Query psy5610
Match_columns 237
No_of_seqs 175 out of 1693
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 21:57:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5610.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5610hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.8 1.3E-18 2.7E-23 136.8 10.3 91 1-97 40-142 (161)
2 PRK08719 ribonuclease H; Revie 99.7 2.3E-17 4.9E-22 128.3 9.9 87 1-96 48-146 (147)
3 COG0328 RnhA Ribonuclease HI [ 99.7 1.1E-17 2.4E-22 129.4 7.6 92 1-97 41-145 (154)
4 PRK00203 rnhA ribonuclease H; 99.7 3.7E-17 8.1E-22 127.8 9.2 90 1-97 41-142 (150)
5 PF00075 RNase_H: RNase H; In 99.7 2E-17 4.3E-22 126.0 6.8 84 2-96 39-132 (132)
6 cd06222 RnaseH RNase H (RNase 99.6 4.1E-14 8.8E-19 105.2 10.9 90 1-95 39-130 (130)
7 KOG3752|consensus 99.4 6.5E-13 1.4E-17 114.8 8.0 91 2-97 255-365 (371)
8 PRK13907 rnhA ribonuclease H; 99.4 3.2E-12 6.9E-17 97.2 9.8 88 1-97 39-127 (128)
9 PF13456 RVT_3: Reverse transc 99.3 2E-11 4.4E-16 85.8 9.7 85 3-96 1-86 (87)
10 PRK07708 hypothetical protein; 99.2 2.1E-10 4.5E-15 94.8 10.3 88 1-97 116-208 (219)
11 PRK07238 bifunctional RNase H/ 99.0 2.8E-09 6.1E-14 95.2 10.2 88 1-97 43-132 (372)
12 PF13966 zf-RVT: zinc-binding 96.9 0.0006 1.3E-08 47.9 2.0 32 171-202 51-83 (86)
13 PF05741 zf-nanos: Nanos RNA b 75.5 1.5 3.3E-05 28.0 1.0 21 180-200 34-54 (55)
14 PF13696 zf-CCHC_2: Zinc knuck 51.9 7.2 0.00016 22.0 0.7 19 179-200 8-26 (32)
15 PHA02031 putative DnaG-like pr 50.5 9.6 0.00021 32.5 1.6 56 179-236 43-100 (266)
16 COG0296 GlgB 1,4-alpha-glucan 47.1 25 0.00054 33.8 3.9 35 55-89 214-249 (628)
17 cd00350 rubredoxin_like Rubred 46.5 9.2 0.0002 21.4 0.6 21 182-202 4-24 (33)
18 COG2093 DNA-directed RNA polym 45.3 15 0.00033 24.0 1.6 17 173-189 12-28 (64)
19 TIGR03847 conserved hypothetic 41.0 17 0.00036 28.9 1.5 22 178-201 155-176 (177)
20 PF00098 zf-CCHC: Zinc knuckle 39.0 27 0.00058 16.7 1.5 17 181-200 2-18 (18)
21 PF14169 YdjO: Cold-inducible 38.9 22 0.00048 23.0 1.6 21 174-194 34-56 (59)
22 PF13917 zf-CCHC_3: Zinc knuck 38.4 18 0.0004 21.7 1.1 19 179-200 4-22 (42)
23 PF08274 PhnA_Zn_Ribbon: PhnA 37.3 14 0.0003 20.5 0.4 22 180-201 3-25 (30)
24 PF06696 Strep_SA_rep: Strepto 35.2 33 0.00072 18.1 1.6 17 1-17 7-23 (25)
25 PRK12380 hydrogenase nickel in 34.9 14 0.00031 27.1 0.3 26 180-205 71-96 (113)
26 KOG0466|consensus 34.3 53 0.0012 28.9 3.6 37 172-208 102-142 (466)
27 PF15322 PMSI1: Protein missin 33.9 23 0.0005 30.3 1.3 14 157-170 215-228 (311)
28 TIGR00100 hypA hydrogenase nic 32.3 23 0.0005 26.1 1.0 26 180-205 71-96 (115)
29 KOG4602|consensus 32.1 23 0.0005 29.9 1.1 23 179-201 268-290 (318)
30 PRK03824 hypA hydrogenase nick 31.5 25 0.00054 26.7 1.1 11 193-203 105-115 (135)
31 PF14205 Cys_rich_KTR: Cystein 29.9 25 0.00054 22.3 0.7 23 181-203 6-36 (55)
32 TIGR01206 lysW lysine biosynth 29.8 33 0.00071 21.8 1.2 22 181-202 4-29 (54)
33 COG3341 Predicted double-stran 28.6 65 0.0014 26.6 3.1 90 2-97 107-201 (225)
34 PF03119 DNA_ligase_ZBD: NAD-d 26.8 27 0.00058 18.9 0.4 20 181-200 1-22 (28)
35 PRK09710 lar restriction allev 26.6 30 0.00066 22.8 0.7 24 180-203 7-35 (64)
36 PRK03681 hypA hydrogenase nick 25.7 35 0.00076 25.1 1.0 26 180-205 71-97 (114)
37 cd00729 rubredoxin_SM Rubredox 25.5 35 0.00076 19.3 0.7 10 179-188 18-27 (34)
38 PF14255 Cys_rich_CPXG: Cystei 25.0 35 0.00075 21.5 0.7 8 181-188 2-9 (52)
39 PF13395 HNH_4: HNH endonuclea 24.9 34 0.00073 21.4 0.7 14 182-195 1-24 (54)
40 COG1326 Uncharacterized archae 24.7 34 0.00074 27.7 0.8 27 179-205 6-40 (201)
41 PF07282 OrfB_Zn_ribbon: Putat 24.4 42 0.00091 21.9 1.1 23 179-201 28-52 (69)
42 KOG1123|consensus 24.2 92 0.002 29.5 3.5 31 13-45 530-560 (776)
43 PF13248 zf-ribbon_3: zinc-rib 23.8 46 0.001 17.4 1.0 7 181-187 4-10 (26)
44 KOG1812|consensus 23.4 2.4E+02 0.0052 25.5 6.0 38 3-45 49-86 (384)
45 PRK00420 hypothetical protein; 23.3 53 0.0011 24.2 1.5 27 161-188 21-49 (112)
46 PRK00464 nrdR transcriptional 22.8 41 0.00089 26.3 0.9 9 181-189 2-10 (154)
47 PRK06393 rpoE DNA-directed RNA 22.5 61 0.0013 21.4 1.5 11 178-188 16-26 (64)
48 COG0266 Nei Formamidopyrimidin 21.8 2.9E+02 0.0062 23.8 5.9 26 82-107 171-196 (273)
49 PF01396 zf-C4_Topoisom: Topoi 21.8 45 0.00098 19.4 0.8 27 181-207 3-33 (39)
50 PF05605 zf-Di19: Drought indu 21.7 34 0.00075 21.3 0.2 18 179-196 2-19 (54)
51 PF11290 DUF3090: Protein of u 21.4 51 0.0011 26.2 1.2 18 177-194 152-170 (171)
52 PF09538 FYDLN_acid: Protein o 21.4 73 0.0016 23.3 1.9 20 172-192 20-39 (108)
53 PF01155 HypA: Hydrogenase exp 21.1 30 0.00065 25.3 -0.1 25 180-204 71-95 (113)
54 PF09862 DUF2089: Protein of u 20.8 53 0.0011 24.3 1.1 19 182-202 1-19 (113)
55 PF03604 DNA_RNApol_7kD: DNA d 20.5 88 0.0019 17.5 1.7 14 174-187 12-25 (32)
56 KOG3456|consensus 20.0 62 0.0013 23.6 1.3 27 162-188 84-113 (120)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.78 E-value=1.3e-18 Score=136.78 Aligned_cols=91 Identities=29% Similarity=0.333 Sum_probs=72.0
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc---------ccC--CChHH-HHHHHHHHHhhcCC
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN---------IFS--LNPIA-GEIRDLILTNKSKL 68 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~---------~~~--~~~~~-~~i~~~~~~l~~~~ 68 (237)
++|++||+.|++.||+.+ . .....|.|+|||++++++++. |+. ..|+. +++.+.+..+.+..
T Consensus 40 ~TNnraEl~Aii~aL~~~-----~-~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~ 113 (161)
T PRK06548 40 ATNNIAELTAVRELLIAT-----R-HTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR 113 (161)
T ss_pred CCHHHHHHHHHHHHHHhh-----h-cCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC
Confidence 479999999999999863 2 234579999999999999994 222 23444 45555555555566
Q ss_pred cEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610 69 NVRFIWVPSHVGIAGNEEADRLAKEALTS 97 (237)
Q Consensus 69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~~ 97 (237)
.|+|.|||||+|..|||.||.||++++..
T Consensus 114 ~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 114 NIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred ceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999877
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.73 E-value=2.3e-17 Score=128.34 Aligned_cols=87 Identities=29% Similarity=0.342 Sum_probs=67.4
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc---------ccCCC--hHH-HHHHHHHHHhhcCC
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN---------IFSLN--PIA-GEIRDLILTNKSKL 68 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~---------~~~~~--~~~-~~i~~~~~~l~~~~ 68 (237)
++|++||+.|++.||+.+. . ...|+|||++++++++. |...+ ++. .+++..+..+....
T Consensus 48 ~Tnn~aEl~A~~~aL~~~~-----~----~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~ 118 (147)
T PRK08719 48 TDNAELELLALIEALEYAR-----D----GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARK 118 (147)
T ss_pred ccHHHHHHHHHHHHHHHcC-----C----CCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCC
Confidence 3799999999999999952 2 13799999999999843 22221 222 34555556565667
Q ss_pred cEEEEEecCCCCCcCChHHHHHHHHhhh
Q psy5610 69 NVRFIWVPSHVGIAGNEEADRLAKEALT 96 (237)
Q Consensus 69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~ 96 (237)
+|+|.|||||+|++||+.||+||+.|+.
T Consensus 119 ~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 119 YVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred cEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 7999999999999999999999999875
No 3
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.72 E-value=1.1e-17 Score=129.43 Aligned_cols=92 Identities=22% Similarity=0.310 Sum_probs=72.7
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC----CC-------hH-HHHHHHHHHHhhcC-
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS----LN-------PI-AGEIRDLILTNKSK- 67 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~----~~-------~~-~~~i~~~~~~l~~~- 67 (237)
++|++||+.|++.||+++ ...+...|.|+|||++++++|+.|.. .+ |+ ..++++.+..+.+.
T Consensus 41 tTNNraEl~A~i~AL~~l-----~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~ 115 (154)
T COG0328 41 TTNNRAELRALIEALEAL-----KELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRH 115 (154)
T ss_pred ccChHHHHHHHHHHHHHH-----HhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhC
Confidence 589999999999999995 44577899999999999999995422 11 11 12344444444444
Q ss_pred CcEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610 68 LNVRFIWVPSHVGIAGNEEADRLAKEALTS 97 (237)
Q Consensus 68 ~~v~~~wvp~H~g~~gNe~ad~~a~~a~~~ 97 (237)
..|.+.|||||.|.++||.||+||+.++..
T Consensus 116 ~~v~~~WVkgH~g~~~NeraD~LA~~~~~~ 145 (154)
T COG0328 116 ELVFWEWVKGHAGHPENERADQLAREAARA 145 (154)
T ss_pred CeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence 489999999999999999999999999877
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.71 E-value=3.7e-17 Score=127.84 Aligned_cols=90 Identities=19% Similarity=0.319 Sum_probs=69.8
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc---------C--CChHH-HHHHHHHHHhhcCC
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF---------S--LNPIA-GEIRDLILTNKSKL 68 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~---------~--~~~~~-~~i~~~~~~l~~~~ 68 (237)
.+|++||+.|++.||+.+ . ....+.|+|||++++++|..+. . ..++. .++.+.+.++....
T Consensus 41 ~TN~~aEL~Ai~~AL~~~-----~--~~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~ 113 (150)
T PRK00203 41 TTNNRMELMAAIEALEAL-----K--EPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRH 113 (150)
T ss_pred CcHHHHHHHHHHHHHHHc-----C--CCCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccC
Confidence 478999999999999984 2 2357999999999999999632 1 12332 23334444444556
Q ss_pred cEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610 69 NVRFIWVPSHVGIAGNEEADRLAKEALTS 97 (237)
Q Consensus 69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~~ 97 (237)
+|.|.|||||+|++||+.||+||++|...
T Consensus 114 ~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 114 QIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred ceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999877
No 5
>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=99.71 E-value=2e-17 Score=126.05 Aligned_cols=84 Identities=42% Similarity=0.649 Sum_probs=66.7
Q ss_pred hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcc-----cC-C--C-hHHHHHHHHHHHhhcCCcEEE
Q psy5610 2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI-----FS-L--N-PIAGEIRDLILTNKSKLNVRF 72 (237)
Q Consensus 2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~-----~~-~--~-~~~~~i~~~~~~l~~~~~v~~ 72 (237)
|+++||+.||..||+. . ....++|||||+++++.+..+ .. . . ++..+|.+++ .....|.|
T Consensus 39 s~~~aEl~Ai~~AL~~-----~---~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~---~~~~~v~~ 107 (132)
T PF00075_consen 39 SNNRAELQAIIEALKA-----L---EHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL---SRGIKVRF 107 (132)
T ss_dssp CHHHHHHHHHHHHHHT-----H---STSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH---HHSSEEEE
T ss_pred chhhhheehHHHHHHH-----h---hcccccccccHHHHHHHHHHhccccccccccccccchhheeecc---ccceEEee
Confidence 7899999999999995 2 128999999999999988872 21 1 1 4556666555 34677999
Q ss_pred EEecCCCCC-cCChHHHHHHHHhhh
Q psy5610 73 IWVPSHVGI-AGNEEADRLAKEALT 96 (237)
Q Consensus 73 ~wvp~H~g~-~gNe~ad~~a~~a~~ 96 (237)
.|||||+|+ .||+.||+|||+|+.
T Consensus 108 ~~V~~H~~~~~~N~~aD~lAk~a~~ 132 (132)
T PF00075_consen 108 RWVPGHSGVPQGNERADRLAKEAAQ 132 (132)
T ss_dssp EESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred eeccCcCCCchhHHHHHHHHHHhcC
Confidence 999999999 699999999999863
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=99.56 E-value=4.1e-14 Score=105.24 Aligned_cols=90 Identities=32% Similarity=0.420 Sum_probs=70.3
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC-CC-hHHHHHHHHHHHhhcCCcEEEEEecCC
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-LN-PIAGEIRDLILTNKSKLNVRFIWVPSH 78 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~-~~-~~~~~i~~~~~~l~~~~~v~~~wvp~H 78 (237)
.|++.||+.|+..||+++ ...+...+.|++||+.+++.+.++.. .. .....+.++...+.....++|.|||+|
T Consensus 39 ~s~~~aEl~al~~al~~~-----~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h 113 (130)
T cd06222 39 TTNNRAELLALIEALELA-----LELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGH 113 (130)
T ss_pred CcHHHHHHHHHHHHHHHH-----HhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCC
Confidence 478999999999999995 45678999999999999999998653 22 222233232222235667999999999
Q ss_pred CCCcCChHHHHHHHHhh
Q psy5610 79 VGIAGNEEADRLAKEAL 95 (237)
Q Consensus 79 ~g~~gNe~ad~~a~~a~ 95 (237)
+|..+|+.||.||+.+.
T Consensus 114 ~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 114 SGIEGNERADALAKEAA 130 (130)
T ss_pred CCCcchHHHHHHHHhhC
Confidence 99999999999999873
No 7
>KOG3752|consensus
Probab=99.40 E-value=6.5e-13 Score=114.85 Aligned_cols=91 Identities=25% Similarity=0.221 Sum_probs=69.4
Q ss_pred hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC-----------CCh----HH--HHHHHHHHHh
Q psy5610 2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-----------LNP----IA--GEIRDLILTN 64 (237)
Q Consensus 2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~-----------~~~----~~--~~i~~~~~~l 64 (237)
+|++||+.||..||+.+ ...+..+++|.|||+.++++|+.|.. .++ ++ +.....+..|
T Consensus 255 tNnrAEl~Av~~ALkka-----~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l 329 (371)
T KOG3752|consen 255 TNNRAELIAAIEALKKA-----RSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDEL 329 (371)
T ss_pred cccHHHHHHHHHHHHHH-----HhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHH
Confidence 68999999999999995 44466699999999999999997653 122 01 1222223333
Q ss_pred hc---CCcEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610 65 KS---KLNVRFIWVPSHVGIAGNEEADRLAKEALTS 97 (237)
Q Consensus 65 ~~---~~~v~~~wvp~H~g~~gNe~ad~~a~~a~~~ 97 (237)
.+ ..+|.+.|||||.|+.||++||.+|+++...
T Consensus 330 ~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 330 EQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred HhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 33 3679999999999999999999999998654
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.38 E-value=3.2e-12 Score=97.18 Aligned_cols=88 Identities=23% Similarity=0.294 Sum_probs=66.4
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccCCChHHHHHHHHHHHhh-cCCcEEEEEecCCC
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNK-SKLNVRFIWVPSHV 79 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~~~~~~~~i~~~~~~l~-~~~~v~~~wvp~H~ 79 (237)
++|..||+.|++.||+.+ ...+...+.|++||+.+++.+++.....+....+.+.+..+. ....+.|.|||+
T Consensus 39 ~tn~~AE~~All~aL~~a-----~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r-- 111 (128)
T PRK13907 39 MSNHEAEYHALLAALKYC-----TEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS-- 111 (128)
T ss_pred cCCcHHHHHHHHHHHHHH-----HhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc--
Confidence 578999999999999995 445667899999999999999985443332333333333333 344588899996
Q ss_pred CCcCChHHHHHHHHhhhc
Q psy5610 80 GIAGNEEADRLAKEALTS 97 (237)
Q Consensus 80 g~~gNe~ad~~a~~a~~~ 97 (237)
++|+.||.+|+.|...
T Consensus 112 --~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 112 --SQNKVADELARKAILQ 127 (128)
T ss_pred --hhchhHHHHHHHHHhc
Confidence 5999999999998753
No 9
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.31 E-value=2e-11 Score=85.79 Aligned_cols=85 Identities=25% Similarity=0.198 Sum_probs=62.2
Q ss_pred hhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc-CCChHHHHHHHHHHHhhcCCcEEEEEecCCCCC
Q psy5610 3 TSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-SLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGI 81 (237)
Q Consensus 3 ~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~-~~~~~~~~i~~~~~~l~~~~~v~~~wvp~H~g~ 81 (237)
|..||+.|++.||+. +...+.+++.|+|||+.+++.|++.. ..+++...+.+....+.....+.|.||| .
T Consensus 1 ~~~aE~~al~~al~~-----a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r 71 (87)
T PF13456_consen 1 PLEAEALALLEALQL-----AWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----R 71 (87)
T ss_dssp HHHHHHHHHHHHHHH-----HHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------G
T ss_pred CcHHHHHHHHHHHHH-----HHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----h
Confidence 468999999999999 56678899999999999999999863 3333333333333333455679999999 8
Q ss_pred cCChHHHHHHHHhhh
Q psy5610 82 AGNEEADRLAKEALT 96 (237)
Q Consensus 82 ~gNe~ad~~a~~a~~ 96 (237)
++|..||.|||.|..
T Consensus 72 ~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 72 EQNKVADALAKFALS 86 (87)
T ss_dssp GGSHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHHhh
Confidence 999999999998863
No 10
>PRK07708 hypothetical protein; Validated
Probab=99.17 E-value=2.1e-10 Score=94.85 Aligned_cols=88 Identities=20% Similarity=0.170 Sum_probs=68.5
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCc--eEEEEeccHHHHHHHhc-ccCCChHHHHHHHHHHHhhcCC--cEEEEEe
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRA--YLVICSDSLSALQTLQN-IFSLNPIAGEIRDLILTNKSKL--NVRFIWV 75 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~--~~~I~tDs~~~i~~l~~-~~~~~~~~~~i~~~~~~l~~~~--~v~~~wv 75 (237)
++|+.||+.|++.||+.+.. .+.+ .|.|++||+.+++.+++ +...++..+.+.+.+..+.++. .+.|.||
T Consensus 116 ~TNN~AEy~Ali~aL~~A~e-----~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~V 190 (219)
T PRK07708 116 YDNNEAEYAALYYAMQELEE-----LGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPI 190 (219)
T ss_pred ccCcHHHHHHHHHHHHHHHH-----cCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEEC
Confidence 47899999999999999643 3433 48999999999999997 4455665666655555544333 4788999
Q ss_pred cCCCCCcCChHHHHHHHHhhhc
Q psy5610 76 PSHVGIAGNEEADRLAKEALTS 97 (237)
Q Consensus 76 p~H~g~~gNe~ad~~a~~a~~~ 97 (237)
| ...|+.||.||++|...
T Consensus 191 p----R~~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 191 S----RKQNKEADQLATQALEG 208 (219)
T ss_pred C----chhhhHHHHHHHHHHhc
Confidence 8 57899999999999987
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.99 E-value=2.8e-09 Score=95.15 Aligned_cols=88 Identities=19% Similarity=0.292 Sum_probs=67.6
Q ss_pred ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc-CCChHHHHHHHHHHHhh-cCCcEEEEEecCC
Q psy5610 1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-SLNPIAGEIRDLILTNK-SKLNVRFIWVPSH 78 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~-~~~~~~~~i~~~~~~l~-~~~~v~~~wvp~H 78 (237)
.+|+.||+.|++.||+.+ ...+...+.|++||+.+++.+.+.+ .+++-...+.+.+..+. ....++|.|||+
T Consensus 43 ~tnn~AE~~All~gL~~a-----~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r- 116 (372)
T PRK07238 43 ATNNVAEYRGLIAGLEAA-----AELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR- 116 (372)
T ss_pred CCchHHHHHHHHHHHHHH-----HhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc-
Confidence 378899999999999995 4456779999999999999999743 34433333333344443 345699999995
Q ss_pred CCCcCChHHHHHHHHhhhc
Q psy5610 79 VGIAGNEEADRLAKEALTS 97 (237)
Q Consensus 79 ~g~~gNe~ad~~a~~a~~~ 97 (237)
.+|+.||.||+.|...
T Consensus 117 ---~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 117 ---ARNAHADRLANEAMDA 132 (372)
T ss_pred ---hhhhHHHHHHHHHHHh
Confidence 7999999999999766
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.87 E-value=0.0006 Score=47.92 Aligned_cols=32 Identities=22% Similarity=0.514 Sum_probs=26.8
Q ss_pred ccccCCCCCCCCCCCCc-ccccccccccccccH
Q psy5610 171 IHLMKKENPPICVPCGC-VISVKHILTDCQTHS 202 (237)
Q Consensus 171 ~~r~~~~~~p~C~~Cg~-~et~~H~l~~Cp~~~ 202 (237)
+.+.+...++.|..||. .||++|+++.||...
T Consensus 51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred hhccCCccCCccccCCCccccccceeccCcCcc
Confidence 45566778899999996 899999999999753
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=75.49 E-value=1.5 Score=28.00 Aligned_cols=21 Identities=24% Similarity=0.572 Sum_probs=10.0
Q ss_pred CCCCCCCcccccccccccccc
Q psy5610 180 PICVPCGCVISVKHILTDCQT 200 (237)
Q Consensus 180 p~C~~Cg~~et~~H~l~~Cp~ 200 (237)
-.|+.||+..+-.|....||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 479999999899999999996
No 14
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=51.85 E-value=7.2 Score=21.97 Aligned_cols=19 Identities=37% Similarity=0.737 Sum_probs=15.7
Q ss_pred CCCCCCCCcccccccccccccc
Q psy5610 179 PPICVPCGCVISVKHILTDCQT 200 (237)
Q Consensus 179 ~p~C~~Cg~~et~~H~l~~Cp~ 200 (237)
+-.|..|+... |++-.||.
T Consensus 8 ~Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CCEeecCCCCC---ccHhHCCC
Confidence 45788898765 99999997
No 15
>PHA02031 putative DnaG-like primase
Probab=50.55 E-value=9.6 Score=32.48 Aligned_cols=56 Identities=9% Similarity=0.145 Sum_probs=43.3
Q ss_pred CCCCCCCCc--ccccccccccccccHHhhhcCCCCccHHhhcCCCCHHHHHHHHHHhCCC
Q psy5610 179 PPICVPCGC--VISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFLRRTQIK 236 (237)
Q Consensus 179 ~p~C~~Cg~--~et~~H~l~~Cp~~~~~R~~l~~p~~l~~ll~~~~~~~l~~F~~~t~~~ 236 (237)
...|..|++ .+.-.|++. -....++.-+.+|.+..++-+......|.+|+.+-|+.
T Consensus 43 ~ayc~rc~~~~~~~~~~~~~--~~~~~~~~~~~~p~d~~~~~~~~~w~~L~~~L~~kG~~ 100 (266)
T PHA02031 43 VAYCYRCKEGGKVEKTHVRR--VQCADQERFMPWPEDASDISQADAYQSLYGLLLSKGID 100 (266)
T ss_pred HHHHHhhcccchhhHHHHHH--HHHHHHHhhCCCCCChhhhhcCChHHHHHHHHHHCCCC
Confidence 367989986 456677775 45566777788999888877777789999999988764
No 16
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=47.15 E-value=25 Score=33.82 Aligned_cols=35 Identities=26% Similarity=0.411 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhcC-CcEEEEEecCCCCCcCChHHHH
Q psy5610 55 GEIRDLILTNKSK-LNVRFIWVPSHVGIAGNEEADR 89 (237)
Q Consensus 55 ~~i~~~~~~l~~~-~~v~~~wvp~H~g~~gNe~ad~ 89 (237)
...+.++..+.+. .-|-+-|||+|.+..||-++--
T Consensus 214 edfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~f 249 (628)
T COG0296 214 EDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLARF 249 (628)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhhc
Confidence 4566666665544 4699999999999999887643
No 17
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=46.46 E-value=9.2 Score=21.45 Aligned_cols=21 Identities=19% Similarity=0.439 Sum_probs=8.8
Q ss_pred CCCCCcccccccccccccccH
Q psy5610 182 CVPCGCVISVKHILTDCQTHS 202 (237)
Q Consensus 182 C~~Cg~~et~~H~l~~Cp~~~ 202 (237)
|..||...+.++-.+.||.-.
T Consensus 4 C~~CGy~y~~~~~~~~CP~Cg 24 (33)
T cd00350 4 CPVCGYIYDGEEAPWVCPVCG 24 (33)
T ss_pred CCCCCCEECCCcCCCcCcCCC
Confidence 444444333333444444443
No 18
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=45.34 E-value=15 Score=23.98 Aligned_cols=17 Identities=29% Similarity=0.624 Sum_probs=12.1
Q ss_pred ccCCCCCCCCCCCCccc
Q psy5610 173 LMKKENPPICVPCGCVI 189 (237)
Q Consensus 173 r~~~~~~p~C~~Cg~~e 189 (237)
++-..+...||.||.++
T Consensus 12 ~l~~~d~e~CP~Cgs~~ 28 (64)
T COG2093 12 RLTPEDTEICPVCGSTD 28 (64)
T ss_pred ccCCCCCccCCCCCCcc
Confidence 45555667799999754
No 19
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=41.00 E-value=17 Score=28.91 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=15.5
Q ss_pred CCCCCCCCCccccccccccccccc
Q psy5610 178 NPPICVPCGCVISVKHILTDCQTH 201 (237)
Q Consensus 178 ~~p~C~~Cg~~et~~H~l~~Cp~~ 201 (237)
.-|.|+.||.+.+++=- .||+-
T Consensus 155 GRP~CPlCg~PldP~GH--~Cpr~ 176 (177)
T TIGR03847 155 GRPPCPLCGRPIDPDGH--ICPRQ 176 (177)
T ss_pred CCCCCCCCCCCCCCCCc--cCCCC
Confidence 45999999997665522 28763
No 20
>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=38.95 E-value=27 Score=16.74 Aligned_cols=17 Identities=41% Similarity=0.892 Sum_probs=11.8
Q ss_pred CCCCCCcccccccccccccc
Q psy5610 181 ICVPCGCVISVKHILTDCQT 200 (237)
Q Consensus 181 ~C~~Cg~~et~~H~l~~Cp~ 200 (237)
.|..||.. .|+...||.
T Consensus 2 ~C~~C~~~---GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEP---GHIARDCPK 18 (18)
T ss_dssp BCTTTSCS---SSCGCTSSS
T ss_pred cCcCCCCc---CcccccCcc
Confidence 46667753 688888874
No 21
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=38.90 E-value=22 Score=23.03 Aligned_cols=21 Identities=24% Similarity=0.591 Sum_probs=14.8
Q ss_pred cCCCCCCCCCCCCc--ccccccc
Q psy5610 174 MKKENPPICVPCGC--VISVKHI 194 (237)
Q Consensus 174 ~~~~~~p~C~~Cg~--~et~~H~ 194 (237)
|...+.|.|+.|+. ....+++
T Consensus 34 Fs~~~~p~CPlC~s~M~~~~r~L 56 (59)
T PF14169_consen 34 FSFEEEPVCPLCKSPMVSGTRML 56 (59)
T ss_pred cccCCCccCCCcCCccccceeec
Confidence 55678899999996 3455443
No 22
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=38.44 E-value=18 Score=21.68 Aligned_cols=19 Identities=26% Similarity=0.574 Sum_probs=15.3
Q ss_pred CCCCCCCCcccccccccccccc
Q psy5610 179 PPICVPCGCVISVKHILTDCQT 200 (237)
Q Consensus 179 ~p~C~~Cg~~et~~H~l~~Cp~ 200 (237)
...|..||.. .|+.++||.
T Consensus 4 ~~~CqkC~~~---GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQK---GHWTYECPN 22 (42)
T ss_pred CCcCcccCCC---CcchhhCCC
Confidence 4678889854 599999997
No 23
>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=37.30 E-value=14 Score=20.47 Aligned_cols=22 Identities=27% Similarity=0.469 Sum_probs=9.4
Q ss_pred CCCCCCCcc-ccccccccccccc
Q psy5610 180 PICVPCGCV-ISVKHILTDCQTH 201 (237)
Q Consensus 180 p~C~~Cg~~-et~~H~l~~Cp~~ 201 (237)
|.|+.||.. .=.+..++.||..
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~C 25 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPEC 25 (30)
T ss_dssp ---TTT-----EE-SSSEEETTT
T ss_pred CCCCCCCCcceeccCCEEeCCcc
Confidence 678889864 3355666677753
No 24
>PF06696 Strep_SA_rep: Streptococcal surface antigen repeat; InterPro: IPR009578 This family consists of a number of ~25 residue long repeats found commonly in Streptococcal surface antigens although one copy is present in the HPSR2-heavy chain potential motor protein of Giardia lamblia (Giardia intestinalis) (Q24984 from SWISSPROT). This family is often found in conjunction with IPR001899 from INTERPRO.; PDB: 3IOX_A 3IPK_A 2WD6_B 1JMM_A.
Probab=35.21 E-value=33 Score=18.14 Aligned_cols=17 Identities=24% Similarity=0.016 Sum_probs=13.0
Q ss_pred ChhhHHHHHHHHHHHHH
Q psy5610 1 MATSVLELTAILFAIHF 17 (237)
Q Consensus 1 ~~~~~AEl~ai~~al~~ 17 (237)
|+-|++||.++.++...
T Consensus 7 la~YqaeLa~vqk~na~ 23 (25)
T PF06696_consen 7 LAQYQAELARVQKANAD 23 (25)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 45788999998887654
No 25
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=34.95 E-value=14 Score=27.14 Aligned_cols=26 Identities=19% Similarity=0.450 Sum_probs=17.3
Q ss_pred CCCCCCCcccccccccccccccHHhh
Q psy5610 180 PICVPCGCVISVKHILTDCQTHSNIR 205 (237)
Q Consensus 180 p~C~~Cg~~et~~H~l~~Cp~~~~~R 205 (237)
-.|..||....+....+.||......
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCHGER 96 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCCCCC
Confidence 46878887655555555688877543
No 26
>KOG0466|consensus
Probab=34.31 E-value=53 Score=28.94 Aligned_cols=37 Identities=32% Similarity=0.559 Sum_probs=26.7
Q ss_pred cccCCCCCCCCCCCCcc---ccccccc-ccccccHHhhhcC
Q psy5610 172 HLMKKENPPICVPCGCV---ISVKHIL-TDCQTHSNIRAPL 208 (237)
Q Consensus 172 ~r~~~~~~p~C~~Cg~~---et~~H~l-~~Cp~~~~~R~~l 208 (237)
+-.+..|.|.|+.||.. .-++|+- ..||-.+-.=..|
T Consensus 102 ~gS~k~d~~~c~~~g~~~~~klvRHVSfVDCPGHDiLMaTM 142 (466)
T KOG0466|consen 102 FGSSKEDRPPCDRPGCEGKMKLVRHVSFVDCPGHDILMATM 142 (466)
T ss_pred cCCCCCCCCCcccCCCCCceEEEEEEEeccCCchHHHHHHH
Confidence 34567788999999863 4788874 5799887665543
No 27
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=33.95 E-value=23 Score=30.34 Aligned_cols=14 Identities=36% Similarity=0.479 Sum_probs=11.7
Q ss_pred hhhhhccccccccc
Q psy5610 157 SLTRLRIGHTNTTH 170 (237)
Q Consensus 157 ~l~qlrtGH~~~~~ 170 (237)
.|.||||.|-+.++
T Consensus 215 ALsqLrTehrPCtY 228 (311)
T PF15322_consen 215 ALSQLRTEHRPCTY 228 (311)
T ss_pred hhhhhhhccCCccc
Confidence 68999999988873
No 28
>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=32.34 E-value=23 Score=26.09 Aligned_cols=26 Identities=23% Similarity=0.299 Sum_probs=17.6
Q ss_pred CCCCCCCcccccccccccccccHHhh
Q psy5610 180 PICVPCGCVISVKHILTDCQTHSNIR 205 (237)
Q Consensus 180 p~C~~Cg~~et~~H~l~~Cp~~~~~R 205 (237)
-.|..||...++....+.||......
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 71 CECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred EEcccCCCEEecCCcCccCcCCcCCC
Confidence 46888887655554556798877543
No 29
>KOG4602|consensus
Probab=32.13 E-value=23 Score=29.95 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=19.7
Q ss_pred CCCCCCCCccccccccccccccc
Q psy5610 179 PPICVPCGCVISVKHILTDCQTH 201 (237)
Q Consensus 179 ~p~C~~Cg~~et~~H~l~~Cp~~ 201 (237)
+..|+.||...+-.|.+-.||.-
T Consensus 268 ~YVCPiCGATgDnAHTiKyCPl~ 290 (318)
T KOG4602|consen 268 SYVCPICGATGDNAHTIKYCPLA 290 (318)
T ss_pred hhcCccccccCCcccceeccccc
Confidence 35699999988999999999963
No 30
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.48 E-value=25 Score=26.74 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=6.6
Q ss_pred cccccccccHH
Q psy5610 193 HILTDCQTHSN 203 (237)
Q Consensus 193 H~l~~Cp~~~~ 203 (237)
+..+.||....
T Consensus 105 ~~~~~CP~Cgs 115 (135)
T PRK03824 105 HAFLKCPKCGS 115 (135)
T ss_pred ccCcCCcCCCC
Confidence 45556776653
No 31
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=29.85 E-value=25 Score=22.33 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=15.6
Q ss_pred CCCCCCc--c-----c-ccccccccccccHH
Q psy5610 181 ICVPCGC--V-----I-SVKHILTDCQTHSN 203 (237)
Q Consensus 181 ~C~~Cg~--~-----e-t~~H~l~~Cp~~~~ 203 (237)
.||.||. + + -...|.+.||....
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCc
Confidence 5889994 1 3 34567788998753
No 32
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=29.80 E-value=33 Score=21.78 Aligned_cols=22 Identities=23% Similarity=0.366 Sum_probs=15.2
Q ss_pred CCCCCCc----ccccccccccccccH
Q psy5610 181 ICVPCGC----VISVKHILTDCQTHS 202 (237)
Q Consensus 181 ~C~~Cg~----~et~~H~l~~Cp~~~ 202 (237)
.|+.||. +++...-+..||...
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CG 29 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECG 29 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCC
Confidence 6889996 245556677898544
No 33
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=28.60 E-value=65 Score=26.63 Aligned_cols=90 Identities=9% Similarity=0.079 Sum_probs=55.8
Q ss_pred hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEE----eccHHHHHHHhcccC-CChHHHHHHHHHHHhhcCCcEEEEEec
Q psy5610 2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVIC----SDSLSALQTLQNIFS-LNPIAGEIRDLILTNKSKLNVRFIWVP 76 (237)
Q Consensus 2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~----tDs~~~i~~l~~~~~-~~~~~~~i~~~~~~l~~~~~v~~~wvp 76 (237)
+|-.+|.+|++.+|+.++ ...+.+.+++| .||++...-+.+-.. ...+... .-+.++-......+.|+-
T Consensus 107 ~n~s~d~la~ly~~~~~~----~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~~--~e~~~~~~~v~h~~k~i~ 180 (225)
T COG3341 107 SNDSGDVLAKLYGLRYEV----PLDNRKSVINYLTPGNDSWAYFKYVKDKCETKVNLLKD--REFFSIGKGVFHDEKDIN 180 (225)
T ss_pred cCchHHHHHHhccccccc----cccCccceeeccCCcchhHHHHHHHhhhhhhHHHHHHh--HHhhhccchhhhhhhhcc
Confidence 467799999999999963 33355566668 799998877765321 1111110 111110011235678899
Q ss_pred CCCCCcCChHHHHHHHHhhhc
Q psy5610 77 SHVGIAGNEEADRLAKEALTS 97 (237)
Q Consensus 77 ~H~g~~gNe~ad~~a~~a~~~ 97 (237)
-|.....+..++..+.-....
T Consensus 181 ~~~~~~~~~~~~s~~~~~~k~ 201 (225)
T COG3341 181 IHIWIFESKKGNSHVYNTSKK 201 (225)
T ss_pred cccccchhhhhhhhhhchhhh
Confidence 998888888888777655554
No 34
>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=26.85 E-value=27 Score=18.87 Aligned_cols=20 Identities=25% Similarity=0.569 Sum_probs=8.0
Q ss_pred CCCCCCc--ccccccccccccc
Q psy5610 181 ICVPCGC--VISVKHILTDCQT 200 (237)
Q Consensus 181 ~C~~Cg~--~et~~H~l~~Cp~ 200 (237)
.|+.||. ....+=+.+.|+.
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 4889996 2344444555654
No 35
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=26.61 E-value=30 Score=22.75 Aligned_cols=24 Identities=29% Similarity=0.706 Sum_probs=14.9
Q ss_pred CCCCCCCc-cccccc----ccccccccHH
Q psy5610 180 PICVPCGC-VISVKH----ILTDCQTHSN 203 (237)
Q Consensus 180 p~C~~Cg~-~et~~H----~l~~Cp~~~~ 203 (237)
.-||+||. ..+++| +.+.|....+
T Consensus 7 KPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 7 KPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred cCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 45999996 444444 4567776543
No 36
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.67 E-value=35 Score=25.11 Aligned_cols=26 Identities=12% Similarity=0.252 Sum_probs=16.2
Q ss_pred CCCCCCCccc-ccccccccccccHHhh
Q psy5610 180 PICVPCGCVI-SVKHILTDCQTHSNIR 205 (237)
Q Consensus 180 p~C~~Cg~~e-t~~H~l~~Cp~~~~~R 205 (237)
-.|..||... ...+..+.||......
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCCCC
Confidence 4687888743 3345556788876443
No 37
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=25.53 E-value=35 Score=19.28 Aligned_cols=10 Identities=40% Similarity=0.962 Sum_probs=5.7
Q ss_pred CCCCCCCCcc
Q psy5610 179 PPICVPCGCV 188 (237)
Q Consensus 179 ~p~C~~Cg~~ 188 (237)
+..|+.||.+
T Consensus 18 p~~CP~Cg~~ 27 (34)
T cd00729 18 PEKCPICGAP 27 (34)
T ss_pred CCcCcCCCCc
Confidence 3466666653
No 38
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.99 E-value=35 Score=21.48 Aligned_cols=8 Identities=38% Similarity=0.750 Sum_probs=6.5
Q ss_pred CCCCCCcc
Q psy5610 181 ICVPCGCV 188 (237)
Q Consensus 181 ~C~~Cg~~ 188 (237)
.||+||+.
T Consensus 2 ~CPyCge~ 9 (52)
T PF14255_consen 2 QCPYCGEP 9 (52)
T ss_pred CCCCCCCe
Confidence 59999973
No 39
>PF13395 HNH_4: HNH endonuclease
Probab=24.87 E-value=34 Score=21.41 Aligned_cols=14 Identities=36% Similarity=0.809 Sum_probs=9.8
Q ss_pred CCCCCcc---c-------cccccc
Q psy5610 182 CVPCGCV---I-------SVKHIL 195 (237)
Q Consensus 182 C~~Cg~~---e-------t~~H~l 195 (237)
|.+||.. + +++|++
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHii 24 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHII 24 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEe
Confidence 7788862 2 668887
No 40
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.68 E-value=34 Score=27.73 Aligned_cols=27 Identities=19% Similarity=0.391 Sum_probs=17.4
Q ss_pred CCCCCCCCcccc--------cccccccccccHHhh
Q psy5610 179 PPICVPCGCVIS--------VKHILTDCQTHSNIR 205 (237)
Q Consensus 179 ~p~C~~Cg~~et--------~~H~l~~Cp~~~~~R 205 (237)
.-.|+.||..+. -.|.+..|+....-.
T Consensus 6 y~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 6 YIECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 356888883333 466778888766554
No 41
>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=24.42 E-value=42 Score=21.86 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=14.1
Q ss_pred CCCCCCCCcc--ccccccccccccc
Q psy5610 179 PPICVPCGCV--ISVKHILTDCQTH 201 (237)
Q Consensus 179 ~p~C~~Cg~~--et~~H~l~~Cp~~ 201 (237)
+-.|+.||.. .+...-.+.||..
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~C 52 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNC 52 (69)
T ss_pred ccCccCcccccccccccceEEcCCC
Confidence 4568888862 3345556678753
No 42
>KOG1123|consensus
Probab=24.15 E-value=92 Score=29.47 Aligned_cols=31 Identities=23% Similarity=0.277 Sum_probs=24.3
Q ss_pred HHHHHhHHhhhhcCCCceEEEEeccHHHHHHHh
Q psy5610 13 FAIHFSISAHLNNVNRAYLVICSDSLSALQTLQ 45 (237)
Q Consensus 13 ~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~ 45 (237)
.|.++++.+ ....+.+|++|+||-.|++...
T Consensus 530 raCqfLI~~--HE~RgDKiIVFsDnvfALk~YA 560 (776)
T KOG1123|consen 530 RACQFLIKF--HERRGDKIIVFSDNVFALKEYA 560 (776)
T ss_pred HHHHHHHHH--HHhcCCeEEEEeccHHHHHHHH
Confidence 577888774 4457889999999999997644
No 43
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.83 E-value=46 Score=17.40 Aligned_cols=7 Identities=43% Similarity=1.350 Sum_probs=3.9
Q ss_pred CCCCCCc
Q psy5610 181 ICVPCGC 187 (237)
Q Consensus 181 ~C~~Cg~ 187 (237)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555665
No 44
>KOG1812|consensus
Probab=23.37 E-value=2.4e+02 Score=25.48 Aligned_cols=38 Identities=16% Similarity=0.103 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHh
Q psy5610 3 TSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQ 45 (237)
Q Consensus 3 ~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~ 45 (237)
.-.||++|+..+|..+ ...+...+.+++|+.-..+.+.
T Consensus 49 ~~~ae~~al~~~l~ea-----~~~~~~~~~~~~d~~~~~~~v~ 86 (384)
T KOG1812|consen 49 PLEAELMALKRGLTEA-----LELGLNHIVIYCDDELIYESVA 86 (384)
T ss_pred hhhHHHHHHhhccHHH-----HhhccccceEecccHHHHHHHh
Confidence 3468888998888884 4557889999999665555443
No 45
>PRK00420 hypothetical protein; Validated
Probab=23.27 E-value=53 Score=24.22 Aligned_cols=27 Identities=19% Similarity=0.294 Sum_probs=15.5
Q ss_pred hccccccc-c-cccccCCCCCCCCCCCCcc
Q psy5610 161 LRIGHTNT-T-HIHLMKKENPPICVPCGCV 188 (237)
Q Consensus 161 lrtGH~~~-~-~~~r~~~~~~p~C~~Cg~~ 188 (237)
++.+|.+. + .++++ +...-.|+.||..
T Consensus 21 ml~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 21 MLSKHCPVCGLPLFEL-KDGEVVCPVHGKV 49 (112)
T ss_pred HccCCCCCCCCcceec-CCCceECCCCCCe
Confidence 35567664 3 23333 4456678888874
No 46
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=22.80 E-value=41 Score=26.26 Aligned_cols=9 Identities=33% Similarity=0.545 Sum_probs=6.9
Q ss_pred CCCCCCccc
Q psy5610 181 ICVPCGCVI 189 (237)
Q Consensus 181 ~C~~Cg~~e 189 (237)
.||+||.++
T Consensus 2 ~cp~c~~~~ 10 (154)
T PRK00464 2 RCPFCGHPD 10 (154)
T ss_pred cCCCCCCCC
Confidence 699999643
No 47
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=22.51 E-value=61 Score=21.37 Aligned_cols=11 Identities=18% Similarity=0.169 Sum_probs=8.6
Q ss_pred CCCCCCCCCcc
Q psy5610 178 NPPICVPCGCV 188 (237)
Q Consensus 178 ~~p~C~~Cg~~ 188 (237)
+...|+.||..
T Consensus 16 ~~~~Cp~Cgs~ 26 (64)
T PRK06393 16 PEKTCPVHGDE 26 (64)
T ss_pred CCCcCCCCCCC
Confidence 56699999974
No 48
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.84 E-value=2.9e+02 Score=23.81 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=16.5
Q ss_pred cCChHHHHHHHHhhhcCCCCCCCCCh
Q psy5610 82 AGNEEADRLAKEALTSTHPTINKIPI 107 (237)
Q Consensus 82 ~gNe~ad~~a~~a~~~~~~~~~~~~~ 107 (237)
-||-.||++-=.+--.+......++.
T Consensus 171 vGNIYa~E~Lf~agI~P~~~a~~l~~ 196 (273)
T COG0266 171 VGNIYADEILFRAGIHPARPAGDLSL 196 (273)
T ss_pred ccHHHHHHHHHHcCCCcccCccccCH
Confidence 49999999876666554433333443
No 49
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=21.82 E-value=45 Score=19.42 Aligned_cols=27 Identities=19% Similarity=0.358 Sum_probs=16.1
Q ss_pred CCCCCCcc----cccccccccccccHHhhhc
Q psy5610 181 ICVPCGCV----ISVKHILTDCQTHSNIRAP 207 (237)
Q Consensus 181 ~C~~Cg~~----et~~H~l~~Cp~~~~~R~~ 207 (237)
.|+.||.. .+..=.++.|..|-.-+..
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYPECKYT 33 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCCCcCCe
Confidence 58888852 2333366788887544433
No 50
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.70 E-value=34 Score=21.28 Aligned_cols=18 Identities=22% Similarity=0.377 Sum_probs=11.1
Q ss_pred CCCCCCCCcccccccccc
Q psy5610 179 PPICVPCGCVISVKHILT 196 (237)
Q Consensus 179 ~p~C~~Cg~~et~~H~l~ 196 (237)
+-.||+||..-+...++-
T Consensus 2 ~f~CP~C~~~~~~~~L~~ 19 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVE 19 (54)
T ss_pred CcCCCCCCCccCHHHHHH
Confidence 457999997444444443
No 51
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.44 E-value=51 Score=26.17 Aligned_cols=18 Identities=33% Similarity=0.660 Sum_probs=12.7
Q ss_pred CCCCCCCCCCccccc-ccc
Q psy5610 177 ENPPICVPCGCVISV-KHI 194 (237)
Q Consensus 177 ~~~p~C~~Cg~~et~-~H~ 194 (237)
..-|.|+.||.+.++ -|+
T Consensus 152 AGRP~CPlCg~PlDP~GH~ 170 (171)
T PF11290_consen 152 AGRPPCPLCGEPLDPEGHI 170 (171)
T ss_pred CCCCCCCCCCCCCCCCCCc
Confidence 345999999997543 443
No 52
>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=21.42 E-value=73 Score=23.30 Aligned_cols=20 Identities=25% Similarity=0.609 Sum_probs=13.6
Q ss_pred cccCCCCCCCCCCCCcccccc
Q psy5610 172 HLMKKENPPICVPCGCVISVK 192 (237)
Q Consensus 172 ~r~~~~~~p~C~~Cg~~et~~ 192 (237)
|=+|+ ++-.||.||....++
T Consensus 20 YDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 20 YDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCC-CCccCCCCCCccCcc
Confidence 34566 556699999865555
No 53
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=21.10 E-value=30 Score=25.35 Aligned_cols=25 Identities=16% Similarity=0.344 Sum_probs=15.4
Q ss_pred CCCCCCCcccccccccccccccHHh
Q psy5610 180 PICVPCGCVISVKHILTDCQTHSNI 204 (237)
Q Consensus 180 p~C~~Cg~~et~~H~l~~Cp~~~~~ 204 (237)
-.|..||..-+++...+.||.....
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSSSS
T ss_pred EECCCCCCEEecCCCCCCCcCCcCC
Confidence 4687888765555555778877644
No 54
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.80 E-value=53 Score=24.27 Aligned_cols=19 Identities=26% Similarity=0.758 Sum_probs=12.3
Q ss_pred CCCCCcccccccccccccccH
Q psy5610 182 CVPCGCVISVKHILTDCQTHS 202 (237)
Q Consensus 182 C~~Cg~~et~~H~l~~Cp~~~ 202 (237)
||.||.+-.+..+ .||...
T Consensus 1 CPvCg~~l~vt~l--~C~~C~ 19 (113)
T PF09862_consen 1 CPVCGGELVVTRL--KCPSCG 19 (113)
T ss_pred CCCCCCceEEEEE--EcCCCC
Confidence 7888876655554 477654
No 55
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.52 E-value=88 Score=17.48 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=8.9
Q ss_pred cCCCCCCCCCCCCc
Q psy5610 174 MKKENPPICVPCGC 187 (237)
Q Consensus 174 ~~~~~~p~C~~Cg~ 187 (237)
++..+.-.|+.||.
T Consensus 12 ~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 12 LKPGDPIRCPECGH 25 (32)
T ss_dssp BSTSSTSSBSSSS-
T ss_pred cCCCCcEECCcCCC
Confidence 45556667888885
No 56
>KOG3456|consensus
Probab=20.02 E-value=62 Score=23.60 Aligned_cols=27 Identities=30% Similarity=0.420 Sum_probs=18.4
Q ss_pred cccccccccc-c--ccCCCCCCCCCCCCcc
Q psy5610 162 RIGHTNTTHI-H--LMKKENPPICVPCGCV 188 (237)
Q Consensus 162 rtGH~~~~~~-~--r~~~~~~p~C~~Cg~~ 188 (237)
--||+.++|- - -+.+.....|-+||..
T Consensus 84 dGg~~aLGHPkvyInLDk~~~~~CgYCGlr 113 (120)
T KOG3456|consen 84 DGGTPALGHPKVYINLDKPGPHICGYCGLR 113 (120)
T ss_pred cCCCCCCCCCeEEEEcCCCCCcccccchhh
Confidence 4577778874 2 3455567889999963
Done!