENNLVDEAARNSNEAP 64 (220)
Q Consensus 33 ~~~V~l~WVPgH~GI~GNE~AD~~AK~A~~~~ 64 (220)
...+.+.|||- .-|+.||++|++|.+..
T Consensus 182 ~l~~~~~~VpR----~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 182 KLTPVYEPISR----KQNKEADQLATQALEGT 209 (219)
T ss_pred CceEEEEECCc----hhhhHHHHHHHHHHhcC
Confidence 34577888876 56999999999999854
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=79.09 E-value=1.3 Score=39.88 Aligned_cols=26 Identities=31% Similarity=0.567 Sum_probs=22.8
Q ss_pred ceEEEEEeccCCCCCcchhhhHHhhccccC
Q psy16807 34 TVVSFLWIPSHVGIRENNLVDEAARNSNEA 63 (220)
Q Consensus 34 ~~V~l~WVPgH~GI~GNE~AD~~AK~A~~~ 63 (220)
..|.+.|||. ++|+.||.+|+.|...
T Consensus 107 ~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 107 GRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred CceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 4799999998 7899999999998654
No 12
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=78.87 E-value=1.2 Score=30.50 Aligned_cols=26 Identities=27% Similarity=0.316 Sum_probs=20.2
Q ss_pred CceEEEEEeccCCCCCcchhhhHHhhcccc
Q psy16807 33 WTVVSFLWIPSHVGIRENNLVDEAARNSNE 62 (220)
Q Consensus 33 ~~~V~l~WVPgH~GI~GNE~AD~~AK~A~~ 62 (220)
-..+.+.|||- ++|..||.+||.|.+
T Consensus 61 ~~~~~~~~i~r----~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 61 FWNVSVSHIPR----EQNKVADALAKFALS 86 (87)
T ss_dssp CSCEEEEE--G----GGSHHHHHHHHHHHH
T ss_pred ccceEEEEECh----HHhHHHHHHHHHHhh
Confidence 45889999987 789999999998853
No 13
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=58.86 E-value=5 Score=26.31 Aligned_cols=21 Identities=24% Similarity=0.585 Sum_probs=10.0
Q ss_pred CCcccCCCcccccccccccccC
Q psy16807 164 PACHLCNEVPITIKHWLLECPR 185 (220)
Q Consensus 164 p~C~~Cg~~~et~~HiL~~Cp~ 185 (220)
-.|+.||. ..+-.|....||.
T Consensus 34 y~Cp~CgA-tGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGA-TGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT----GGG---GGG-TT
T ss_pred CcCCCCcC-cCccccccccCcC
Confidence 46999999 8999999999996
No 14
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=50.84 E-value=13 Score=18.42 Aligned_cols=17 Identities=35% Similarity=0.884 Sum_probs=12.8
Q ss_pred CcccCCCcccccccccccccC
Q psy16807 165 ACHLCNEVPITIKHWLLECPR 185 (220)
Q Consensus 165 ~C~~Cg~~~et~~HiL~~Cp~ 185 (220)
.|..||. ..|+-.+||.
T Consensus 2 ~C~~C~~----~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGE----PGHIARDCPK 18 (18)
T ss_dssp BCTTTSC----SSSCGCTSSS
T ss_pred cCcCCCC----cCcccccCcc
Confidence 5777877 5788888874
No 15
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=45.10 E-value=20 Score=34.86 Aligned_cols=32 Identities=25% Similarity=0.343 Sum_probs=26.0
Q ss_pred hHHHhh--ccCCceEEEEEeccCCCCCcchhhhH
Q psy16807 24 FRYLLS--DSYWTVVSFLWIPSHVGIRENNLVDE 55 (220)
Q Consensus 24 ~r~~l~--~~~~~~V~l~WVPgH~GI~GNE~AD~ 55 (220)
|+.+.+ -+.|..|=|-|||+|.|..||=++--
T Consensus 216 fk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~f 249 (628)
T COG0296 216 FKALVDAAHQAGIGVILDWVPNHFPPDGNYLARF 249 (628)
T ss_pred HHHHHHHHHHcCCEEEEEecCCcCCCCcchhhhc
Confidence 555555 47899999999999999999987643
No 16
>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=43.89 E-value=8.4 Score=21.99 Aligned_cols=21 Identities=38% Similarity=0.691 Sum_probs=6.8
Q ss_pred CCcccCCCccccccccccccc
Q psy16807 164 PACHLCNEVPITIKHWLLECP 184 (220)
Q Consensus 164 p~C~~Cg~~~et~~HiL~~Cp 184 (220)
|.|+.||.+..=.+..++-||
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp 23 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCP 23 (30)
T ss_dssp ---TTT-----EE-SSSEEET
T ss_pred CCCCCCCCcceeccCCEEeCC
Confidence 678888874333444445555
No 17
>KOG1930|consensus
Probab=38.12 E-value=32 Score=31.83 Aligned_cols=63 Identities=21% Similarity=0.348 Sum_probs=38.9
Q ss_pred eecccCcccCCCCCchhhHhhhhh--------ccccccccc-hhhhhccCCCC-Ccc-cCCC-ccccccccccccc
Q psy16807 121 IKCDTRKWKSSTRDVRAEEIVVCR--------LRIGHCLAT-HQYLLERQNPP-ACH-LCNE-VPITIKHWLLECP 184 (220)
Q Consensus 121 i~~~~~~w~~~~~lsR~~~~~L~q--------lRTGH~~~~-~l~r~~~~~~p-~C~-~Cg~-~~et~~HiL~~Cp 184 (220)
++.+.+.||.+ +++|.+++.|-+ +|-.|+.-. |---++...+| .-. .=|. ++|=|.|||+||.
T Consensus 207 V~DTSKyWYKP-~isREQAIalLrdkePGtFvvRDS~SfrGayGLAlKVstPPPs~~~~~g~~~neLVRHFLIE~s 281 (483)
T KOG1930|consen 207 VKDTSKYWYKP-NISREQAIALLRDKEPGTFVVRDSHSFRGAYGLALKVSTPPPSVQPGDGSDSNELVRHFLIEPS 281 (483)
T ss_pred eecccccccCC-CCCHHHHHHHhhcCCCCeEEEecCCcCCCccceEEEeccCCCcccCCCCCchhhhhhhheeccC
Confidence 34456779975 899999987764 355555533 44345555443 322 2232 2488999999984
No 18
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=36.93 E-value=23 Score=21.84 Aligned_cols=19 Identities=37% Similarity=1.045 Sum_probs=15.6
Q ss_pred CCCcccCCCcccccccccccccC
Q psy16807 163 PPACHLCNEVPITIKHWLLECPR 185 (220)
Q Consensus 163 ~p~C~~Cg~~~et~~HiL~~Cp~ 185 (220)
...|..||. ..|+-++|+.
T Consensus 4 ~~~CqkC~~----~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQ----KGHWTYECPN 22 (42)
T ss_pred CCcCcccCC----CCcchhhCCC
Confidence 467888887 4699999996
No 19
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=36.07 E-value=31 Score=23.19 Aligned_cols=17 Identities=29% Similarity=0.632 Sum_probs=12.2
Q ss_pred cCCChhhHHHHHHHHHhC
Q psy16807 203 LKDDEIIIDSCVNFLKEA 220 (220)
Q Consensus 203 L~~~~~~~~~i~~Fi~~t 220 (220)
...++ .+.+.++|+++|
T Consensus 36 F~~~P-sikSSLkFLRkT 52 (64)
T PF09905_consen 36 FKNNP-SIKSSLKFLRKT 52 (64)
T ss_dssp TTSS---HHHHHHHHHHS
T ss_pred CCCCC-chHHHHHHHhcC
Confidence 34466 489999999997
No 20
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=35.66 E-value=24 Score=23.41 Aligned_cols=15 Identities=27% Similarity=0.753 Sum_probs=12.1
Q ss_pred hccCCCCCcccCCCc
Q psy16807 158 LERQNPPACHLCNEV 172 (220)
Q Consensus 158 ~~~~~~p~C~~Cg~~ 172 (220)
|...+.|.||.|+.+
T Consensus 34 Fs~~~~p~CPlC~s~ 48 (59)
T PF14169_consen 34 FSFEEEPVCPLCKSP 48 (59)
T ss_pred cccCCCccCCCcCCc
Confidence 455678999999984
No 21
>KOG1994|consensus
Probab=33.50 E-value=17 Score=30.86 Aligned_cols=23 Identities=17% Similarity=0.379 Sum_probs=19.4
Q ss_pred CCcccCCCcccccccccccccCc
Q psy16807 164 PACHLCNEVPITIKHWLLECPRL 186 (220)
Q Consensus 164 p~C~~Cg~~~et~~HiL~~Cp~~ 186 (220)
-.|-+||-...|.+-++-+||--
T Consensus 240 ~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 240 YYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred eEEEEeccccCCHHHHHHhCCCC
Confidence 35889998889999999999964
No 22
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=32.98 E-value=32 Score=27.93 Aligned_cols=24 Identities=33% Similarity=0.649 Sum_probs=17.9
Q ss_pred cCCCCCcccCCCcccccccccccccCc
Q psy16807 160 RQNPPACHLCNEVPITIKHWLLECPRL 186 (220)
Q Consensus 160 ~~~~p~C~~Cg~~~et~~HiL~~Cp~~ 186 (220)
....|.|+.||.+.+---|| ||+-
T Consensus 153 aAGRP~CPlCg~PldP~GH~---Cpr~ 176 (177)
T TIGR03847 153 AAGRPPCPLCGRPIDPDGHI---CPRQ 176 (177)
T ss_pred hCCCCCCCCCCCCCCCCCcc---CCCC
Confidence 45689999999955545676 8863
No 23
>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=32.30 E-value=31 Score=21.25 Aligned_cols=18 Identities=11% Similarity=0.180 Sum_probs=13.2
Q ss_pred hhhhhccCCCCCcccCCC
Q psy16807 154 HQYLLERQNPPACHLCNE 171 (220)
Q Consensus 154 ~l~r~~~~~~p~C~~Cg~ 171 (220)
|+..++-.+.+.||.||.
T Consensus 9 ~l~~~RW~~g~~CP~Cg~ 26 (46)
T PF12760_consen 9 YLEEIRWPDGFVCPHCGS 26 (46)
T ss_pred HHHHhcCCCCCCCCCCCC
Confidence 455555556688999998
No 24
>PF10580 Neuromodulin_N: Gap junction protein N-terminal region; InterPro: IPR018947 Neuromodulin is a component of the motile growth cones. It is membrane protein whose expression is widely correlated with successful axon elongation []. It is a crucial component of an effective regeneration response in the nervous system []. Although its function is uncertain, the N-terminal region is well conserved and contains both a calmodulin binding domain, and sites for acylation, membrane attachment and protein kinase C phosphorylation. Structure predictions suggest that the C-terminal region may exist as an extended, negatively-charged rod with some similarity to the side arms of neurofilaments, indicating that the biological role of neuromodulin may depend on its ability to form a dynamic membrane-cytoplasm-calmodulin complex []. This entry represents the neuromodulin N-terminal domain.
Probab=30.20 E-value=60 Score=18.55 Aligned_cols=24 Identities=17% Similarity=0.248 Sum_probs=17.8
Q ss_pred eccCCCCCcchhhhHHhhccccCC
Q psy16807 41 IPSHVGIRENNLVDEAARNSNEAP 64 (220)
Q Consensus 41 VPgH~GI~GNE~AD~~AK~A~~~~ 64 (220)
+-.+..++-||.||+...+-...|
T Consensus 5 ~r~tk~VEKNeeadQkieqDg~KP 28 (32)
T PF10580_consen 5 IRRTKPVEKNEEADQKIEQDGIKP 28 (32)
T ss_pred eeccccccccchhhhhhhhcCCCc
Confidence 334567999999999988765444
No 25
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=29.92 E-value=37 Score=25.30 Aligned_cols=20 Identities=25% Similarity=0.634 Sum_probs=14.4
Q ss_pred hhhccCCCCCcccCCCcccccc
Q psy16807 156 YLLERQNPPACHLCNEVPITIK 177 (220)
Q Consensus 156 ~r~~~~~~p~C~~Cg~~~et~~ 177 (220)
|-+|+ ++-.||.||. ...++
T Consensus 20 YDLnk-~PivCP~CG~-~~~~~ 39 (108)
T PF09538_consen 20 YDLNK-DPIVCPKCGT-EFPPE 39 (108)
T ss_pred ccCCC-CCccCCCCCC-ccCcc
Confidence 45666 5667999999 66665
No 26
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=29.11 E-value=25 Score=26.25 Aligned_cols=23 Identities=22% Similarity=0.554 Sum_probs=14.9
Q ss_pred CCCcccCCCcccccccccccccCc
Q psy16807 163 PPACHLCNEVPITIKHWLLECPRL 186 (220)
Q Consensus 163 ~p~C~~Cg~~~et~~HiL~~Cp~~ 186 (220)
.-.|..||. ...+....+.||.=
T Consensus 70 ~~~C~~Cg~-~~~~~~~~~~CP~C 92 (113)
T PRK12380 70 QAWCWDCSQ-VVEIHQHDAQCPHC 92 (113)
T ss_pred EEEcccCCC-EEecCCcCccCcCC
Confidence 346888887 55555455568864
No 27
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.91 E-value=26 Score=26.20 Aligned_cols=24 Identities=17% Similarity=0.474 Sum_probs=15.1
Q ss_pred CCCcccCCCcccccccccccccCc
Q psy16807 163 PPACHLCNEVPITIKHWLLECPRL 186 (220)
Q Consensus 163 ~p~C~~Cg~~~et~~HiL~~Cp~~ 186 (220)
.-.|..||.......+.++.||.=
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~C 93 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQC 93 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCc
Confidence 456888988333335555678863
No 28
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=28.06 E-value=33 Score=23.18 Aligned_cols=19 Identities=26% Similarity=0.559 Sum_probs=13.6
Q ss_pred CCCCCcccCCCcccccccc
Q psy16807 161 QNPPACHLCNEVPITIKHW 179 (220)
Q Consensus 161 ~~~p~C~~Cg~~~et~~Hi 179 (220)
+.--.||.||....+++|.
T Consensus 4 d~lKPCPFCG~~~~~v~~~ 22 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKAI 22 (64)
T ss_pred ccccCCCCCCCceeEEEec
Confidence 3345799999977777664
No 29
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=27.93 E-value=28 Score=26.07 Aligned_cols=23 Identities=26% Similarity=0.585 Sum_probs=15.2
Q ss_pred CCCcccCCCcccccccccccccCc
Q psy16807 163 PPACHLCNEVPITIKHWLLECPRL 186 (220)
Q Consensus 163 ~p~C~~Cg~~~et~~HiL~~Cp~~ 186 (220)
.-.|..||. .-++....+.||.=
T Consensus 70 ~~~C~~Cg~-~~~~~~~~~~CP~C 92 (115)
T TIGR00100 70 ECECEDCSE-EVSPEIDLYRCPKC 92 (115)
T ss_pred EEEcccCCC-EEecCCcCccCcCC
Confidence 456888887 55555445678864
No 30
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=26.27 E-value=41 Score=22.62 Aligned_cols=19 Identities=16% Similarity=0.450 Sum_probs=11.9
Q ss_pred hccCCCCCcccCCCcccccc
Q psy16807 158 LERQNPPACHLCNEVPITIK 177 (220)
Q Consensus 158 ~~~~~~p~C~~Cg~~~et~~ 177 (220)
+-..+...||.||. .+..+
T Consensus 13 l~~~d~e~CP~Cgs-~~~te 31 (64)
T COG2093 13 LTPEDTEICPVCGS-TDLTE 31 (64)
T ss_pred cCCCCCccCCCCCC-cccch
Confidence 33345566999999 54443
No 31
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.06 E-value=32 Score=26.59 Aligned_cols=7 Identities=29% Similarity=1.023 Sum_probs=3.7
Q ss_pred CcccCCC
Q psy16807 165 ACHLCNE 171 (220)
Q Consensus 165 ~C~~Cg~ 171 (220)
.|..||.
T Consensus 72 ~C~~CG~ 78 (135)
T PRK03824 72 KCRNCGN 78 (135)
T ss_pred ECCCCCC
Confidence 4555554
No 32
>PF13395 HNH_4: HNH endonuclease
Probab=25.91 E-value=30 Score=22.09 Aligned_cols=15 Identities=27% Similarity=0.709 Sum_probs=10.5
Q ss_pred cccCCCc---c------ccccccc
Q psy16807 166 CHLCNEV---P------ITIKHWL 180 (220)
Q Consensus 166 C~~Cg~~---~------et~~HiL 180 (220)
|++||.. . -+++||+
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHii 24 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHII 24 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEe
Confidence 7788873 1 3778886
No 33
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=25.63 E-value=26 Score=23.00 Aligned_cols=29 Identities=24% Similarity=0.425 Sum_probs=21.9
Q ss_pred CCCcccCCCcccccccccccccCcHHHHhhcC
Q psy16807 163 PPACHLCNEVPITIKHWLLECPRLNALRRKFK 194 (220)
Q Consensus 163 ~p~C~~Cg~~~et~~HiL~~Cp~~~~~R~~l~ 194 (220)
...|..||.+.-+..|-|+ -.++.|..|+
T Consensus 10 ~t~CrRCGk~i~tl~~SL~---Gad~lr~klG 38 (60)
T PF10892_consen 10 ETPCRRCGKSIRTLSRSLI---GADDLRVKLG 38 (60)
T ss_pred eehhhhhCccHHHHHHHhh---ChHHHHHHHc
Confidence 4568899998888899887 4456676664
No 34
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=24.79 E-value=33 Score=19.87 Aligned_cols=18 Identities=39% Similarity=1.180 Sum_probs=14.2
Q ss_pred CCcccCCCcccccccccccccC
Q psy16807 164 PACHLCNEVPITIKHWLLECPR 185 (220)
Q Consensus 164 p~C~~Cg~~~et~~HiL~~Cp~ 185 (220)
=.|..|+. .. |++-+||.
T Consensus 9 Y~C~~C~~-~G---H~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQ-KG---HWIQDCPT 26 (32)
T ss_pred CEeecCCC-CC---ccHhHCCC
Confidence 35888887 33 99999997
No 35
>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=24.59 E-value=47 Score=22.01 Aligned_cols=24 Identities=17% Similarity=0.483 Sum_probs=13.4
Q ss_pred CCCCcccCCCcccc-cccccccccC
Q psy16807 162 NPPACHLCNEVPIT-IKHWLLECPR 185 (220)
Q Consensus 162 ~~p~C~~Cg~~~et-~~HiL~~Cp~ 185 (220)
.|-.|+.||...+. ...=.+.||.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~ 51 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPN 51 (69)
T ss_pred CccCccCcccccccccccceEEcCC
Confidence 35668778874333 3333456764
No 36
>COG4744 Uncharacterized conserved protein [Function unknown]
Probab=23.07 E-value=47 Score=24.99 Aligned_cols=12 Identities=17% Similarity=0.578 Sum_probs=9.7
Q ss_pred EEEEeccCCCCCcchh
Q psy16807 37 SFLWIPSHVGIRENNL 52 (220)
Q Consensus 37 ~l~WVPgH~GI~GNE~ 52 (220)
+++|||| +|||.
T Consensus 108 r~I~Vp~----~~~~~ 119 (121)
T COG4744 108 RVIYVPE----EGNEA 119 (121)
T ss_pred eEEEecC----CCCcC
Confidence 5899999 77774
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=23.04 E-value=38 Score=21.94 Aligned_cols=26 Identities=23% Similarity=0.602 Sum_probs=13.4
Q ss_pred hccCCCCCcccCCCcccccccccccccCcHHHHhhc
Q psy16807 158 LERQNPPACHLCNEVPITIKHWLLECPRLNALRRKF 193 (220)
Q Consensus 158 ~~~~~~p~C~~Cg~~~et~~HiL~~Cp~~~~~R~~l 193 (220)
..-..++.||.||. .|+.-.+.|+-+
T Consensus 19 ~~S~~PatCP~C~a----------~~~~srnLrRHl 44 (54)
T PF09237_consen 19 SQSEQPATCPICGA----------VIRQSRNLRRHL 44 (54)
T ss_dssp CTTS--EE-TTT------------EESSHHHHHHHH
T ss_pred hccCCCCCCCcchh----------hccchhhHHHHH
Confidence 33445789999998 366666666544
No 38
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=22.45 E-value=33 Score=19.02 Aligned_cols=21 Identities=19% Similarity=0.501 Sum_probs=7.3
Q ss_pred CcccCCCc-ccccccccccccC
Q psy16807 165 ACHLCNEV-PITIKHWLLECPR 185 (220)
Q Consensus 165 ~C~~Cg~~-~et~~HiL~~Cp~ 185 (220)
.||.||.. ....+=+.+.|+.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--
T ss_pred CcCCCCCEeEcCCCCEeEECCC
Confidence 48999983 2223333344654
No 39
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.83 E-value=54 Score=21.59 Aligned_cols=31 Identities=19% Similarity=0.296 Sum_probs=21.8
Q ss_pred hhccCCCCCcccCCCcccccccccccccCcHH
Q psy16807 157 LLERQNPPACHLCNEVPITIKHWLLECPRLNA 188 (220)
Q Consensus 157 r~~~~~~p~C~~Cg~~~et~~HiL~~Cp~~~~ 188 (220)
+.....-..|+.||+ ..=+-|+=..|..|..
T Consensus 21 ~l~~~~~~~c~~cG~-~~l~Hrvc~~cg~Y~g 51 (57)
T COG0333 21 ALKAPTLSVCPNCGE-YKLPHRVCLKCGYYKG 51 (57)
T ss_pred hhhCccceeccCCCC-cccCceEcCCCCCccC
Confidence 333334478999999 7777787788887753
No 40
>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=21.62 E-value=52 Score=24.59 Aligned_cols=22 Identities=32% Similarity=0.529 Sum_probs=11.9
Q ss_pred CCCcccCCCc--ccccccccccccCc
Q psy16807 163 PPACHLCNEV--PITIKHWLLECPRL 186 (220)
Q Consensus 163 ~p~C~~Cg~~--~et~~HiL~~Cp~~ 186 (220)
.|.||.|+.. .++-+ ++-||-=
T Consensus 2 lp~CP~C~seytY~dg~--~~iCpeC 25 (109)
T TIGR00686 2 LPPCPKCNSEYTYHDGT--QLICPSC 25 (109)
T ss_pred CCcCCcCCCcceEecCC--eeECccc
Confidence 3678888763 23333 3456643
No 41
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.72 E-value=64 Score=21.51 Aligned_cols=26 Identities=23% Similarity=0.580 Sum_probs=15.3
Q ss_pred CCCCcccCCCccccccc-ccccccCcH
Q psy16807 162 NPPACHLCNEVPITIKH-WLLECPRLN 187 (220)
Q Consensus 162 ~~p~C~~Cg~~~et~~H-iL~~Cp~~~ 187 (220)
+.+.|.+||......++ +.|.||.=-
T Consensus 8 ~~~~CtSCg~~i~p~e~~v~F~CPnCG 34 (61)
T COG2888 8 DPPVCTSCGREIAPGETAVKFPCPNCG 34 (61)
T ss_pred CCceeccCCCEeccCCceeEeeCCCCC
Confidence 46889999984312222 225688754
No 42
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.41 E-value=67 Score=19.38 Aligned_cols=15 Identities=20% Similarity=0.671 Sum_probs=10.6
Q ss_pred hhccCCCCCcccCCC
Q psy16807 157 LLERQNPPACHLCNE 171 (220)
Q Consensus 157 r~~~~~~p~C~~Cg~ 171 (220)
.+.-.+...||.||.
T Consensus 20 ~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 20 SISEDDPVPCPECGS 34 (42)
T ss_pred EcCCCCCCcCCCCCC
Confidence 333355788999998
No 43
>KOG4602|consensus
Probab=20.36 E-value=53 Score=28.42 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=19.6
Q ss_pred CCCcccCCCcccccccccccccCc
Q psy16807 163 PPACHLCNEVPITIKHWLLECPRL 186 (220)
Q Consensus 163 ~p~C~~Cg~~~et~~HiL~~Cp~~ 186 (220)
+-.|+.||. ..+-.|.+-.||.-
T Consensus 268 ~YVCPiCGA-TgDnAHTiKyCPl~ 290 (318)
T KOG4602|consen 268 SYVCPICGA-TGDNAHTIKYCPLA 290 (318)
T ss_pred hhcCccccc-cCCcccceeccccc
Confidence 346999999 88999999999974
Done!