Query psy15839
Match_columns 293
No_of_seqs 260 out of 1526
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 22:39:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15839.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15839hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.9 1.5E-23 3.3E-28 175.0 14.9 123 57-181 5-141 (161)
2 COG0328 RnhA Ribonuclease HI [ 99.9 3.3E-23 7.2E-28 170.4 13.6 126 57-183 3-146 (154)
3 PRK08719 ribonuclease H; Revie 99.9 1.1E-22 2.4E-27 168.1 14.0 120 57-181 4-146 (147)
4 PF00075 RNase_H: RNase H; In 99.9 8E-23 1.7E-27 165.0 11.1 116 57-180 3-131 (132)
5 PRK00203 rnhA ribonuclease H; 99.9 3.4E-22 7.4E-27 165.9 13.9 125 57-184 3-144 (150)
6 cd06222 RnaseH RNase H (RNase 99.8 2E-18 4.3E-23 135.7 14.1 121 60-180 2-130 (130)
7 KOG3752|consensus 99.8 1.6E-18 3.5E-23 158.8 12.1 132 49-180 202-363 (371)
8 PRK13907 rnhA ribonuclease H; 99.8 1.2E-17 2.5E-22 134.8 13.0 120 58-181 2-126 (128)
9 PRK07708 hypothetical protein; 99.6 6.2E-15 1.3E-19 129.3 15.2 124 55-182 71-208 (219)
10 PRK07238 bifunctional RNase H/ 99.6 3.9E-14 8.5E-19 134.1 14.7 120 57-180 2-130 (372)
11 PF13456 RVT_3: Reverse transc 99.3 6.8E-12 1.5E-16 93.4 9.1 85 92-180 1-85 (87)
12 PF13966 zf-RVT: zinc-binding 75.4 1.9 4.1E-05 31.8 1.7 38 244-281 38-82 (86)
13 PF05380 Peptidase_A17: Pao re 74.8 11 0.00023 31.2 6.4 60 48-109 68-143 (159)
14 PRK10933 trehalose-6-phosphate 70.0 9.3 0.0002 38.4 5.7 98 48-166 4-108 (551)
15 COG0296 GlgB 1,4-alpha-glucan 67.4 6.8 0.00015 39.8 4.1 35 138-172 213-247 (628)
16 PF00336 DNA_pol_viral_C: DNA 67.2 7.2 0.00016 33.9 3.6 88 59-163 96-183 (245)
17 PF00098 zf-CCHC: Zinc knuckle 58.2 9.4 0.0002 19.7 1.7 17 264-280 2-18 (18)
18 cd01285 nucleoside_deaminase N 56.2 56 0.0012 25.0 6.7 54 69-122 17-75 (109)
19 COG3341 Predicted double-stran 53.9 42 0.00092 29.4 6.1 86 91-181 107-200 (225)
20 COG0295 Cdd Cytidine deaminase 50.8 36 0.00078 27.6 4.9 53 68-121 25-81 (134)
21 KOG1812|consensus 50.8 45 0.00098 31.9 6.4 44 90-133 47-90 (384)
22 PRK10860 tRNA-specific adenosi 50.3 61 0.0013 27.4 6.4 51 70-120 34-88 (172)
23 cd01284 Riboflavin_deaminase-r 47.6 74 0.0016 24.9 6.2 48 68-119 18-66 (115)
24 COG4566 TtrR Response regulato 45.8 1.1E+02 0.0024 26.5 7.2 68 99-169 15-91 (202)
25 TIGR02403 trehalose_treC alpha 41.5 55 0.0012 32.8 5.6 72 95-166 24-102 (543)
26 cd01286 deoxycytidylate_deamin 39.4 1.2E+02 0.0025 24.2 6.3 26 92-119 68-93 (131)
27 COG0590 CumB Cytosine/adenosin 38.4 1E+02 0.0022 25.4 5.9 51 70-120 29-84 (152)
28 PRK08298 cytidine deaminase; V 33.7 75 0.0016 25.7 4.3 51 70-121 24-78 (136)
29 TIGR01354 cyt_deam_tetra cytid 32.8 1.1E+02 0.0025 24.2 5.2 52 69-121 21-76 (127)
30 PF15322 PMSI1: Protein missin 31.8 27 0.00058 31.8 1.5 16 238-253 213-228 (311)
31 PF14255 Cys_rich_CPXG: Cystei 31.8 21 0.00045 24.0 0.6 17 264-280 2-18 (52)
32 PRK06848 hypothetical protein; 29.0 1.3E+02 0.0028 24.4 5.0 53 68-121 26-82 (139)
33 smart00642 Aamy Alpha-amylase 28.7 1.5E+02 0.0033 24.5 5.6 29 138-166 69-97 (166)
34 KOG1817|consensus 27.8 1.6E+02 0.0034 28.8 5.9 46 61-108 454-502 (533)
35 PF00383 dCMP_cyt_deam_1: Cyti 27.0 2.3E+02 0.005 20.8 5.9 51 68-119 23-78 (102)
36 COG0117 RibD Pyrimidine deamin 27.0 1.2E+02 0.0025 25.0 4.3 40 68-107 27-66 (146)
37 PF01396 zf-C4_Topoisom: Topoi 24.8 39 0.00084 21.1 0.9 22 264-285 3-31 (39)
38 PRK12411 cytidine deaminase; P 23.2 1.9E+02 0.0041 23.2 4.9 52 69-121 24-79 (132)
39 COG2093 DNA-directed RNA polym 21.9 59 0.0013 22.7 1.4 20 255-274 11-30 (64)
40 PF08274 PhnA_Zn_Ribbon: PhnA 21.8 32 0.00069 20.3 0.1 18 263-280 3-24 (30)
41 PF09345 DUF1987: Domain of un 21.6 1.4E+02 0.003 22.8 3.6 25 137-161 61-85 (99)
42 PRK12568 glycogen branching en 20.7 1.1E+02 0.0024 31.9 3.8 32 138-169 318-349 (730)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.91 E-value=1.5e-23 Score=174.97 Aligned_cols=123 Identities=24% Similarity=0.215 Sum_probs=93.7
Q ss_pred eEEEEEecCCC-CCC-eeEEEEECCeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC---
Q psy15839 57 VVDLSLYGSKT-IQN-TSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK--- 131 (293)
Q Consensus 57 ~~~iytDGS~~-~~~-~G~~v~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~--- 131 (293)
.+.||||||+. +++ .|+|++..+.....+....+||+.|||.||+.||+.+.. ....|.|+|||++|+++|++|
T Consensus 5 ~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~ 83 (161)
T PRK06548 5 EIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYS 83 (161)
T ss_pred EEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHH
Confidence 57899999988 444 677766443222223334679999999999999987653 345799999999999999952
Q ss_pred -----C-C-Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839 132 -----N-T-SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG 181 (293)
Q Consensus 132 -----~-~-~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~ 181 (293)
+ + ++ + ..+++++.+..+... ..|+|.|||||+|++|||.||+||++|+.
T Consensus 84 Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~ 141 (161)
T PRK06548 84 WKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAAN 141 (161)
T ss_pred HHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 2 2 23 3 357777777776654 47999999999999999999999999874
No 2
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.90 E-value=3.3e-23 Score=170.38 Aligned_cols=126 Identities=20% Similarity=0.177 Sum_probs=100.8
Q ss_pred eEEEEEecCCC-CCC-eeEEEE--ECCeeEEe--ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhc
Q psy15839 57 VVDLSLYGSKT-IQN-TSCAVY--AGGSAKSY--ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN 130 (293)
Q Consensus 57 ~~~iytDGS~~-~~~-~G~~v~--~~~~~~~~--~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~ 130 (293)
.+.||||||+. |+| .|+|++ .++..+.+ +.. .+||++||+.|++.||+.+.+.+...|.|+|||++|+++|..
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~ 81 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR 81 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence 57899999998 555 455644 34433323 333 789999999999999999998888999999999999999995
Q ss_pred C---CCC--------hh-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCc
Q psy15839 131 K---NTS--------IP-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 183 (293)
Q Consensus 131 ~---~~~--------~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~ 183 (293)
+ ++. .| ...++++.+.++......|.+.|||||+|.++||.||+||++|+..+
T Consensus 82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 4 111 13 35677888888877788999999999999999999999999997654
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.89 E-value=1.1e-22 Score=168.05 Aligned_cols=120 Identities=21% Similarity=0.238 Sum_probs=90.8
Q ss_pred eEEEEEecCCC-CCC----eeEEEE--ECCe----eEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHH
Q psy15839 57 VVDLSLYGSKT-IQN----TSCAVY--AGGS----AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSAL 125 (293)
Q Consensus 57 ~~~iytDGS~~-~~~----~G~~v~--~~~~----~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai 125 (293)
.+.||||||+. +++ .|+|++ .++. ....++....|+++|||.|++.||+.+.+. ..|+|||++|+
T Consensus 4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi 79 (147)
T PRK08719 4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCV 79 (147)
T ss_pred eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHH
Confidence 46799999997 332 477754 3321 223345556799999999999999999753 37999999999
Q ss_pred HHhh--------cCCC-C-h-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839 126 TSIA--------NKNT-S-I-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG 181 (293)
Q Consensus 126 ~~l~--------~~~~-~-~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~ 181 (293)
++|+ +.+. + + + ...++++.+..+.. ...|+|.|||||+|++|||.||+||++|+.
T Consensus 80 ~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 80 RGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9994 3443 3 2 2 24567777777665 567999999999999999999999999863
No 4
>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=99.89 E-value=8e-23 Score=165.00 Aligned_cols=116 Identities=28% Similarity=0.348 Sum_probs=86.9
Q ss_pred eEEEEEecCCC-C-CCeeEEE-EECCeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhc---
Q psy15839 57 VVDLSLYGSKT-I-QNTSCAV-YAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN--- 130 (293)
Q Consensus 57 ~~~iytDGS~~-~-~~~G~~v-~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~--- 130 (293)
.+.||||||+. + +..|+|+ +..+......++ ..+++.|||.||..||+.+ . ...+.|+|||+++++.|..
T Consensus 3 ~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~~ 78 (132)
T PF00075_consen 3 AIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWLH 78 (132)
T ss_dssp SEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHHH
T ss_pred cEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhcc
Confidence 46799999977 3 3345554 454543344455 8899999999999999944 3 3899999999999998887
Q ss_pred --CCC-C--h-hHHHHHHHHHHHHhhCCceEEEEEeCCCCCC-hhhHHHHHHHhhcc
Q psy15839 131 --KNT-S--I-PLIAHILNTWHTLKSCGKKVAFLWCPSHTGI-SGNEIVDRATRQLD 180 (293)
Q Consensus 131 --~~~-~--~-~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~a~ 180 (293)
.+. . + ++..+|++.+ ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus 79 ~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 79 GNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred ccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 332 1 2 3555555443 45899999999999999 69999999999985
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.88 E-value=3.4e-22 Score=165.91 Aligned_cols=125 Identities=16% Similarity=0.173 Sum_probs=91.7
Q ss_pred eEEEEEecCCC-CCC-eeEEEE--ECCeeEEe-ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC
Q psy15839 57 VVDLSLYGSKT-IQN-TSCAVY--AGGSAKSY-ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK 131 (293)
Q Consensus 57 ~~~iytDGS~~-~~~-~G~~v~--~~~~~~~~-~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~ 131 (293)
.+.||||||+. +++ .|+|++ .++....+ +.....|++.|||.|++.||+.+.+ ...+.|+|||++++++|..+
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w 80 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW 80 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence 47899999998 444 566654 33433222 2334678999999999999998865 35799999999999999963
Q ss_pred --------CC--Ch-hH-HHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCcc
Q psy15839 132 --------NT--SI-PL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEF 184 (293)
Q Consensus 132 --------~~--~~-~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~ 184 (293)
+. .+ ++ ..++++.+..+.. ...|.|.|||||+|++||+.||+|||+|...+.
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 22 22 22 2345555555443 378999999999999999999999999976543
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=99.79 E-value=2e-18 Score=135.72 Aligned_cols=121 Identities=23% Similarity=0.231 Sum_probs=92.8
Q ss_pred EEEecCCCC--CCeeEEEEE--CCeeEEe---ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCC
Q psy15839 60 LSLYGSKTI--QNTSCAVYA--GGSAKSY---ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN 132 (293)
Q Consensus 60 iytDGS~~~--~~~G~~v~~--~~~~~~~---~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~ 132 (293)
+|||||... ++.|+|++. .+....+ ......+++.||+.|++.||+.+.......+.|++||+.++..+.+..
T Consensus 2 ~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~ 81 (130)
T cd06222 2 IYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWY 81 (130)
T ss_pred EEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccc
Confidence 799999984 467887653 2222222 222577899999999999999998878899999999999999999876
Q ss_pred C-ChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhcc
Q psy15839 133 T-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD 180 (293)
Q Consensus 133 ~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~ 180 (293)
. ..+....++..+..+...+..++|.|||+|+|+.+|+.||.|||+|.
T Consensus 82 ~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 82 EGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred cCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 4 22223333334444445788999999999999999999999999873
No 7
>KOG3752|consensus
Probab=99.78 E-value=1.6e-18 Score=158.76 Aligned_cols=132 Identities=22% Similarity=0.180 Sum_probs=99.9
Q ss_pred CCCCCCC--CeEEEEEecCCC-CC----CeeEEEEECCe---eEEeecC-CCCchhHHHHHHHHHHHHHhhcCCCccEEE
Q psy15839 49 PPWYSDF--PVVDLSLYGSKT-IQ----NTSCAVYAGGS---AKSYILN-NINSIFTAELLALVFCLDSVKNRPDVNTLI 117 (293)
Q Consensus 49 ~~W~~~~--~~~~iytDGS~~-~~----~~G~~v~~~~~---~~~~~~~-~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I 117 (293)
..|..+. ....||||||+. +| .+|+||+.++. .+...+. ..+++|.|||.||..||+.+.+....++.|
T Consensus 202 k~~~d~e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I 281 (371)
T KOG3752|consen 202 KLENDREEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVI 281 (371)
T ss_pred hcccccccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEE
Confidence 3444443 347799999988 33 48999987653 4566666 789999999999999999999888889999
Q ss_pred EeCcHHHHHHhhcCC--------C--Ch-h-H-----HHHHHHHHHHHhh--CCceEEEEEeCCCCCChhhHHHHHHHhh
Q psy15839 118 VCDSMSALTSIANKN--------T--SI-P-L-----IAHILNTWHTLKS--CGKKVAFLWCPSHTGISGNEIVDRATRQ 178 (293)
Q Consensus 118 ~tDS~~ai~~l~~~~--------~--~~-~-~-----~~~i~~~~~~l~~--~~~~v~~~WVpgH~gi~gNe~AD~lAk~ 178 (293)
.|||++++++|+.|- . .+ + + .......+..|.+ .+..|++.|||||.|+.|||+||.||++
T Consensus 282 ~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARk 361 (371)
T KOG3752|consen 282 RTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARK 361 (371)
T ss_pred EechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhh
Confidence 999999999999762 1 11 1 0 1122223333333 3689999999999999999999999999
Q ss_pred cc
Q psy15839 179 LD 180 (293)
Q Consensus 179 a~ 180 (293)
++
T Consensus 362 gs 363 (371)
T KOG3752|consen 362 GS 363 (371)
T ss_pred hh
Confidence 85
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.76 E-value=1.2e-17 Score=134.84 Aligned_cols=120 Identities=17% Similarity=0.120 Sum_probs=91.4
Q ss_pred EEEEEecCCC-C-CCeeEEEEEC--CeeEEee-cCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCC
Q psy15839 58 VDLSLYGSKT-I-QNTSCAVYAG--GSAKSYI-LNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN 132 (293)
Q Consensus 58 ~~iytDGS~~-~-~~~G~~v~~~--~~~~~~~-~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~ 132 (293)
+.||||||+. + +..|+|++.. +....++ .....+++.||+.|++.||+.+.+.+...+.|+|||+.+++.+++.+
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~ 81 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY 81 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence 5799999988 3 4477776532 2222222 23456889999999999999999988889999999999999999976
Q ss_pred CChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839 133 TSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG 181 (293)
Q Consensus 133 ~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~ 181 (293)
...+-...+++.+..+......+.|.|||. ++|+.||.||++|..
T Consensus 82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 533333444445555566778888999996 599999999999864
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.64 E-value=6.2e-15 Score=129.31 Aligned_cols=124 Identities=12% Similarity=0.010 Sum_probs=89.5
Q ss_pred CCeEEEEEecCCC--CCCeeEEEE--ECCe--eEE----eecCCCCchhHHHHHHHHHHHHHhhcCCCcc--EEEEeCcH
Q psy15839 55 FPVVDLSLYGSKT--IQNTSCAVY--AGGS--AKS----YILNNINSIFTAELLALVFCLDSVKNRPDVN--TLIVCDSM 122 (293)
Q Consensus 55 ~~~~~iytDGS~~--~~~~G~~v~--~~~~--~~~----~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~--i~I~tDS~ 122 (293)
++.+.+|+|||+. .+..|+|++ .++. ... ..+....+++.||+.|++.||+.+.+.+.+. |.|++||+
T Consensus 71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSq 150 (219)
T PRK07708 71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQ 150 (219)
T ss_pred CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccH
Confidence 4467899999986 345777753 3322 211 2355557899999999999999999887654 89999999
Q ss_pred HHHHHhhcCCC-ChhHHHHHHHHHHHHh-hCCceEEEEEeCCCCCChhhHHHHHHHhhccCC
Q psy15839 123 SALTSIANKNT-SIPLIAHILNTWHTLK-SCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA 182 (293)
Q Consensus 123 ~ai~~l~~~~~-~~~~~~~i~~~~~~l~-~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~ 182 (293)
.+++.+.+.+. .++....+++.+..+. .....+.|.||| .+.|+.||+||++|...
T Consensus 151 lVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 151 VVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEG 208 (219)
T ss_pred HHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence 99999999875 4443333444443333 334457889998 57899999999999864
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.57 E-value=3.9e-14 Score=134.09 Aligned_cols=120 Identities=14% Similarity=0.113 Sum_probs=91.6
Q ss_pred eEEEEEecCCC-C-CCeeEEEE--ECC-e-e-EEe-ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHh
Q psy15839 57 VVDLSLYGSKT-I-QNTSCAVY--AGG-S-A-KSY-ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI 128 (293)
Q Consensus 57 ~~~iytDGS~~-~-~~~G~~v~--~~~-~-~-~~~-~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l 128 (293)
.+.||||||+. + +..|+|++ ..+ . . ..+ ..-...+++.||+.|++.||+.+.+.+...|.|++||+.+++.+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i 81 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM 81 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence 46799999988 4 34677754 332 2 1 122 22236778899999999999999998888999999999999999
Q ss_pred hcCCC-ChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhcc
Q psy15839 129 ANKNT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD 180 (293)
Q Consensus 129 ~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~ 180 (293)
.+.+. +++-...+...+..+..+...++|.|||. .+|+.||.||++|.
T Consensus 82 ~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~ 130 (372)
T PRK07238 82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAM 130 (372)
T ss_pred CCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHH
Confidence 98775 44433334444555667778999999995 79999999999985
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.34 E-value=6.8e-12 Score=93.38 Aligned_cols=85 Identities=18% Similarity=0.131 Sum_probs=65.4
Q ss_pred hhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCCChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHH
Q psy15839 92 IFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEI 171 (293)
Q Consensus 92 ~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~ 171 (293)
+..||+.|+..||+.+.+.+..+|.|.|||+.+++.|++..........+...+..+......+.|.||| .++|..
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~ 76 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV 76 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence 4689999999999999999999999999999999999998642112223444445556678999999999 799999
Q ss_pred HHHHHhhcc
Q psy15839 172 VDRATRQLD 180 (293)
Q Consensus 172 AD~lAk~a~ 180 (293)
||.|||.|.
T Consensus 77 A~~LA~~a~ 85 (87)
T PF13456_consen 77 ADALAKFAL 85 (87)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 999999874
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=75.37 E-value=1.9 Score=31.81 Aligned_cols=38 Identities=16% Similarity=-0.032 Sum_probs=25.4
Q ss_pred HhhCcccc--c-cccccCCCCCCCCcccCC-Cccc---cccCCCC
Q psy15839 244 VRIGHTRL--T-HSYLFTRSDPPSCQSSQL-SSQS---SEDKSKS 281 (293)
Q Consensus 244 lRTGH~~l--~-~~~r~~~~~~p~C~~Cg~-~~~~---l~~Cp~~ 281 (293)
-|.-|.++ + -+.+.+...++.|..|+. .|+. +++||.-
T Consensus 38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a 82 (86)
T PF13966_consen 38 WRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFA 82 (86)
T ss_pred eeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCc
Confidence 34445555 2 245667778899999996 4433 9999864
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=74.82 E-value=11 Score=31.23 Aligned_cols=60 Identities=15% Similarity=0.099 Sum_probs=35.8
Q ss_pred CCCCCCCC----CeEEEEEecCCCCCCeeEEEEE---CCe--eEEe-----ecC--CCCchhHHHHHHHHHHHHHhhc
Q psy15839 48 FPPWYSDF----PVVDLSLYGSKTIQNTSCAVYA---GGS--AKSY-----ILN--NINSIFTAELLALVFCLDSVKN 109 (293)
Q Consensus 48 ~~~W~~~~----~~~~iytDGS~~~~~~G~~v~~---~~~--~~~~-----~~~--~~~~~~~AEl~Ai~~AL~~~~~ 109 (293)
+|.+.... ..+-+|+|+|. .+.|+.+|. .+. ...+ +.. ...|+-+-||.|+..|.+++..
T Consensus 68 iPR~i~~~~~~~~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 68 IPRCIPISDYRSVELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred CCcccccccccceeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 66554421 13568999995 345555542 221 1111 111 2458999999999999998853
No 14
>PRK10933 trehalose-6-phosphate hydrolase; Provisional
Probab=70.02 E-value=9.3 Score=38.35 Aligned_cols=98 Identities=12% Similarity=0.130 Sum_probs=62.7
Q ss_pred CCCCCCCCCeEEEEEecCCCCCCeeEEEEECCeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEe-------C
Q psy15839 48 FPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVC-------D 120 (293)
Q Consensus 48 ~~~W~~~~~~~~iytDGS~~~~~~G~~v~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~t-------D 120 (293)
.|.|++.--.+.||+|.-...++-| .+.+.+|...|+++.+.+...|.|-- |
T Consensus 4 ~~~W~~~~v~Yqi~~~~f~d~~~~~---------------------~Gdl~gi~~~ldyl~~lGv~~i~l~P~~~~~~~~ 62 (551)
T PRK10933 4 LPHWWQNGVIYQIYPKSFQDTTGSG---------------------TGDLRGVTQRLDYLQKLGVDAIWLTPFYVSPQVD 62 (551)
T ss_pred cchhhhcCeEEEEEchHhhcCCCCC---------------------CcCHHHHHHhhHHHHhCCCCEEEECCCCCCCCCC
Confidence 4669887777889998754422222 14588999999999988877766522 1
Q ss_pred cHHHHHHhhcCCCChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCC
Q psy15839 121 SMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGI 166 (293)
Q Consensus 121 S~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi 166 (293)
+-+.+.-....-..-.....+.++++.++++|.+|-+-.|+.|++.
T Consensus 63 ~gY~~~d~~~id~~~Gt~~d~~~lv~~~h~~gi~vilD~V~NH~s~ 108 (551)
T PRK10933 63 NGYDVANYTAIDPTYGTLDDFDELVAQAKSRGIRIILDMVFNHTST 108 (551)
T ss_pred CCCCcccCCCcCcccCCHHHHHHHHHHHHHCCCEEEEEECCCCccC
Confidence 1111000000000001345677888889999999999999999875
No 15
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=67.43 E-value=6.8 Score=39.81 Aligned_cols=35 Identities=20% Similarity=0.297 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHH
Q psy15839 138 IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIV 172 (293)
Q Consensus 138 ~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~A 172 (293)
-..+...++..++.|..|-+-|||+|.+..||-++
T Consensus 213 Pedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 213 PEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 35677788888999999999999999999888755
No 16
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=67.25 E-value=7.2 Score=33.89 Aligned_cols=88 Identities=20% Similarity=0.189 Sum_probs=47.3
Q ss_pred EEEEecCCCCCCeeEEEEECCeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCCChhHH
Q psy15839 59 DLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLI 138 (293)
Q Consensus 59 ~iytDGS~~~~~~G~~v~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~~~~~~ 138 (293)
.|++|+.-. |.|+........+....--.++.|||+|...|.-+... ++ |.|||..|+ .+..++-++.
T Consensus 96 ~VfaDATpT----gwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~~----r~-l~tDnt~Vl---srkyts~PW~ 163 (245)
T PF00336_consen 96 QVFADATPT----GWGISITGQRMRGTFSKPLPIHTAELLAACLARLMSGA----RC-LGTDNTVVL---SRKYTSFPWL 163 (245)
T ss_pred ceeccCCCC----cceeeecCceeeeeecccccchHHHHHHHHHHHhccCC----cE-EeecCcEEE---ecccccCcHH
Confidence 477776543 33333322222222222346889999999888776643 34 899998654 3444443422
Q ss_pred HHHHHHHHHHhhCCceEEEEEeCCC
Q psy15839 139 AHILNTWHTLKSCGKKVAFLWCPSH 163 (293)
Q Consensus 139 ~~i~~~~~~l~~~~~~v~~~WVpgH 163 (293)
.... .+.+ -..+.|..||+-
T Consensus 164 lac~--A~wi---Lrgts~~yVPS~ 183 (245)
T PF00336_consen 164 LACA--ANWI---LRGTSFYYVPSK 183 (245)
T ss_pred HHHH--HHHh---hcCceEEEeccc
Confidence 1111 0111 134678899963
No 17
>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=58.15 E-value=9.4 Score=19.70 Aligned_cols=17 Identities=18% Similarity=0.265 Sum_probs=14.4
Q ss_pred CCcccCCCccccccCCC
Q psy15839 264 SCQSSQLSSQSSEDKSK 280 (293)
Q Consensus 264 ~C~~Cg~~~~~l~~Cp~ 280 (293)
.|..||...+...+||.
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 58889998888999984
No 18
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=56.16 E-value=56 Score=24.98 Aligned_cols=54 Identities=9% Similarity=-0.044 Sum_probs=34.0
Q ss_pred CCeeEEEEEC-CeeEEeecCC----CCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcH
Q psy15839 69 QNTSCAVYAG-GSAKSYILNN----INSIFTAELLALVFCLDSVKNRPDVNTLIVCDSM 122 (293)
Q Consensus 69 ~~~G~~v~~~-~~~~~~~~~~----~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~ 122 (293)
..+|+.++.+ +.....+... ......||+.||..+.+...........+|+.-+
T Consensus 17 ~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~E 75 (109)
T cd01285 17 VPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLE 75 (109)
T ss_pred CcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCC
Confidence 3577777766 4333333222 2345689999999998876543456677877543
No 19
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=53.88 E-value=42 Score=29.43 Aligned_cols=86 Identities=16% Similarity=0.024 Sum_probs=56.7
Q ss_pred chhHHHHHHHHHHHHHhhcCCCccEEE-E----eCcHHHHHHhhcCC-CChhHHHHHHHHHHHHhh--CCceEEEEEeCC
Q psy15839 91 SIFTAELLALVFCLDSVKNRPDVNTLI-V----CDSMSALTSIANKN-TSIPLIAHILNTWHTLKS--CGKKVAFLWCPS 162 (293)
Q Consensus 91 ~~~~AEl~Ai~~AL~~~~~~~~~~i~I-~----tDS~~ai~~l~~~~-~~~~~~~~i~~~~~~l~~--~~~~v~~~WVpg 162 (293)
++..+|.+|++.+|+.+...+.++..| + .||++.++-+.+-. ..-.+ .. ..+... .+....+.|+--
T Consensus 107 ~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k~~~---~~--~~e~~~~~~~v~h~~k~i~~ 181 (225)
T COG3341 107 SNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETKVNL---LK--DREFFSIGKGVFHDEKDINI 181 (225)
T ss_pred cCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHhhhhhhHHHH---HH--hHHhhhccchhhhhhhhccc
Confidence 455899999999999998766555555 6 69998887776542 11100 00 011111 224455678888
Q ss_pred CCCChhhHHHHHHHhhccC
Q psy15839 163 HTGISGNEIVDRATRQLDG 181 (293)
Q Consensus 163 H~gi~gNe~AD~lAk~a~~ 181 (293)
|..+..+..++.++.....
T Consensus 182 ~~~~~~~~~~~s~~~~~~k 200 (225)
T COG3341 182 HIWIFESKKGNSHVYNTSK 200 (225)
T ss_pred ccccchhhhhhhhhhchhh
Confidence 9999999888888876654
No 20
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=50.85 E-value=36 Score=27.59 Aligned_cols=53 Identities=15% Similarity=0.048 Sum_probs=34.3
Q ss_pred CCCeeEEEEECCeeEEeecC----CCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCc
Q psy15839 68 IQNTSCAVYAGGSAKSYILN----NINSIFTAELLALVFCLDSVKNRPDVNTLIVCDS 121 (293)
Q Consensus 68 ~~~~G~~v~~~~~~~~~~~~----~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS 121 (293)
+=.||+++...+....+|.. ....-.-||-.||.+|+.. -......|.+++|+
T Consensus 25 ~F~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 25 KFKVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred CCcEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 33588887755543333322 1222247999999999987 44456788999988
No 21
>KOG1812|consensus
Probab=50.82 E-value=45 Score=31.93 Aligned_cols=44 Identities=25% Similarity=0.246 Sum_probs=35.8
Q ss_pred CchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCC
Q psy15839 90 NSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT 133 (293)
Q Consensus 90 ~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~ 133 (293)
.+...||+.|+..+|..+...+...+.+++|+......+.....
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~ 90 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREK 90 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhh
Confidence 56789999999999999999999999999997666554444433
No 22
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=50.31 E-value=61 Score=27.35 Aligned_cols=51 Identities=12% Similarity=0.001 Sum_probs=30.3
Q ss_pred CeeEEEEECCeeEEeecC----CCCchhHHHHHHHHHHHHHhhcCCCccEEEEeC
Q psy15839 70 NTSCAVYAGGSAKSYILN----NINSIFTAELLALVFCLDSVKNRPDVNTLIVCD 120 (293)
Q Consensus 70 ~~G~~v~~~~~~~~~~~~----~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tD 120 (293)
.+|+.++.++.....+.. .......||+.||..|.+.+........++|+-
T Consensus 34 pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~~~~~l~g~tlY~T 88 (172)
T PRK10860 34 PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVT 88 (172)
T ss_pred CEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhcCCCCcCCcEEEee
Confidence 477777765543333211 111234799999999987665444445666663
No 23
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=47.59 E-value=74 Score=24.87 Aligned_cols=48 Identities=13% Similarity=0.020 Sum_probs=29.9
Q ss_pred CCCeeEEEEEC-CeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEe
Q psy15839 68 IQNTSCAVYAG-GSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVC 119 (293)
Q Consensus 68 ~~~~G~~v~~~-~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~t 119 (293)
+..+|+.++.+ +.....+.........||+.||..|.+. .....++|+
T Consensus 18 ~~pvGaviv~~~g~iv~~g~n~~~~~~HAE~~ai~~a~~~----~l~g~tly~ 66 (115)
T cd01284 18 NPPVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEK----LARGATLYV 66 (115)
T ss_pred CCCEEEEEEeCCCeEEEEecCCCCCcccHHHHHHHHHhhc----CCCCeEEEE
Confidence 34578877765 4434444333334568999999998874 234556666
No 24
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=45.81 E-value=1.1e+02 Score=26.50 Aligned_cols=68 Identities=10% Similarity=0.035 Sum_probs=45.2
Q ss_pred HHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCC---------CChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhh
Q psy15839 99 ALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN---------TSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGN 169 (293)
Q Consensus 99 Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~---------~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gN 169 (293)
++..||..+.+...-++..|++.+.-+....... -+|-.- .+....|...|...-+..+-||.+|+--
T Consensus 15 ~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sG---lelq~~L~~~~~~~PVIfiTGhgDIpma 91 (202)
T COG4566 15 SVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSG---LELQDRLAERGIRLPVIFLTGHGDIPMA 91 (202)
T ss_pred HHHHHHHHHHHhCCceeeeecCHHHHHhhccCCCCCeEEEecCCCCCch---HHHHHHHHhcCCCCCEEEEeCCCChHHH
Confidence 5667888887777778889999988887742221 011111 1233455677888888889999998753
No 25
>TIGR02403 trehalose_treC alpha,alpha-phosphotrehalase. Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.
Probab=41.52 E-value=55 Score=32.80 Aligned_cols=72 Identities=15% Similarity=0.036 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHhhcCCCccEEEEe-------CcHHHHHHhhcCCCChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCC
Q psy15839 95 AELLALVFCLDSVKNRPDVNTLIVC-------DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGI 166 (293)
Q Consensus 95 AEl~Ai~~AL~~~~~~~~~~i~I~t-------DS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi 166 (293)
+-+.+|..-|+++.+.+...|.+-- |+-+.+.-....-..-....++..+++.++++|.+|-+-+|+.|++.
T Consensus 24 G~~~gi~~~l~yl~~lG~~~i~l~Pi~~~~~~~~gY~~~d~~~id~~~Gt~~~~~~lv~~ah~~gi~vilD~v~NH~~~ 102 (543)
T TIGR02403 24 GDLRGIIEKLDYLKKLGVDYIWLNPFYVSPQKDNGYDVSDYYAINPLFGTMADFEELVSEAKKRNIKIMLDMVFNHTST 102 (543)
T ss_pred cCHHHHHHhHHHHHHcCCCEEEECCcccCCCCCCCCCccccCccCcccCCHHHHHHHHHHHHHCCCEEEEEECcccccc
Confidence 3466788888888887766665422 11111100000000011345677788888999999999999999974
No 26
>cd01286 deoxycytidylate_deaminase Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.
Probab=39.38 E-value=1.2e+02 Score=24.22 Aligned_cols=26 Identities=12% Similarity=-0.022 Sum_probs=17.5
Q ss_pred hhHHHHHHHHHHHHHhhcCCCccEEEEe
Q psy15839 92 IFTAELLALVFCLDSVKNRPDVNTLIVC 119 (293)
Q Consensus 92 ~~~AEl~Ai~~AL~~~~~~~~~~i~I~t 119 (293)
...||..||..|.+. .......+||+
T Consensus 68 ~~HAE~~Ai~~a~~~--~~~~~~~tLyv 93 (131)
T cd01286 68 TVHAEQNAILQAARH--GVSLEGATLYV 93 (131)
T ss_pred CCCHHHHHHHHHhHc--CCCcCCeEEEE
Confidence 457999999988764 22234566665
No 27
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=38.42 E-value=1e+02 Score=25.39 Aligned_cols=51 Identities=10% Similarity=0.053 Sum_probs=30.4
Q ss_pred CeeEEEEECC-eeEEeec----CCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeC
Q psy15839 70 NTSCAVYAGG-SAKSYIL----NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCD 120 (293)
Q Consensus 70 ~~G~~v~~~~-~~~~~~~----~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tD 120 (293)
.+|+.++..+ .....+- ....-.-.||+.||..|-+.+........++|+-
T Consensus 29 PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyvT 84 (152)
T COG0590 29 PVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYVT 84 (152)
T ss_pred CEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEEe
Confidence 4677777633 2332221 1111224799999999999987644555666663
No 28
>PRK08298 cytidine deaminase; Validated
Probab=33.67 E-value=75 Score=25.74 Aligned_cols=51 Identities=10% Similarity=-0.022 Sum_probs=30.8
Q ss_pred CeeEEEEECCeeEEeecCCC----CchhHHHHHHHHHHHHHhhcCCCccEEEEeCc
Q psy15839 70 NTSCAVYAGGSAKSYILNNI----NSIFTAELLALVFCLDSVKNRPDVNTLIVCDS 121 (293)
Q Consensus 70 ~~G~~v~~~~~~~~~~~~~~----~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS 121 (293)
.||+++...+..+..|..-+ ..-.-||..||..|+..-. .....|.|.+|.
T Consensus 24 ~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G~-~~~~~i~v~~~~ 78 (136)
T PRK08298 24 GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQK-RVTHSICVAREN 78 (136)
T ss_pred ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCCC-ceEEEEEEEcCC
Confidence 78888876554444443221 1224799999999886532 224556677666
No 29
>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.
Probab=32.79 E-value=1.1e+02 Score=24.18 Aligned_cols=52 Identities=12% Similarity=-0.081 Sum_probs=31.4
Q ss_pred CCeeEEEEECCeeEEeecCCC----CchhHHHHHHHHHHHHHhhcCCCccEEEEeCc
Q psy15839 69 QNTSCAVYAGGSAKSYILNNI----NSIFTAELLALVFCLDSVKNRPDVNTLIVCDS 121 (293)
Q Consensus 69 ~~~G~~v~~~~~~~~~~~~~~----~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS 121 (293)
..+|+++...+.....+...+ .-...||..||..|...-.. ....+.|..+.
T Consensus 21 ~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~~-~i~~i~vv~~~ 76 (127)
T TIGR01354 21 FKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGYR-KFVAIAVADSA 76 (127)
T ss_pred CeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCCC-CeEEEEEEeCC
Confidence 347777775543332232222 12247999999999876432 46678888766
No 30
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=31.78 E-value=27 Score=31.78 Aligned_cols=16 Identities=25% Similarity=0.225 Sum_probs=14.3
Q ss_pred HHhHHhHhhCcccccc
Q psy15839 238 EVVLTRVRIGHTRLTH 253 (293)
Q Consensus 238 ~~~L~qlRTGH~~l~~ 253 (293)
...|.||||.|-..+|
T Consensus 213 vGALsqLrTehrPCtY 228 (311)
T PF15322_consen 213 VGALSQLRTEHRPCTY 228 (311)
T ss_pred cchhhhhhhccCCccc
Confidence 5689999999999985
No 31
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=31.76 E-value=21 Score=24.00 Aligned_cols=17 Identities=18% Similarity=0.110 Sum_probs=12.2
Q ss_pred CCcccCCCccccccCCC
Q psy15839 264 SCQSSQLSSQSSEDKSK 280 (293)
Q Consensus 264 ~C~~Cg~~~~~l~~Cp~ 280 (293)
.||+||+....++++..
T Consensus 2 ~CPyCge~~~~~iD~s~ 18 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSA 18 (52)
T ss_pred CCCCCCCeeEEEEecCC
Confidence 59999988766555543
No 32
>PRK06848 hypothetical protein; Validated
Probab=29.04 E-value=1.3e+02 Score=24.39 Aligned_cols=53 Identities=9% Similarity=-0.049 Sum_probs=31.4
Q ss_pred CCCeeEEEEECCeeEEeecCC----CCchhHHHHHHHHHHHHHhhcCCCccEEEEeCc
Q psy15839 68 IQNTSCAVYAGGSAKSYILNN----INSIFTAELLALVFCLDSVKNRPDVNTLIVCDS 121 (293)
Q Consensus 68 ~~~~G~~v~~~~~~~~~~~~~----~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS 121 (293)
+..||+++...+..+..|..- .....-||-.||..|+..-. .....|.+.+++
T Consensus 26 ~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~g~-~~i~~i~~v~~~ 82 (139)
T PRK06848 26 WHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISEGD-HEIDTIVAVRHP 82 (139)
T ss_pred CCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHcCC-CceEEEEEEecC
Confidence 456898887665444444221 11223799999999986522 234556566554
No 33
>smart00642 Aamy Alpha-amylase domain.
Probab=28.68 E-value=1.5e+02 Score=24.54 Aligned_cols=29 Identities=17% Similarity=0.085 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhhCCceEEEEEeCCCCCC
Q psy15839 138 IAHILNTWHTLKSCGKKVAFLWCPSHTGI 166 (293)
Q Consensus 138 ~~~i~~~~~~l~~~~~~v~~~WVpgH~gi 166 (293)
..++.++++.++++|..|-+-.|+.|++.
T Consensus 69 ~~d~~~lv~~~h~~Gi~vilD~V~NH~~~ 97 (166)
T smart00642 69 MEDFKELVDAAHARGIKVILDVVINHTSD 97 (166)
T ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCCCC
Confidence 46677888889999999999999999887
No 34
>KOG1817|consensus
Probab=27.79 E-value=1.6e+02 Score=28.80 Aligned_cols=46 Identities=28% Similarity=0.307 Sum_probs=30.9
Q ss_pred EEecCCC--CCC-eeEEEEECCeeEEeecCCCCchhHHHHHHHHHHHHHhh
Q psy15839 61 SLYGSKT--IQN-TSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVK 108 (293)
Q Consensus 61 ytDGS~~--~~~-~G~~v~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~ 108 (293)
|++|.+. ++. .-++++.++ +..+.+.+.++..||+.|+..||+-..
T Consensus 454 ~V~~~~gpa~~r~y~Vavyf~g--krlat~~G~nik~Ae~rAA~~ALe~~~ 502 (533)
T KOG1817|consen 454 KVLGAKGPANDRNYKVAVYFKG--KRLATGVGSNIKQAEMRAAMQALENLK 502 (533)
T ss_pred EEecccCCCCCCceEEEEEECC--EEEeeccCchHhHHHHHHHHHHHHHHH
Confidence 5565433 222 345666666 444555577899999999999999775
No 35
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=27.04 E-value=2.3e+02 Score=20.79 Aligned_cols=51 Identities=12% Similarity=0.010 Sum_probs=30.5
Q ss_pred CCCeeEEEEE-CCeeEEeecCC----CCchhHHHHHHHHHHHHHhhcCCCccEEEEe
Q psy15839 68 IQNTSCAVYA-GGSAKSYILNN----INSIFTAELLALVFCLDSVKNRPDVNTLIVC 119 (293)
Q Consensus 68 ~~~~G~~v~~-~~~~~~~~~~~----~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~t 119 (293)
+..+|+.++. ++.....+... ....-.||..||..+.+. .........+|+
T Consensus 23 ~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~-~~~~~~~~~lyv 78 (102)
T PF00383_consen 23 NFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN-GGSSLKGCTLYV 78 (102)
T ss_dssp SSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT-TSSGETTEEEEE
T ss_pred CCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh-ccccccCccccc
Confidence 4468888888 44444444322 122348999999999887 222234566766
No 36
>COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism]
Probab=26.97 E-value=1.2e+02 Score=25.01 Aligned_cols=40 Identities=15% Similarity=0.110 Sum_probs=25.9
Q ss_pred CCCeeEEEEECCeeEEeecCCCCchhHHHHHHHHHHHHHh
Q psy15839 68 IQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSV 107 (293)
Q Consensus 68 ~~~~G~~v~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~ 107 (293)
|+.||+.|+.++.....+.....-.-.||..|+..|=+.+
T Consensus 27 NP~VG~VIV~~~~Ivg~G~h~~aG~pHAEv~Al~~ag~~a 66 (146)
T COG0117 27 NPSVGCVIVKDGEIVGEGYHEKAGGPHAEVCALRMAGEAA 66 (146)
T ss_pred CCceeEEEEECCEEEeeeecCCCCCCcHHHHHHHHcCccc
Confidence 6779999998885544443222223379999998884433
No 37
>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=24.77 E-value=39 Score=21.08 Aligned_cols=22 Identities=18% Similarity=0.114 Sum_probs=14.5
Q ss_pred CCcccCCCcc-------ccccCCCCchhh
Q psy15839 264 SCQSSQLSSQ-------SSEDKSKSPEQR 285 (293)
Q Consensus 264 ~C~~Cg~~~~-------~l~~Cp~~~~~R 285 (293)
.|+.||.... ..+.|+.|++=+
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~ 31 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYPECK 31 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCCCcC
Confidence 5888885421 277888887643
No 38
>PRK12411 cytidine deaminase; Provisional
Probab=23.19 E-value=1.9e+02 Score=23.22 Aligned_cols=52 Identities=21% Similarity=0.075 Sum_probs=30.5
Q ss_pred CCeeEEEEECCeeEEeecCCCCc----hhHHHHHHHHHHHHHhhcCCCccEEEEeCc
Q psy15839 69 QNTSCAVYAGGSAKSYILNNINS----IFTAELLALVFCLDSVKNRPDVNTLIVCDS 121 (293)
Q Consensus 69 ~~~G~~v~~~~~~~~~~~~~~~~----~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS 121 (293)
-.||+++...+.....|..-+.. ..-||..||..|+..- ......|.|.+|.
T Consensus 24 ~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~g-~~~i~~i~v~~~~ 79 (132)
T PRK12411 24 FQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEG-DKEFVAIAIVADT 79 (132)
T ss_pred CceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHCC-CCceEEEEEEeCC
Confidence 35777776555433333221111 2379999999987542 2245677787765
No 39
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=21.91 E-value=59 Score=22.71 Aligned_cols=20 Identities=15% Similarity=0.189 Sum_probs=14.2
Q ss_pred cccCCCCCCCCcccCCCccc
Q psy15839 255 YLFTRSDPPSCQSSQLSSQS 274 (293)
Q Consensus 255 ~r~~~~~~p~C~~Cg~~~~~ 274 (293)
+|+--.|...||.||.+..+
T Consensus 11 k~l~~~d~e~CP~Cgs~~~t 30 (64)
T COG2093 11 KRLTPEDTEICPVCGSTDLT 30 (64)
T ss_pred cccCCCCCccCCCCCCcccc
Confidence 35666677779999987433
No 40
>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=21.84 E-value=32 Score=20.35 Aligned_cols=18 Identities=11% Similarity=0.065 Sum_probs=7.1
Q ss_pred CCCcccCCCcc----ccccCCC
Q psy15839 263 PSCQSSQLSSQ----SSEDKSK 280 (293)
Q Consensus 263 p~C~~Cg~~~~----~l~~Cp~ 280 (293)
|.|+.|+...+ .++-||-
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~ 24 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPE 24 (30)
T ss_dssp ---TTT-----EE-SSSEEETT
T ss_pred CCCCCCCCcceeccCCEEeCCc
Confidence 67888886532 2777774
No 41
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=21.62 E-value=1.4e+02 Score=22.80 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhhCCceEEEEEeC
Q psy15839 137 LIAHILNTWHTLKSCGKKVAFLWCP 161 (293)
Q Consensus 137 ~~~~i~~~~~~l~~~~~~v~~~WVp 161 (293)
.+..|.+.++.+.++|..|.+.|.=
T Consensus 61 ~l~~i~~~Le~~~~~g~~V~v~Wyy 85 (99)
T PF09345_consen 61 ALMDIFDLLEDAAQKGGKVTVNWYY 85 (99)
T ss_pred HHHHHHHHHHHHHhcCCcEEEEEEE
Confidence 4456777777778899999999985
No 42
>PRK12568 glycogen branching enzyme; Provisional
Probab=20.73 E-value=1.1e+02 Score=31.92 Aligned_cols=32 Identities=13% Similarity=0.128 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhhCCceEEEEEeCCCCCChhh
Q psy15839 138 IAHILNTWHTLKSCGKKVAFLWCPSHTGISGN 169 (293)
Q Consensus 138 ~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gN 169 (293)
...+...++.+++.|..|-+-|||.|++-.++
T Consensus 318 ~~dfk~lV~~~H~~Gi~VIlD~V~nH~~~d~~ 349 (730)
T PRK12568 318 PDGFAQFVDACHRAGIGVILDWVSAHFPDDAH 349 (730)
T ss_pred HHHHHHHHHHHHHCCCEEEEEeccccCCcccc
Confidence 56777888899999999999999999986544
Done!