Query 039495
Match_columns 327
No_of_seqs 237 out of 1319
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 10:16:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039495.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039495hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13907 rnhA ribonuclease H; 99.9 5.4E-25 1.2E-29 183.8 13.0 127 167-295 1-127 (128)
2 PRK07238 bifunctional RNase H/ 99.8 1.8E-20 4E-25 183.1 14.2 137 167-304 2-140 (372)
3 PRK07708 hypothetical protein; 99.8 4.1E-20 8.8E-25 168.2 15.0 135 163-297 69-210 (219)
4 PF13456 RVT_3: Reverse transc 99.8 1.9E-19 4.2E-24 138.7 9.1 86 209-294 1-86 (87)
5 cd06222 RnaseH RNase H (RNase 99.8 1.1E-18 2.4E-23 140.5 13.5 125 169-293 1-130 (130)
6 COG0328 RnhA Ribonuclease HI [ 99.8 5E-19 1.1E-23 151.8 11.0 127 167-296 3-146 (154)
7 PRK00203 rnhA ribonuclease H; 99.6 2.8E-15 6E-20 128.9 11.9 126 167-297 3-144 (150)
8 PF00075 RNase_H: RNase H; In 99.6 3.5E-15 7.5E-20 124.0 11.8 119 167-293 3-131 (132)
9 PRK08719 ribonuclease H; Revie 99.6 3.9E-15 8.5E-20 127.7 12.2 123 167-294 4-146 (147)
10 PRK06548 ribonuclease H; Provi 99.6 1.4E-14 3E-19 125.9 13.9 123 167-296 5-143 (161)
11 KOG3752 Ribonuclease H [Replic 98.8 4.7E-08 1E-12 94.0 11.7 127 165-294 210-364 (371)
12 KOG1812 Predicted E3 ubiquitin 95.2 0.028 6.1E-07 55.6 5.2 116 180-295 16-138 (384)
13 COG0590 CumB Cytosine/adenosin 55.0 29 0.00062 29.8 5.3 56 181-236 26-83 (152)
14 cd01285 nucleoside_deaminase N 53.4 41 0.0009 26.8 5.7 56 181-236 15-72 (109)
15 TIGR01354 cyt_deam_tetra cytid 49.8 46 0.001 27.5 5.6 56 182-238 20-76 (127)
16 COG0295 Cdd Cytidine deaminase 49.0 46 0.00099 28.2 5.4 55 183-238 26-81 (134)
17 cd01284 Riboflavin_deaminase-r 48.8 49 0.0011 27.0 5.5 41 181-223 17-57 (115)
18 cd00786 cytidine_deaminase-lik 44.1 91 0.002 24.2 6.3 42 181-222 16-60 (96)
19 PRK10860 tRNA-specific adenosi 37.0 77 0.0017 27.8 5.3 39 184-223 34-74 (172)
20 PF00383 dCMP_cyt_deam_1: Cyti 35.3 63 0.0014 24.9 4.1 44 180-223 21-66 (102)
21 cd01283 cytidine_deaminase Cyt 30.4 1.1E+02 0.0023 24.4 4.8 42 181-222 16-58 (112)
22 PF04920 DUF656: Family of unk 27.8 32 0.00069 27.8 1.1 36 64-100 33-68 (126)
23 TIGR02571 ComEB ComE operon pr 25.4 2.2E+02 0.0047 24.4 6.0 13 209-221 67-79 (151)
24 COG3981 Predicted acetyltransf 24.3 3.2E+02 0.007 24.2 6.8 27 214-240 116-142 (174)
25 PRK12411 cytidine deaminase; P 23.6 2.2E+02 0.0048 23.8 5.6 56 182-238 23-79 (132)
26 PRK05578 cytidine deaminase; V 23.0 1.9E+02 0.0042 24.1 5.1 54 184-238 25-79 (131)
27 PRK06848 hypothetical protein; 21.0 2.7E+02 0.0059 23.5 5.7 54 183-237 27-81 (139)
28 PF03259 Robl_LC7: Roadblock/L 20.8 1.4E+02 0.003 22.1 3.6 59 183-241 14-76 (91)
29 PF08119 Toxin_31: Scorpion ac 20.8 39 0.00084 21.3 0.3 7 41-47 26-32 (37)
No 1
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.92 E-value=5.4e-25 Score=183.79 Aligned_cols=127 Identities=21% Similarity=0.197 Sum_probs=115.4
Q ss_pred cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495 167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE 246 (327)
Q Consensus 167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~ 246 (327)
++++|||||+..+++.+|+|+|+||..|.+... ...+..|+++||++|+++||+.|.+.|+++|+|+|||++|+++++
T Consensus 1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~--~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~ 78 (128)
T PRK13907 1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLS--LPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVE 78 (128)
T ss_pred CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEE--ecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHh
Confidence 479999999999999999999999999877643 234567999999999999999999999999999999999999999
Q ss_pred CCCCCCCchhhhHHHHHHHhccCCccceeeccCcccHHHHHHHHHHhhC
Q 039495 247 LPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQ 295 (327)
Q Consensus 247 ~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~LAk~A~~~ 295 (327)
+.......+..++++++.++..|..+.+.|++|++|..||.||+.|+..
T Consensus 79 ~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 79 KEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQ 127 (128)
T ss_pred HHHhcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHhc
Confidence 9776556788999999999999999999999999999999999999753
No 2
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.84 E-value=1.8e-20 Score=183.07 Aligned_cols=137 Identities=22% Similarity=0.225 Sum_probs=121.9
Q ss_pred cEEEEEeeeecCCCCceeEEEEEEcCCCc-eEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhh
Q 039495 167 WVKLNIEGSSSRAQGSAGAGGIVRDESGK-WILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCL 245 (327)
Q Consensus 167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~-~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i 245 (327)
.+++|||||+.++++.+|+|+|++|++|. ++..++..++..|+++||+.||+.||+++.+.|.++|+|++||++|++.+
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 37899999999999999999999999764 55666677777899999999999999999999999999999999999999
Q ss_pred cCCCCCC-CchhhhHHHHHHHhccCCccceeeccCcccHHHHHHHHHHhhCCCCCeEEec
Q 039495 246 ELPASFL-DPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFD 304 (327)
Q Consensus 246 ~~~~~~~-s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~LAk~A~~~~~~~~~~~~ 304 (327)
++.+... ..+..++.+++.++++|..+.+.||+|++|..||.||+.|+..... .+|++
T Consensus 82 ~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~~~~-~~~~~ 140 (372)
T PRK07238 82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAG-GEPWG 140 (372)
T ss_pred CCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHhhcc-CCCcc
Confidence 9987544 4577889999999999999999999999999999999999987763 35654
No 3
>PRK07708 hypothetical protein; Validated
Probab=99.84 E-value=4.1e-20 Score=168.22 Aligned_cols=135 Identities=16% Similarity=0.112 Sum_probs=114.1
Q ss_pred CCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEe--ccccccC-CccchHHHHHHHHHhhHHHHhhCceE--EEEEEc
Q 039495 163 PPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWIL--GYSKNLG-TSNSLASELWALYHGLNLVWERGFRK--VLVECN 237 (327)
Q Consensus 163 P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~--~~~~~~~-~~s~~~AE~~Al~~AL~~A~~~g~~~--Vi~EsD 237 (327)
+.++.+++|||||+..+++.+|+|+|++++.|.... ..+..++ ..|+++||+.|++.||+.|.++|+++ |+|++|
T Consensus 69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D 148 (219)
T PRK07708 69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD 148 (219)
T ss_pred cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence 334569999999999999999999999998776443 3334454 47999999999999999999999976 899999
Q ss_pred cHhhHHhhcCCCCCCC-chhhhHHHHHHHhccCC-ccceeeccCcccHHHHHHHHHHhhCCC
Q 039495 238 SHEAVKCLELPASFLD-PNRALILSCREYLCRNW-DCKLQLILREANSCANWLAAHCENQPL 297 (327)
Q Consensus 238 S~~VV~~i~~~~~~~s-~~~~li~eI~~ll~~f~-~v~~~hI~R~~N~~AD~LAk~A~~~~~ 297 (327)
|++|++++++.+.... .+..+.+.++.++++|. .+.+.||+|++|..||.||+.|++...
T Consensus 149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGTV 210 (219)
T ss_pred cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhcCC
Confidence 9999999999876554 45678888888888775 478899999999999999999998654
No 4
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.80 E-value=1.9e-19 Score=138.68 Aligned_cols=86 Identities=35% Similarity=0.475 Sum_probs=76.6
Q ss_pred chHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcCCCCCCCchhhhHHHHHHHhccCCccceeeccCcccHHHHHH
Q 039495 209 SLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWL 288 (327)
Q Consensus 209 ~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~L 288 (327)
|++||++|++.||++|.++|+++|+|||||+.+|+++++.....+.+..++.+|+.++..|+++.+.||+|++|..||.|
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~L 80 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADAL 80 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHHHHH
Confidence 58999999999999999999999999999999999999998777799999999999999999999999999999999999
Q ss_pred HHHHhh
Q 039495 289 AAHCEN 294 (327)
Q Consensus 289 Ak~A~~ 294 (327)
||.|++
T Consensus 81 A~~a~~ 86 (87)
T PF13456_consen 81 AKFALS 86 (87)
T ss_dssp HHHHHH
T ss_pred HHHHhh
Confidence 999976
No 5
>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=99.80 E-value=1.1e-18 Score=140.53 Aligned_cols=125 Identities=26% Similarity=0.251 Sum_probs=112.5
Q ss_pred EEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcCC
Q 039495 169 KLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELP 248 (327)
Q Consensus 169 K~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~~ 248 (327)
+||+|||+....+.+|+|+++++..+.............+++++|++|+..||+.+...+.+++.|++||+.+++.+++.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~ 80 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW 80 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence 58999999988899999999999999888766555566799999999999999999999999999999999999999987
Q ss_pred CC-CCCchhhhHHHHHHHhccCCccceeeccC----cccHHHHHHHHHHh
Q 039495 249 AS-FLDPNRALILSCREYLCRNWDCKLQLILR----EANSCANWLAAHCE 293 (327)
Q Consensus 249 ~~-~~s~~~~li~eI~~ll~~f~~v~~~hI~R----~~N~~AD~LAk~A~ 293 (327)
.. ....+..++.+++.++..+..+.+.|++| +.|..||.||+.++
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 65 34567788899999988889999999999 99999999999874
No 6
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.79 E-value=5e-19 Score=151.80 Aligned_cols=127 Identities=22% Similarity=0.185 Sum_probs=108.2
Q ss_pred cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495 167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE 246 (327)
Q Consensus 167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~ 246 (327)
.+.+|+|||+.+++|.+|+|+|++...+.. ..+.....+|++++|++|+++||+.+.+.+...|.++|||++|++.|+
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~--~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~ 80 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEK--ELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT 80 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceE--EEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence 478999999999999999999999666665 333344478999999999999999999999999999999999999999
Q ss_pred CCC----C---------CCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCC
Q 039495 247 LPA----S---------FLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQP 296 (327)
Q Consensus 247 ~~~----~---------~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~ 296 (327)
.+ . .+-....+++++.+++..+..+.+.||+ +..|+.||.||+.+....
T Consensus 81 -~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 81 -RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred -HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 22 1 1122346799999999999899999998 889999999999998754
No 7
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.63 E-value=2.8e-15 Score=128.89 Aligned_cols=126 Identities=18% Similarity=0.090 Sum_probs=98.4
Q ss_pred cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495 167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE 246 (327)
Q Consensus 167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~ 246 (327)
.+.+|||||+..+++.+|+|+|+...++... ++...+..|++.||++|+..||+.+.+ ...|.|.|||+++++.|+
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~--~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~ 78 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKE--LSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGIT 78 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEE--EecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHH
Confidence 3789999999999999999999987554432 233345679999999999999998765 357999999999999998
Q ss_pred C--------CCC----CCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCCC
Q 039495 247 L--------PAS----FLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQPL 297 (327)
Q Consensus 247 ~--------~~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~~ 297 (327)
+ ... .+-....++++|.+++.. ..+.|.||+ ++.|..||.||+.|.....
T Consensus 79 ~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 79 EWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 5 111 122345678888888765 578888888 7779999999999987543
No 8
>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=99.63 E-value=3.5e-15 Score=123.95 Aligned_cols=119 Identities=24% Similarity=0.296 Sum_probs=94.3
Q ss_pred cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495 167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE 246 (327)
Q Consensus 167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~ 246 (327)
-+.+++|||+..+++.+|+|+++.+. . .++..++..|++.||++|+.+||+ +... +++.|.|||+.+++.++
T Consensus 3 ~~~iytDgS~~~~~~~~~~g~v~~~~--~---~~~~~~~~~s~~~aEl~Ai~~AL~-~~~~--~~v~I~tDS~~v~~~l~ 74 (132)
T PF00075_consen 3 AIIIYTDGSCRPNPGKGGAGYVVWGG--R---NFSFRLGGQSNNRAELQAIIEALK-ALEH--RKVTIYTDSQYVLNALN 74 (132)
T ss_dssp SEEEEEEEEECTTTTEEEEEEEEETT--E---EEEEEEESECHHHHHHHHHHHHHH-THST--SEEEEEES-HHHHHHHH
T ss_pred cEEEEEeCCccCCCCceEEEEEEECC--e---EEEecccccchhhhheehHHHHHH-Hhhc--ccccccccHHHHHHHHH
Confidence 37899999999999999999977433 2 222333467999999999999999 5422 99999999999999888
Q ss_pred C-----CCCCCCchhhhHHHHHHHhccCCccceeeccCc-----ccHHHHHHHHHHh
Q 039495 247 L-----PASFLDPNRALILSCREYLCRNWDCKLQLILRE-----ANSCANWLAAHCE 293 (327)
Q Consensus 247 ~-----~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~-----~N~~AD~LAk~A~ 293 (327)
. ..........++.++.+++.....+.|.||+.+ .|..||.|||.|+
T Consensus 75 ~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 75 KWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp THHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HhccccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 8 443333333577888888877888999999998 6889999999986
No 9
>PRK08719 ribonuclease H; Reviewed
Probab=99.62 E-value=3.9e-15 Score=127.74 Aligned_cols=123 Identities=21% Similarity=0.229 Sum_probs=97.9
Q ss_pred cEEEEEeeeecCCCC---ceeEEEEEEcCCCceEeccccccC-CccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhH
Q 039495 167 WVKLNIEGSSSRAQG---SAGAGGIVRDESGKWILGYSKNLG-TSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAV 242 (327)
Q Consensus 167 ~lK~NvDgS~~~~~~---~aG~G~ViRD~~G~~l~~~~~~~~-~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV 242 (327)
.+++|||||+..+++ ++|+|+++.+.+|..+...+..+. ..|++.||+.|+..||+.+.+.. .|.|||++++
T Consensus 4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~~----~i~tDS~yvi 79 (147)
T PRK08719 4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDGD----VIYSDSDYCV 79 (147)
T ss_pred eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCCC----EEEechHHHH
Confidence 478999999988766 789999999988876543333343 46999999999999999987653 7999999999
Q ss_pred Hhhc--------CCCC----CCCchhhhHHHHHHHhccCCccceeeccC----cccHHHHHHHHHHhh
Q 039495 243 KCLE--------LPAS----FLDPNRALILSCREYLCRNWDCKLQLILR----EANSCANWLAAHCEN 294 (327)
Q Consensus 243 ~~i~--------~~~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~R----~~N~~AD~LAk~A~~ 294 (327)
+.++ +.+. .+-.+..+++.|..+.+ ...++|.||++ ..|..||.||+.|..
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 9995 3322 22335678888888876 56789999999 569999999999864
No 10
>PRK06548 ribonuclease H; Provisional
Probab=99.60 E-value=1.4e-14 Score=125.92 Aligned_cols=123 Identities=19% Similarity=0.159 Sum_probs=95.7
Q ss_pred cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495 167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE 246 (327)
Q Consensus 167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~ 246 (327)
.+.+|||||+.++++.+|+|+++.+. + . .....+..|++.||++|+++||+.+. .+..+|.|.|||+++++.++
T Consensus 5 ~~~IytDGa~~gnpg~~G~g~~~~~~-~-~---~~g~~~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i~ 78 (161)
T PRK06548 5 EIIAATDGSSLANPGPSGWAWYVDEN-T-W---DSGGWDIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSLT 78 (161)
T ss_pred EEEEEEeeccCCCCCceEEEEEEeCC-c-E---EccCCCCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHHH
Confidence 38999999999999999999999753 2 1 12333457999999999999998554 45568999999999999999
Q ss_pred C--------CC----CCCCchhhhHHHHHHHhccCCccceeeccC----cccHHHHHHHHHHhhCC
Q 039495 247 L--------PA----SFLDPNRALILSCREYLCRNWDCKLQLILR----EANSCANWLAAHCENQP 296 (327)
Q Consensus 247 ~--------~~----~~~s~~~~li~eI~~ll~~f~~v~~~hI~R----~~N~~AD~LAk~A~~~~ 296 (327)
. .+ ..+-....|+++|..++... .++|.||+- ..|..||.||+.+....
T Consensus 79 ~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 3 22 12224578999999988763 677877654 56999999999998643
No 11
>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]
Probab=98.79 E-value=4.7e-08 Score=94.04 Aligned_cols=127 Identities=20% Similarity=0.144 Sum_probs=92.9
Q ss_pred CCcEEEEEeeeecCC---CCceeEEEEEEcCCCceEeccccc-c-CCccchHHHHHHHHHhhHHHHhhCceEEEEEEccH
Q 039495 165 TNWVKLNIEGSSSRA---QGSAGAGGIVRDESGKWILGYSKN-L-GTSNSLASELWALYHGLNLVWERGFRKVLVECNSH 239 (327)
Q Consensus 165 ~g~lK~NvDgS~~~~---~~~aG~G~ViRD~~G~~l~~~~~~-~-~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~ 239 (327)
.+.+.+|+||++..+ ..++|+|+.+=+..-. ..+.. . +..|++.||+.|+.+||+.|++....+|+|.|||+
T Consensus 210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~---N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~ 286 (371)
T KOG3752|consen 210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHEL---NVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSE 286 (371)
T ss_pred ccceEEEecCccccCCCCCCcceeEEeeCCCCcc---cccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechH
Confidence 345789999999875 3568888877553211 11222 2 56799999999999999999999999999999999
Q ss_pred hhHHhhcC-------------CCCC----CCchhhhHHHHHHHhcc--CCccceeeccC----cccHHHHHHHHHHhh
Q 039495 240 EAVKCLEL-------------PASF----LDPNRALILSCREYLCR--NWDCKLQLILR----EANSCANWLAAHCEN 294 (327)
Q Consensus 240 ~VV~~i~~-------------~~~~----~s~~~~li~eI~~ll~~--f~~v~~~hI~R----~~N~~AD~LAk~A~~ 294 (327)
+++++|+. ...+ .......+.++.+|.+. ...+++.||+- ..|..||.||+.+..
T Consensus 287 ~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 287 YFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred HHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 99999983 1111 01123466777777766 35677777765 469999999999843
No 12
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.23 E-value=0.028 Score=55.64 Aligned_cols=116 Identities=17% Similarity=0.119 Sum_probs=83.6
Q ss_pred CCceeEEEEEEcC-CCceEeccccccC---CccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcCCCCCCC--
Q 039495 180 QGSAGAGGIVRDE-SGKWILGYSKNLG---TSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLD-- 253 (327)
Q Consensus 180 ~~~aG~G~ViRD~-~G~~l~~~~~~~~---~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~~~~~~s-- 253 (327)
...+|.|+.+.|. +....+....... ..++.+||++|+..+|..+.++|+.++.+.+|+..+...+.+......
T Consensus 16 ~~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~ 95 (384)
T KOG1812|consen 16 ILLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHR 95 (384)
T ss_pred hhcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHH
Confidence 3568889999885 5555443333322 258999999999999999999999999999998888887776654333
Q ss_pred chhhhHHHHHHHhccCCccceeeccCc-ccHHHHHHHHHHhhC
Q 039495 254 PNRALILSCREYLCRNWDCKLQLILRE-ANSCANWLAAHCENQ 295 (327)
Q Consensus 254 ~~~~li~eI~~ll~~f~~v~~~hI~R~-~N~~AD~LAk~A~~~ 295 (327)
.+..+..+.+.+...+....-..+++. ....|-.||+.+...
T Consensus 96 ~~~~l~~~v~~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 96 KIVLLVELVQRIREQLTSSEPILVPKNADIKFAYKLAREAIVS 138 (384)
T ss_pred HHHHHHHHHHHHHHHhhcccceecccchhhHHHHHHHHHhhcc
Confidence 355666666666666655555556554 456688999999874
No 13
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=55.04 E-value=29 Score=29.83 Aligned_cols=56 Identities=13% Similarity=0.194 Sum_probs=39.2
Q ss_pred CceeEEEEEEcCCCceEecc-ccccCC-ccchHHHHHHHHHhhHHHHhhCceEEEEEE
Q 039495 181 GSAGAGGIVRDESGKWILGY-SKNLGT-SNSLASELWALYHGLNLVWERGFRKVLVEC 236 (327)
Q Consensus 181 ~~aG~G~ViRD~~G~~l~~~-~~~~~~-~s~~~AE~~Al~~AL~~A~~~g~~~Vi~Es 236 (327)
|...+|+||.+.+|.++... ...... -...+||..|++.|-+......+...++++
T Consensus 26 ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyv 83 (152)
T COG0590 26 GEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYV 83 (152)
T ss_pred CCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEE
Confidence 35668999999889888733 333333 234599999999999888765555555555
No 14
>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=53.40 E-value=41 Score=26.79 Aligned_cols=56 Identities=14% Similarity=0.125 Sum_probs=35.6
Q ss_pred CceeEEEEEEcCCCceEecc-cccc-CCccchHHHHHHHHHhhHHHHhhCceEEEEEE
Q 039495 181 GSAGAGGIVRDESGKWILGY-SKNL-GTSNSLASELWALYHGLNLVWERGFRKVLVEC 236 (327)
Q Consensus 181 ~~aG~G~ViRD~~G~~l~~~-~~~~-~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~Es 236 (327)
+...+|.++.|.+|+++... .... .......||..|+..+.+.-....+....+++
T Consensus 15 ~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~ 72 (109)
T cd01285 15 GEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYT 72 (109)
T ss_pred CCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEE
Confidence 45678889999889887733 3322 23467899999998876643322234444444
No 15
>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=49.79 E-value=46 Score=27.54 Aligned_cols=56 Identities=14% Similarity=0.157 Sum_probs=39.3
Q ss_pred ceeEEEEEEcCCCceEeccccccC-CccchHHHHHHHHHhhHHHHhhCceEEEEEEcc
Q 039495 182 SAGAGGIVRDESGKWILGYSKNLG-TSNSLASELWALYHGLNLVWERGFRKVLVECNS 238 (327)
Q Consensus 182 ~aG~G~ViRD~~G~~l~~~~~~~~-~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS 238 (327)
....|.++++.+|+++.+...-.. ......||..|+..+...- ...+..+.+-.+.
T Consensus 20 ~~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g-~~~i~~i~vv~~~ 76 (127)
T TIGR01354 20 NFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAG-YRKFVAIAVADSA 76 (127)
T ss_pred CCeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcC-CCCeEEEEEEeCC
Confidence 345788899999999886654332 3356789999999887652 2356777777654
No 16
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=48.98 E-value=46 Score=28.20 Aligned_cols=55 Identities=20% Similarity=0.317 Sum_probs=42.1
Q ss_pred eeEEEEEEcCCCceEecccc-ccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEcc
Q 039495 183 AGAGGIVRDESGKWILGYSK-NLGTSNSLASELWALYHGLNLVWERGFRKVLVECNS 238 (327)
Q Consensus 183 aG~G~ViRD~~G~~l~~~~~-~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS 238 (327)
--+|+++|..+|++..+... .....--.-||--|+..++.. -...+..|.+.+|.
T Consensus 26 F~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 26 FKVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred CcEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 34688899999988886643 333446788999999999877 55667888888887
No 17
>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=48.80 E-value=49 Score=27.02 Aligned_cols=41 Identities=15% Similarity=0.097 Sum_probs=28.8
Q ss_pred CceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHH
Q 039495 181 GSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNL 223 (327)
Q Consensus 181 ~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~ 223 (327)
+...+|.|+-+.+|+++........ ...+||..|+..+.+.
T Consensus 17 ~~~pvGaviv~~~g~iv~~g~n~~~--~~~HAE~~ai~~a~~~ 57 (115)
T cd01284 17 PNPPVGCVIVDDDGEIVGEGYHRKA--GGPHAEVNALASAGEK 57 (115)
T ss_pred CCCCEEEEEEeCCCeEEEEecCCCC--CcccHHHHHHHHHhhc
Confidence 3456888888888988873322222 5689999999888654
No 18
>cd00786 cytidine_deaminase-like Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. 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.
Probab=44.06 E-value=91 Score=24.17 Aligned_cols=42 Identities=17% Similarity=0.121 Sum_probs=27.0
Q ss_pred CceeEEEEEEcC-CCceEe-cccccc-CCccchHHHHHHHHHhhH
Q 039495 181 GSAGAGGIVRDE-SGKWIL-GYSKNL-GTSNSLASELWALYHGLN 222 (327)
Q Consensus 181 ~~aG~G~ViRD~-~G~~l~-~~~~~~-~~~s~~~AE~~Al~~AL~ 222 (327)
+...+|.++.+. +|.++. +..... .......||..|+..+.+
T Consensus 16 ~~~pVGaviv~~~~g~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~ 60 (96)
T cd00786 16 SNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGS 60 (96)
T ss_pred CCCCEEEEEEEeCCCCeEeeeEeccCCCCCCeeCHHHHHHHHHHH
Confidence 455677777775 566665 333222 234678999999987754
No 19
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=37.03 E-value=77 Score=27.80 Aligned_cols=39 Identities=21% Similarity=0.379 Sum_probs=24.7
Q ss_pred eEEEEEEcCCCceEe-ccccccCCc-cchHHHHHHHHHhhHH
Q 039495 184 GAGGIVRDESGKWIL-GYSKNLGTS-NSLASELWALYHGLNL 223 (327)
Q Consensus 184 G~G~ViRD~~G~~l~-~~~~~~~~~-s~~~AE~~Al~~AL~~ 223 (327)
.+|+||.+ +|+++. +.....+.. ...+||..|+..|.+.
T Consensus 34 pvGAVIV~-~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~ 74 (172)
T PRK10860 34 PVGAVLVH-NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLV 74 (172)
T ss_pred CEEEEEEe-CCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHh
Confidence 46667775 577776 333333322 4568999999988653
No 20
>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=35.34 E-value=63 Score=24.92 Aligned_cols=44 Identities=25% Similarity=0.422 Sum_probs=29.3
Q ss_pred CCceeEEEEEEcCCCceEe-cccccc-CCccchHHHHHHHHHhhHH
Q 039495 180 QGSAGAGGIVRDESGKWIL-GYSKNL-GTSNSLASELWALYHGLNL 223 (327)
Q Consensus 180 ~~~aG~G~ViRD~~G~~l~-~~~~~~-~~~s~~~AE~~Al~~AL~~ 223 (327)
.+...+|+++.+++|..+. +..... +......||..|+..+-+.
T Consensus 21 ~~~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~ 66 (102)
T PF00383_consen 21 CGNFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN 66 (102)
T ss_dssp TTSSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT
T ss_pred cCCCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh
Confidence 3556789999997666665 444333 2335679999998887765
No 21
>cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. 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. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.
Probab=30.40 E-value=1.1e+02 Score=24.36 Aligned_cols=42 Identities=14% Similarity=0.172 Sum_probs=31.0
Q ss_pred CceeEEEEEEcCCCceEeccccccC-CccchHHHHHHHHHhhH
Q 039495 181 GSAGAGGIVRDESGKWILGYSKNLG-TSNSLASELWALYHGLN 222 (327)
Q Consensus 181 ~~aG~G~ViRD~~G~~l~~~~~~~~-~~s~~~AE~~Al~~AL~ 222 (327)
+...+|+++++.+|.++.+...... ......||..|+..+..
T Consensus 16 ~~~~vga~i~~~~g~i~~G~n~e~~~~~~~~hAE~~ai~~~~~ 58 (112)
T cd01283 16 SNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVS 58 (112)
T ss_pred CCCeEEEEEEECCCCEEEeEEeecCCCCCCcCHHHHHHHHHHH
Confidence 4567888888888998876654433 34677999999888765
No 22
>PF04920 DUF656: Family of unknown function (DUF656) ; InterPro: IPR007004 This is a family of hypothetical proteins, the majority is from Beet necrotic yellow vein virus.
Probab=27.78 E-value=32 Score=27.80 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=22.5
Q ss_pred eecccceEEEEecccccccCccccCCcchhhhhhccc
Q 039495 64 KIVGPVDVVVSKELYGKACGSHEKGDVNPATETMLSE 100 (327)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (327)
-|+||.+++++.+.------.. .-|++||++++.++
T Consensus 33 idigplgvl~ni~~lfhms~ir-~~di~p~LNkI~si 68 (126)
T PF04920_consen 33 IDIGPLGVLCNIGVLFHMSVIR-RRDIFPWLNKITSI 68 (126)
T ss_pred hcccceeEEEecceeEEEEEEe-ecchhhhhhhccee
Confidence 3689999999966532111122 34888988876443
No 23
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=25.39 E-value=2.2e+02 Score=24.41 Aligned_cols=13 Identities=23% Similarity=0.304 Sum_probs=10.7
Q ss_pred chHHHHHHHHHhh
Q 039495 209 SLASELWALYHGL 221 (327)
Q Consensus 209 ~~~AE~~Al~~AL 221 (327)
..+||..||..+.
T Consensus 67 ~~HAE~nAI~~a~ 79 (151)
T TIGR02571 67 TIHAEMNALLQCA 79 (151)
T ss_pred ccCHHHHHHHHHH
Confidence 3699999999874
No 24
>COG3981 Predicted acetyltransferase [General function prediction only]
Probab=24.28 E-value=3.2e+02 Score=24.16 Aligned_cols=27 Identities=33% Similarity=0.438 Sum_probs=22.9
Q ss_pred HHHHHHhhHHHHhhCceEEEEEEccHh
Q 039495 214 LWALYHGLNLVWERGFRKVLVECNSHE 240 (327)
Q Consensus 214 ~~Al~~AL~~A~~~g~~~Vi~EsDS~~ 240 (327)
-..|+.||+.|+.+|+.+|.+=.|...
T Consensus 116 ~emLkl~L~~ar~lgi~~Vlvtcd~dN 142 (174)
T COG3981 116 KEMLKLALEKARELGIKKVLVTCDKDN 142 (174)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEeCCCC
Confidence 356899999999999999999888643
No 25
>PRK12411 cytidine deaminase; Provisional
Probab=23.59 E-value=2.2e+02 Score=23.77 Aligned_cols=56 Identities=14% Similarity=0.181 Sum_probs=38.2
Q ss_pred ceeEEEEEEcCCCceEeccccccC-CccchHHHHHHHHHhhHHHHhhCceEEEEEEcc
Q 039495 182 SAGAGGIVRDESGKWILGYSKNLG-TSNSLASELWALYHGLNLVWERGFRKVLVECNS 238 (327)
Q Consensus 182 ~aG~G~ViRD~~G~~l~~~~~~~~-~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS 238 (327)
....|+.++..+|+++.+...-.. ..-..-||..|+..++.. -...+..|.+-++.
T Consensus 23 ~~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~-g~~~i~~i~v~~~~ 79 (132)
T PRK12411 23 KFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSE-GDKEFVAIAIVADT 79 (132)
T ss_pred CCceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHC-CCCceEEEEEEeCC
Confidence 345788899999999887653332 224568999998887643 23456777777754
No 26
>PRK05578 cytidine deaminase; Validated
Probab=23.00 E-value=1.9e+02 Score=24.11 Aligned_cols=54 Identities=9% Similarity=0.097 Sum_probs=38.1
Q ss_pred eEEEEEEcCCCceEecccccc-CCccchHHHHHHHHHhhHHHHhhCceEEEEEEcc
Q 039495 184 GAGGIVRDESGKWILGYSKNL-GTSNSLASELWALYHGLNLVWERGFRKVLVECNS 238 (327)
Q Consensus 184 G~G~ViRD~~G~~l~~~~~~~-~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS 238 (327)
..|..+++.+|++..+...-. ...-..-||..|+..++.. -...+..+.+-+|.
T Consensus 25 ~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~-G~~~i~~i~vv~~~ 79 (131)
T PRK05578 25 PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISE-GGGRLVAIACVGET 79 (131)
T ss_pred ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHc-CCCceEEEEEEecC
Confidence 578889999999998775432 2235678999999888743 23356777777765
No 27
>PRK06848 hypothetical protein; Validated
Probab=21.01 E-value=2.7e+02 Score=23.50 Aligned_cols=54 Identities=9% Similarity=0.112 Sum_probs=36.0
Q ss_pred eeEEEEEEcCCCceEeccccccC-CccchHHHHHHHHHhhHHHHhhCceEEEEEEc
Q 039495 183 AGAGGIVRDESGKWILGYSKNLG-TSNSLASELWALYHGLNLVWERGFRKVLVECN 237 (327)
Q Consensus 183 aG~G~ViRD~~G~~l~~~~~~~~-~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsD 237 (327)
..+|+.++..+|++..+...-.. .....-||-.|+..++.. -...+..+.+-++
T Consensus 27 f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~-g~~~i~~i~~v~~ 81 (139)
T PRK06848 27 HHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISE-GDHEIDTIVAVRH 81 (139)
T ss_pred CcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHc-CCCceEEEEEEec
Confidence 46788899999999887654332 235678999999888754 2224555554443
No 28
>PF03259 Robl_LC7: Roadblock/LC7 domain; InterPro: IPR004942 This family includes proteins that are about 100 amino acids long and have been shown to be related []. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions []. This family also includes Golgi-associated MP1 adapter protein (Q9Y2Q5 from SWISSPROT) and MglB from Myxococcus xanthus (Q50883 from SWISSPROT), a protein involved in gliding motility []. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.; PDB: 2B95_B 1Z09_A 2E8J_B 2HZ5_B 3KYE_A 2ZL1_B 1SKO_B 3CPT_B 1VEU_B 1VET_B ....
Probab=20.76 E-value=1.4e+02 Score=22.12 Aligned_cols=59 Identities=19% Similarity=0.175 Sum_probs=31.7
Q ss_pred eeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHH-Hhh---CceEEEEEEccHhh
Q 039495 183 AGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLV-WER---GFRKVLVECNSHEA 241 (327)
Q Consensus 183 aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A-~~~---g~~~Vi~EsDS~~V 241 (327)
+--|.++-|.+|..+..............|.+.+++.+.+.+ .+. .++.+.++++...+
T Consensus 14 gv~~~~l~~~dG~~i~~~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~~~~i 76 (91)
T PF03259_consen 14 GVRGAVLVDKDGLVIASSGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETEKGEI 76 (91)
T ss_dssp TEEEEEEEETTSEEEEETSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEE
T ss_pred CeeEEEEEcCCCCEEEEecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEECCCEE
Confidence 345788889999998861111111122233333333333322 223 47899999987654
No 29
>PF08119 Toxin_31: Scorpion acidic alpha-KTx toxin family; InterPro: IPR012635 This entry represents proteins that are acidic alpha-KTx short chain scorpion toxins. These toxins are named parabutoxins, that binds and inhibit voltage-sensitive potassium channels and inhibit the vertebrate potassium channel Kv1.1 with low affinity. Furthermore, they lack the crucial pore-plugging lysine. In addition, the second important residue of the dyad, the hydrophobic residue (Phe or Tyr) is also missing [].; GO: 0019870 potassium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region
Probab=20.76 E-value=39 Score=21.33 Aligned_cols=7 Identities=71% Similarity=1.578 Sum_probs=5.7
Q ss_pred hcCCCCC
Q 039495 41 VCDGPAA 47 (327)
Q Consensus 41 ~~~~~~~ 47 (327)
|||||..
T Consensus 26 vcdgpqk 32 (37)
T PF08119_consen 26 VCDGPQK 32 (37)
T ss_pred cccCCcc
Confidence 8999964
Done!