Query psy5302
Match_columns 333
No_of_seqs 300 out of 1643
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 23:05:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5302hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.9 9.9E-23 2.2E-27 168.0 12.7 123 97-228 2-146 (154)
2 PRK06548 ribonuclease H; Provi 99.9 1.5E-22 3.3E-27 169.7 12.7 122 96-228 3-143 (161)
3 PRK08719 ribonuclease H; Revie 99.9 3.3E-22 7.1E-27 166.2 13.4 121 97-226 3-146 (147)
4 PF00075 RNase_H: RNase H; In 99.9 1.6E-22 3.5E-27 165.2 10.4 117 97-225 2-131 (132)
5 PRK00203 rnhA ribonuclease H; 99.9 3.9E-22 8.5E-27 166.9 12.3 120 98-229 3-144 (150)
6 KOG3752|consensus 99.8 4.5E-18 9.8E-23 156.4 10.8 126 96-227 210-365 (371)
7 cd06222 RnaseH RNase H (RNase 99.7 3E-17 6.4E-22 131.2 14.1 118 100-225 1-130 (130)
8 PRK13907 rnhA ribonuclease H; 99.7 3.8E-16 8.2E-21 127.2 13.0 116 99-227 2-127 (128)
9 PRK07708 hypothetical protein; 99.7 2.7E-15 5.9E-20 132.4 15.2 141 79-228 56-209 (219)
10 PRK07238 bifunctional RNase H/ 99.5 7.6E-13 1.6E-17 126.9 13.9 118 98-228 2-133 (372)
11 PF13456 RVT_3: Reverse transc 99.2 7.4E-11 1.6E-15 88.7 10.1 82 133-226 1-86 (87)
12 COG3341 Predicted double-stran 97.1 0.00084 1.8E-08 58.1 5.0 171 51-228 14-202 (225)
13 PF13966 zf-RVT: zinc-binding 96.4 0.0024 5.1E-08 48.0 2.3 40 292-331 39-82 (86)
14 PF05380 Peptidase_A17: Pao re 79.9 4.5 9.8E-05 33.8 5.5 52 97-150 80-143 (159)
15 PF01693 Cauli_VI: Caulimoviru 76.6 0.18 3.8E-06 32.7 -3.2 35 51-85 9-43 (44)
16 PF00336 DNA_pol_viral_C: DNA 57.2 13 0.00028 32.4 3.4 90 94-207 90-182 (245)
17 COG0296 GlgB 1,4-alpha-glucan 43.6 27 0.00057 36.0 3.8 34 184-217 213-247 (628)
18 PF05741 zf-nanos: Nanos RNA b 37.0 18 0.0004 24.6 1.0 21 310-330 34-54 (55)
19 PF08274 PhnA_Zn_Ribbon: PhnA 35.0 16 0.00034 21.6 0.4 21 310-330 3-24 (30)
20 PF13696 zf-CCHC_2: Zinc knuck 31.8 28 0.0006 20.9 1.1 20 309-331 8-27 (32)
21 TIGR00100 hypA hydrogenase nic 31.1 23 0.0005 27.9 0.9 20 310-329 71-90 (115)
22 PF01396 zf-C4_Topoisom: Topoi 30.4 34 0.00073 21.4 1.4 22 311-332 3-28 (39)
23 PF13917 zf-CCHC_3: Zinc knuck 30.1 33 0.00072 21.9 1.3 18 309-329 4-21 (42)
24 PF00098 zf-CCHC: Zinc knuckle 29.3 45 0.00098 17.0 1.5 17 311-330 2-18 (18)
25 KOG3752|consensus 29.3 23 0.00049 33.8 0.7 92 51-150 35-142 (371)
26 PRK03824 hypA hydrogenase nick 27.8 28 0.00062 28.3 0.9 8 310-317 108-115 (135)
27 COG2093 DNA-directed RNA polym 27.1 45 0.00097 23.3 1.6 18 303-320 12-29 (64)
28 PRK03681 hypA hydrogenase nick 25.5 32 0.0007 27.1 0.8 7 311-317 72-78 (114)
29 KOG1812|consensus 23.5 2E+02 0.0044 27.7 6.0 38 131-173 47-84 (384)
30 KOG2212|consensus 20.4 71 0.0015 30.4 2.1 44 56-106 73-116 (504)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.89 E-value=9.9e-23 Score=167.95 Aligned_cols=123 Identities=22% Similarity=0.234 Sum_probs=96.5
Q ss_pred CcEEEEecCCCC--CCCcceEEe--cCc--eeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHH
Q psy5302 97 DSTVIYTDASKT--DVAVSSAFC--SQD--IKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSA 170 (333)
Q Consensus 97 ~~~~iytDGS~~--~~~~G~g~~--~~~--~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~ 170 (333)
..+.||||||+. +|..|+|+| .+. ...+.... .+|+++||+.|++.||+.+.+.+.. . |.|+|||++|
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~---~--v~l~tDS~yv 75 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGAC---E--VTLYTDSKYV 75 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCc---e--EEEEecHHHH
Confidence 358999999975 455788877 232 23455555 8999999999999999999985543 4 9999999999
Q ss_pred HHHHcCCCCC----------------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302 171 LQTLQNVFSL----------------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST 228 (333)
Q Consensus 171 ~~~l~~~~~~----------------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~ 228 (333)
+++|..|..+ .++++++.+++ .....|.+.|||||+|.++||+||+||+.|+...
T Consensus 76 ~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~---~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 76 VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELL---KRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHhhccccCccccccCccccHHHHHHHHHHH---hhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 9999855221 12455555554 5555899999999999999999999999998765
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.89 E-value=1.5e-22 Score=169.68 Aligned_cols=122 Identities=25% Similarity=0.237 Sum_probs=90.0
Q ss_pred CCcEEEEecCCCCC--CCcceEEe-cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302 96 VDSTVIYTDASKTD--VAVSSAFC-SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ 172 (333)
Q Consensus 96 ~~~~~iytDGS~~~--~~~G~g~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~ 172 (333)
+..+.||||||+.. +..|+|++ .+....+.. ....|++.|||.|++.||+.+.... ..|.|+|||++|++
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~-~~~~TNnraEl~Aii~aL~~~~~~~------~~v~I~TDS~yvi~ 75 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGG-WDIATNNIAELTAVRELLIATRHTD------RPILILSDSKYVIN 75 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccC-CCCCCHHHHHHHHHHHHHHhhhcCC------ceEEEEeChHHHHH
Confidence 34599999999864 44788877 322222222 2368999999999999998654321 23999999999999
Q ss_pred HHcC---------CCCC-------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302 173 TLQN---------VFSL-------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST 228 (333)
Q Consensus 173 ~l~~---------~~~~-------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~ 228 (333)
++.. |... .+++++|..++ ....|.|.|||||+|++|||.||+||++|+...
T Consensus 76 ~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~----~~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 76 SLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLM----ENRNIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHH----hcCceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 9983 3322 23555555554 234799999999999999999999999999765
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.88 E-value=3.3e-22 Score=166.21 Aligned_cols=121 Identities=22% Similarity=0.263 Sum_probs=87.7
Q ss_pred CcEEEEecCCCCCCC-----cceEEe--c--Cce--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEe
Q psy5302 97 DSTVIYTDASKTDVA-----VSSAFC--S--QDI--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICS 165 (333)
Q Consensus 97 ~~~~iytDGS~~~~~-----~G~g~~--~--~~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~s 165 (333)
..++||||||+..++ .|+|++ . +.. ..+..+....|++.||+.|++.||+.+.. . ..|+|
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~-------~--~~i~t 73 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD-------G--DVIYS 73 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC-------C--CEEEe
Confidence 568999999986433 488876 2 232 24455656689999999999999999854 2 57999
Q ss_pred CcHHHHHHHcC---------CCCCch--H-HHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhc
Q psy5302 166 DSLSALQTLQN---------VFSLNP--I-ASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALT 226 (333)
Q Consensus 166 Ds~~~~~~l~~---------~~~~~~--~-~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~ 226 (333)
||++|+++++. |....+ + -.++++.+........|+|.|||||+|++|||.||+||++|+.
T Consensus 74 DS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 74 DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred chHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 99999999842 222211 1 1233333332223567999999999999999999999999975
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=99.88 E-value=1.6e-22 Score=165.23 Aligned_cols=117 Identities=38% Similarity=0.529 Sum_probs=90.4
Q ss_pred CcEEEEecCCCCC--CCcceEEe-cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHHH
Q psy5302 97 DSTVIYTDASKTD--VAVSSAFC-SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQT 173 (333)
Q Consensus 97 ~~~~iytDGS~~~--~~~G~g~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~~ 173 (333)
..++||||||+.. +..|+|++ .++...+..++ ..+++.|||.||..||+ +.. . . . +.|+|||++++..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~-~-~---~--v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE-H-R---K--VTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS-T-S---E--EEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh-c-c---c--ccccccHHHHHHH
Confidence 4689999999653 33566665 33345555566 88999999999999999 442 2 2 3 9999999999998
Q ss_pred HcC-----CC-CC--c-hHHHHHHHHHHhhcCCCceEEEEecCCCCC-ccchhhhHHHHHHh
Q psy5302 174 LQN-----VF-SL--N-PIASEIRNLILENKSKLSIRFIWVPSHVGI-AGNEEADRLAKEAL 225 (333)
Q Consensus 174 l~~-----~~-~~--~-~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~-~gNe~AD~lAk~a~ 225 (333)
+.. .. .. . ++..+|++++ ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus 73 l~~~~~~~~~~~~~~~~~i~~~i~~~~---~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 73 LNKWLHGNGWKKTSNGRPIKNEIWELL---SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHTHHHHTTSBSCTSSSBHTHHHHHHH---HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHhccccccccccccccchhheeecc---ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 777 22 11 2 4777888887 44788999999999999 69999999999987
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.88 E-value=3.9e-22 Score=166.94 Aligned_cols=120 Identities=19% Similarity=0.215 Sum_probs=90.4
Q ss_pred cEEEEecCCCCC--CCcceEEe--cCc-e-eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHH
Q psy5302 98 STVIYTDASKTD--VAVSSAFC--SQD-I-KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSAL 171 (333)
Q Consensus 98 ~~~iytDGS~~~--~~~G~g~~--~~~-~-~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~ 171 (333)
.+.||||||+.. +..|+|+| .++ . ..+... ...|++.|||.|++.||+.+... . . |.|+|||++++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~~--~---~--v~I~tDS~yvi 74 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKEP--C---E--VTLYTDSQYVR 74 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCCC--C---e--EEEEECHHHHH
Confidence 489999999864 34778876 222 2 223333 46789999999999999987542 1 3 99999999999
Q ss_pred HHHcCC---------CCC-------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCCC
Q psy5302 172 QTLQNV---------FSL-------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTH 229 (333)
Q Consensus 172 ~~l~~~---------~~~-------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~~ 229 (333)
++|..| ... .+++++|.+++ ....|.|.|||||+|++||+.||+|||+|+....
T Consensus 75 ~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~----~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 75 QGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL----KRHQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHh----ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 999863 211 13556666554 3368999999999999999999999999998763
No 6
>KOG3752|consensus
Probab=99.75 E-value=4.5e-18 Score=156.37 Aligned_cols=126 Identities=27% Similarity=0.287 Sum_probs=98.0
Q ss_pred CCcEEEEecCCCCCC-----CcceEEe--cC-ceeEEeecC-CCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeC
Q psy5302 96 VDSTVIYTDASKTDV-----AVSSAFC--SQ-DIKFSTRLH-SLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSD 166 (333)
Q Consensus 96 ~~~~~iytDGS~~~~-----~~G~g~~--~~-~~~~~~~l~-~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sD 166 (333)
.+..++|||||+..+ .+|+|++ ++ ....++.+. ..+++|.|||.|+..||+.+.+.... + ++|.||
T Consensus 210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~---k--v~I~TD 284 (371)
T KOG3752|consen 210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNIN---K--VVIRTD 284 (371)
T ss_pred ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCC---c--EEEEec
Confidence 344899999997642 3899988 32 345677765 78999999999999999999886654 4 999999
Q ss_pred cHHHHHHHcCCCCC-----------ch----------HHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302 167 SLSALQTLQNVFSL-----------NP----------IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225 (333)
Q Consensus 167 s~~~~~~l~~~~~~-----------~~----------~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~ 225 (333)
|+.++++|+.|.+. ++ .+..+.++++. ....+|.+.||+||.|+.|||+||.||++++
T Consensus 285 S~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~-~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs 363 (371)
T KOG3752|consen 285 SEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQE-ISNKKVQQEYVGGHSGILGNEMADALARKGS 363 (371)
T ss_pred hHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhh-hccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence 99999999876542 11 33444444411 1468999999999999999999999999986
Q ss_pred cC
Q psy5302 226 TS 227 (333)
Q Consensus 226 ~~ 227 (333)
..
T Consensus 364 ~~ 365 (371)
T KOG3752|consen 364 TL 365 (371)
T ss_pred hh
Confidence 54
No 7
>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=99.75 E-value=3e-17 Score=131.24 Aligned_cols=118 Identities=31% Similarity=0.389 Sum_probs=90.6
Q ss_pred EEEecCCCCCC--CcceEEe--cC-c-ee-EEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302 100 VIYTDASKTDV--AVSSAFC--SQ-D-IK-FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ 172 (333)
Q Consensus 100 ~iytDGS~~~~--~~G~g~~--~~-~-~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~ 172 (333)
.+|||||...+ ++|+|++ +. . .. .........+++.+|+.|++.||+.+...... . +.|++||+.++.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~---~--i~i~~Ds~~~~~ 75 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGK---K--VNIYTDSQYVIN 75 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCc---e--EEEEECHHHHHH
Confidence 48999998654 6888877 22 2 22 22222257899999999999999999865544 4 999999999999
Q ss_pred HHcCCCC-Cc----hHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302 173 TLQNVFS-LN----PIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225 (333)
Q Consensus 173 ~l~~~~~-~~----~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~ 225 (333)
.++++.. .. .++..+.+++ .....+.|.|||+|+|..+|+.||.|||+|.
T Consensus 76 ~~~~~~~~~~~~~~~~~~~i~~~~---~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 76 ALTGWYEGKPVKNVDLWQRLLALL---KRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HhhccccCCChhhHHHHHHHHHHH---hCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 9998764 11 2445555544 5678899999999999999999999999874
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.69 E-value=3.8e-16 Score=127.20 Aligned_cols=116 Identities=23% Similarity=0.326 Sum_probs=89.0
Q ss_pred EEEEecCCCCC--CCcceEEe--cC-c-eeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302 99 TVIYTDASKTD--VAVSSAFC--SQ-D-IKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ 172 (333)
Q Consensus 99 ~~iytDGS~~~--~~~G~g~~--~~-~-~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~ 172 (333)
+.||||||... +..|+|+| +. + ...++.. ...+++.||+.|++.||+.+...+.. . +.|+|||+.++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g~~---~--v~i~sDS~~vi~ 75 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHNYN---I--VSFRTDSQLVER 75 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCCCC---E--EEEEechHHHHH
Confidence 67999999764 45889987 32 2 2233322 35789999999999999999987765 4 999999999999
Q ss_pred HHcCCCCCc----hHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcC
Q psy5302 173 TLQNVFSLN----PIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTS 227 (333)
Q Consensus 173 ~l~~~~~~~----~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~ 227 (333)
.+++..... ++++++..++ .....+.|.|||. +.|+.||.||++|...
T Consensus 76 ~~~~~~~~~~~~~~l~~~~~~l~---~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 76 AVEKEYAKNKMFAPLLEEALQYI---KSFDLFFIKWIPS----SQNKVADELARKAILQ 127 (128)
T ss_pred HHhHHHhcChhHHHHHHHHHHHH---hcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence 999855432 3555555554 5566788899995 6999999999999753
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.66 E-value=2.7e-15 Score=132.41 Aligned_cols=141 Identities=17% Similarity=0.187 Sum_probs=99.1
Q ss_pred ChHHHHHHHHHHHhhCCCCcEEEEecCCCC--CCCcceEEe--c--Ccee----EEeecCCCcchHHHHHHHHHHHHHHH
Q psy5302 79 PKEEINISFQELLQQVPVDSTVIYTDASKT--DVAVSSAFC--S--QDIK----FSTRLHSLLSICNAELTSILFAIHFL 148 (333)
Q Consensus 79 ~~~~a~~~~~~~~~~~~~~~~~iytDGS~~--~~~~G~g~~--~--~~~~----~~~~l~~~~s~~~AEl~Ai~~al~~~ 148 (333)
+.+|.++...++ ...++.+++|+|||.. ++.+|+|++ . +... ....++...+++.||+.|++.||+.+
T Consensus 56 ~~k~~~~~~~~~--~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A 133 (219)
T PRK07708 56 SLKELKKLSKEV--EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQEL 133 (219)
T ss_pred eHHHHhhhhhhh--ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHH
Confidence 444555444443 2334679999999975 456888876 2 2222 12345556899999999999999999
Q ss_pred hhhccCcCCcceEEEEeCcHHHHHHHcCCC-CCchHHHHHHHHHHh--hcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302 149 LSSCLNEHTQACFVICSDSLSALQTLQNVF-SLNPIASEIRNLILE--NKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225 (333)
Q Consensus 149 ~~~~~~~~~~~~i~I~sDs~~~~~~l~~~~-~~~~~~~~i~~~~~~--~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~ 225 (333)
...+.+ ...|.|++||+.+++.+++.. ..++....+.+.+.. ......+.|.||| +..|+.||+||++|+
T Consensus 134 ~e~g~~---~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al 206 (219)
T PRK07708 134 EELGVK---HEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQAL 206 (219)
T ss_pred HHcCCC---cceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHH
Confidence 997765 234899999999999998854 344444444333322 2334457889998 788999999999999
Q ss_pred cCC
Q psy5302 226 TST 228 (333)
Q Consensus 226 ~~~ 228 (333)
...
T Consensus 207 ~~~ 209 (219)
T PRK07708 207 EGT 209 (219)
T ss_pred hcC
Confidence 865
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.46 E-value=7.6e-13 Score=126.87 Aligned_cols=118 Identities=18% Similarity=0.271 Sum_probs=89.1
Q ss_pred cEEEEecCCCCC--CCcceEEe--c--Cc-e--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcH
Q psy5302 98 STVIYTDASKTD--VAVSSAFC--S--QD-I--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSL 168 (333)
Q Consensus 98 ~~~iytDGS~~~--~~~G~g~~--~--~~-~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~ 168 (333)
.+.||||||... +.+|+|++ + +. . .....++ ..|++.||+.|++.||+.+.+.+.+ . |.|++||+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~---~--v~i~~DS~ 75 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGAT---E--VEVRMDSK 75 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCC---e--EEEEeCcH
Confidence 378999999764 45888877 3 22 2 2233344 6788999999999999999987765 4 99999999
Q ss_pred HHHHHHcCCCC-Cch----HHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302 169 SALQTLQNVFS-LNP----IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST 228 (333)
Q Consensus 169 ~~~~~l~~~~~-~~~----~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~ 228 (333)
.++..+++... ++. ++.++.++ ......|.|.||| ..+|+.||.||+.|....
T Consensus 76 lvi~~i~~~~~~~~~~l~~~~~~i~~l---~~~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 76 LVVEQMSGRWKVKHPDMKPLAAQAREL---ASQFGRVTYTWIP----RARNAHADRLANEAMDAA 133 (372)
T ss_pred HHHHHhCCCCccCChHHHHHHHHHHHH---HhcCCceEEEECC----chhhhHHHHHHHHHHHhh
Confidence 99999987543 333 23334443 3566789999999 489999999999997655
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.24 E-value=7.4e-11 Score=88.70 Aligned_cols=82 Identities=26% Similarity=0.333 Sum_probs=65.4
Q ss_pred hHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHHHHcCCCCC-c---hHHHHHHHHHHhhcCCCceEEEEecCC
Q psy5302 133 ICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSL-N---PIASEIRNLILENKSKLSIRFIWVPSH 208 (333)
Q Consensus 133 ~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~~l~~~~~~-~---~~~~~i~~~~~~~~~~~~v~~~wVp~H 208 (333)
+..||+.|+..||+.+.+.+.. + |.|.|||+.++..+++.... + .++..|..++ .....+.|.|||
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~---~--i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~---~~~~~~~~~~i~-- 70 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIR---K--IIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLL---DRFWNVSVSHIP-- 70 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-S---C--EEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHH---CCCSCEEEEE----
T ss_pred CcHHHHHHHHHHHHHHHHCCCC---E--EEEEecCccccccccccccccccccccchhhhhhh---ccccceEEEEEC--
Confidence 4689999999999999998876 5 99999999999999887432 2 3566666665 668899999999
Q ss_pred CCCccchhhhHHHHHHhc
Q psy5302 209 VGIAGNEEADRLAKEALT 226 (333)
Q Consensus 209 ~g~~gNe~AD~lAk~a~~ 226 (333)
.++|..||.|||.|..
T Consensus 71 --r~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 71 --REQNKVADALAKFALS 86 (87)
T ss_dssp --GGGSHHHHHHHHHHHH
T ss_pred --hHHhHHHHHHHHHHhh
Confidence 8999999999999864
No 12
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=97.08 E-value=0.00084 Score=58.13 Aligned_cols=171 Identities=8% Similarity=0.017 Sum_probs=107.0
Q ss_pred CCCCCCCCCCCCCCccccccccccCCCCChHHHHHHHHHHHh----hCCCCcEEEEecCCCC--CCCcceEEecCce--e
Q psy5302 51 PAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQ----QVPVDSTVIYTDASKT--DVAVSSAFCSQDI--K 122 (333)
Q Consensus 51 ~~p~~~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~~~~~~~~----~~~~~~~~iytDGS~~--~~~~G~g~~~~~~--~ 122 (333)
+.|+++..|.+|..+|.+..++.+|++.+.|+|...+..-+. ....+.+.-+.+|+.. ++..++-++.+.. .
T Consensus 14 R~tGIyktW~Ec~~qVkGy~ga~YKsf~s~EeA~a~~~g~i~~~tp~~~~e~~i~~~~G~y~~~p~t~~~k~yr~k~~~~ 93 (225)
T COG3341 14 RKTGIYKTWDECEKQVKGYPGAKYKSFKSYEEAEAYCEGNIESVTPYLDFEYIISWAKGDYDAKPGTQEFKEYRGKCTIE 93 (225)
T ss_pred cccceeccHHHHHHHhcCCCcccccccccHHHHHHHhccCccccCcccchhccceeccCCccccCCCcceeEEecccccc
Confidence 579999999999999999999999999999999966552111 1123445667778753 2223333332211 1
Q ss_pred -----EEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEE----eCcHHHHHHHcCCCCC-chHHHHHHHHHH
Q psy5302 123 -----FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVIC----SDSLSALQTLQNVFSL-NPIASEIRNLIL 192 (333)
Q Consensus 123 -----~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~----sDs~~~~~~l~~~~~~-~~~~~~i~~~~~ 192 (333)
..... ...++..+|.+|++.+|+.+.....+ +.++++ .||++...-+.+-... ..+... .+..
T Consensus 94 ~~~lt~~~~~-~~~~n~s~d~la~ly~~~~~~~~~nr----k~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~~-~e~~- 166 (225)
T COG3341 94 YSWLTESSEF-SIKSNDSGDVLAKLYGLRYEVPLDNR----KSVINYLTPGNDSWAYFKYVKDKCETKVNLLKD-REFF- 166 (225)
T ss_pred ceeeeeeccc-ccccCchHHHHHHhccccccccccCc----cceeeccCCcchhHHHHHHHhhhhhhHHHHHHh-HHhh-
Confidence 11111 23456689999999999998875433 224446 6888777666543311 111111 1110
Q ss_pred hhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302 193 ENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST 228 (333)
Q Consensus 193 ~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~ 228 (333)
....+....+.|+--|.++.-+..++.++.......
T Consensus 167 ~~~~~v~h~~k~i~~~~~~~~~~~~~s~~~~~~k~~ 202 (225)
T COG3341 167 SIGKGVFHDEKDINIHIWIFESKKGNSHVYNTSKKE 202 (225)
T ss_pred hccchhhhhhhhcccccccchhhhhhhhhhchhhhh
Confidence 012234566788999999988888888887766655
No 13
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.36 E-value=0.0024 Score=47.96 Aligned_cols=40 Identities=20% Similarity=0.347 Sum_probs=29.3
Q ss_pred eecccccc---cccccCCCCCCCCCCCCC-ccccceeccccCCC
Q psy5302 292 RIGHTNTT---HIHLMKKENPPICVPCGC-VMSVKHIHINRLPN 331 (333)
Q Consensus 292 RTGH~~l~---~~~r~~~~~~~~C~~Cg~-~et~~H~l~~Cp~~ 331 (333)
+.-|..+. -+.+.+...++.|..|+. .||++|+|++||..
T Consensus 39 ~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a 82 (86)
T PF13966_consen 39 RALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFA 82 (86)
T ss_pred eeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCc
Confidence 34445542 234556667799999995 89999999999975
No 14
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=79.91 E-value=4.5 Score=33.83 Aligned_cols=52 Identities=17% Similarity=0.282 Sum_probs=33.6
Q ss_pred CcEEEEecCCCCCCCcceEEe-----cCcee-----EEeec-C-CCcchHHHHHHHHHHHHHHHhh
Q psy5302 97 DSTVIYTDASKTDVAVSSAFC-----SQDIK-----FSTRL-H-SLLSICNAELTSILFAIHFLLS 150 (333)
Q Consensus 97 ~~~~iytDGS~~~~~~G~g~~-----~~~~~-----~~~~l-~-~~~s~~~AEl~Ai~~al~~~~~ 150 (333)
..+.+|+|+|.. +.|+.++ ++... ...++ + ...|+-+-||.|+..|.+++..
T Consensus 80 ~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 468999999953 4454444 12221 11112 1 2458999999999999988865
No 15
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=76.58 E-value=0.18 Score=32.70 Aligned_cols=35 Identities=17% Similarity=0.119 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCCCCccccccccccCCCCChHHHHH
Q psy5302 51 PAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINI 85 (333)
Q Consensus 51 ~~p~~~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~ 85 (333)
.+|+++..|..|.++|++......|++.+.++|..
T Consensus 9 ~~~GIy~~W~~~~~~v~g~~ga~~k~F~t~~eA~~ 43 (44)
T PF01693_consen 9 RQPGIYTSWAECKKQVSGYPGAIYKSFKTREEAEE 43 (44)
T ss_dssp SS-EEECCHHHHHHHCTT-TT-EEEEESSHHHHHH
T ss_pred CCCCeECCHHHHHHHhCCCCCceECCcCCHHHHhh
Confidence 46899999999999999998888999999999873
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=57.21 E-value=13 Score=32.39 Aligned_cols=90 Identities=20% Similarity=0.222 Sum_probs=50.2
Q ss_pred CCCCcEEEEecCCCCCCCcceEEe-cCc-eeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHH
Q psy5302 94 VPVDSTVIYTDASKTDVAVSSAFC-SQD-IKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSAL 171 (333)
Q Consensus 94 ~~~~~~~iytDGS~~~~~~G~g~~-~~~-~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~ 171 (333)
....--.||+|+.-. |+|+. .++ ..+.+.. .-.+..+||.|.-.|.-+. +. + + |.|||..|+
T Consensus 90 qr~~lc~VfaDATpT----gwgi~i~~~~~~~Tfs~--~l~IhtaELlaaClAr~~~---~~----r--~-l~tDnt~Vl 153 (245)
T PF00336_consen 90 QRPGLCQVFADATPT----GWGISITGQRMRGTFSK--PLPIHTAELLAACLARLMS---GA----R--C-LGTDNTVVL 153 (245)
T ss_pred CCCCCCceeccCCCC----cceeeecCceeeeeecc--cccchHHHHHHHHHHHhcc---CC----c--E-EeecCcEEE
Confidence 344566899998754 44433 222 2333432 3468899999987765443 22 2 4 999998665
Q ss_pred HHHcCCCCCch-HHHHHHHHHHhhcCCCceEEEEecC
Q psy5302 172 QTLQNVFSLNP-IASEIRNLILENKSKLSIRFIWVPS 207 (333)
Q Consensus 172 ~~l~~~~~~~~-~~~~i~~~~~~~~~~~~v~~~wVp~ 207 (333)
.. ....-+ .+-..-+.+ -..+.|..||+
T Consensus 154 sr---kyts~PW~lac~A~wi-----Lrgts~~yVPS 182 (245)
T PF00336_consen 154 SR---KYTSFPWLLACAANWI-----LRGTSFYYVPS 182 (245)
T ss_pred ec---ccccCcHHHHHHHHHh-----hcCceEEEecc
Confidence 32 222212 222223333 23478889995
No 17
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=43.61 E-value=27 Score=35.98 Aligned_cols=34 Identities=24% Similarity=0.486 Sum_probs=27.2
Q ss_pred HHHHHHHHHh-hcCCCceEEEEecCCCCCccchhh
Q psy5302 184 ASEIRNLILE-NKSKLSIRFIWVPSHVGIAGNEEA 217 (333)
Q Consensus 184 ~~~i~~~~~~-~~~~~~v~~~wVp~H~g~~gNe~A 217 (333)
-..++.+++. .+.++.|-+-|||+|.+..||-.+
T Consensus 213 Pedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 213 PEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 4555566654 889999999999999999888755
No 18
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=37.05 E-value=18 Score=24.58 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=10.1
Q ss_pred CCCCCCCCccccceeccccCC
Q psy5302 310 PICVPCGCVMSVKHIHINRLP 330 (333)
Q Consensus 310 ~~C~~Cg~~et~~H~l~~Cp~ 330 (333)
-.|+.||+..+-.|....||+
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 379999999899999999996
No 19
>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=34.99 E-value=16 Score=21.60 Aligned_cols=21 Identities=19% Similarity=0.298 Sum_probs=8.9
Q ss_pred CCCCCCCCccc-cceeccccCC
Q psy5302 310 PICVPCGCVMS-VKHIHINRLP 330 (333)
Q Consensus 310 ~~C~~Cg~~et-~~H~l~~Cp~ 330 (333)
|.|+.|+.+.+ .+.-++-||.
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 67889987643 6666777774
No 20
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=31.80 E-value=28 Score=20.91 Aligned_cols=20 Identities=25% Similarity=0.321 Sum_probs=15.7
Q ss_pred CCCCCCCCCccccceeccccCCC
Q psy5302 309 PPICVPCGCVMSVKHIHINRLPN 331 (333)
Q Consensus 309 ~~~C~~Cg~~et~~H~l~~Cp~~ 331 (333)
.-.|..|+... |++-.||..
T Consensus 8 ~Y~C~~C~~~G---H~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKG---HWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCC---ccHhHCCCC
Confidence 45688888655 999999975
No 21
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=31.09 E-value=23 Score=27.95 Aligned_cols=20 Identities=15% Similarity=0.011 Sum_probs=9.0
Q ss_pred CCCCCCCCccccceeccccC
Q psy5302 310 PICVPCGCVMSVKHIHINRL 329 (333)
Q Consensus 310 ~~C~~Cg~~et~~H~l~~Cp 329 (333)
..|..||..-++....+.||
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP 90 (115)
T TIGR00100 71 CECEDCSEEVSPEIDLYRCP 90 (115)
T ss_pred EEcccCCCEEecCCcCccCc
Confidence 34555554433333344455
No 22
>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=30.40 E-value=34 Score=21.36 Aligned_cols=22 Identities=18% Similarity=0.187 Sum_probs=15.1
Q ss_pred CCCCCCCc----cccceeccccCCCC
Q psy5302 311 ICVPCGCV----MSVKHIHINRLPNL 332 (333)
Q Consensus 311 ~C~~Cg~~----et~~H~l~~Cp~~~ 332 (333)
.|+.||.. .+-.=.++.|..|+
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP 28 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYP 28 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCC
Confidence 68888863 34444778888885
No 23
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=30.07 E-value=33 Score=21.94 Aligned_cols=18 Identities=22% Similarity=0.313 Sum_probs=14.4
Q ss_pred CCCCCCCCCccccceeccccC
Q psy5302 309 PPICVPCGCVMSVKHIHINRL 329 (333)
Q Consensus 309 ~~~C~~Cg~~et~~H~l~~Cp 329 (333)
...|..|+.. .|+-++||
T Consensus 4 ~~~CqkC~~~---GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQK---GHWTYECP 21 (42)
T ss_pred CCcCcccCCC---CcchhhCC
Confidence 4678889854 59999999
No 24
>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=29.32 E-value=45 Score=17.00 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=11.9
Q ss_pred CCCCCCCccccceeccccCC
Q psy5302 311 ICVPCGCVMSVKHIHINRLP 330 (333)
Q Consensus 311 ~C~~Cg~~et~~H~l~~Cp~ 330 (333)
.|..||. ..|+..+||.
T Consensus 2 ~C~~C~~---~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGE---PGHIARDCPK 18 (18)
T ss_dssp BCTTTSC---SSSCGCTSSS
T ss_pred cCcCCCC---cCcccccCcc
Confidence 4666764 4688888984
No 25
>KOG3752|consensus
Probab=29.31 E-value=23 Score=33.78 Aligned_cols=92 Identities=18% Similarity=0.066 Sum_probs=56.7
Q ss_pred CCCCCCCCCCCCCCccccccccccCCCCChHHHHHHHHHHHhhCCCCcEEEEecCCCCC-------C-CcceEE-e----
Q psy5302 51 PAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTD-------V-AVSSAF-C---- 117 (333)
Q Consensus 51 ~~p~~~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~~~~~~~~~~~~~~~~iytDGS~~~-------~-~~G~g~-~---- 117 (333)
...+++..|.+|+.+|+.+....+|.+++.+||.+.+. + . .+ -++=+|... | ..+... +
T Consensus 35 r~~Gvy~tw~e~k~qv~~y~~~~~kkf~t~~eA~sf~~-~-~-~~-----t~~~~s~~~~~~~vs~g~~~~~~a~~~~~~ 106 (371)
T KOG3752|consen 35 RKTGVYSTWDECKEQVDGYGNARYKKFTTEEEAQSFVR-I-T-RP-----TFTKSSSPQRTDAVSSGPQRQSVASFTSNM 106 (371)
T ss_pred cccccccchHHHHHHHhhcCccchhccccHHHHHHHhc-C-C-Cc-----ccccccccccccccccCCcceeeeeeccch
Confidence 35789999999999999999899999999999986443 2 0 00 012222211 1 111111 0
Q ss_pred -cCce-e-EEeecCCCcchHHHHHHHHHHHHHHHhh
Q psy5302 118 -SQDI-K-FSTRLHSLLSICNAELTSILFAIHFLLS 150 (333)
Q Consensus 118 -~~~~-~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~ 150 (333)
.+.. . ....+...++++.+|..+..+++.....
T Consensus 107 ~~~~~~~~~~s~~~~~~~~~~a~~~~~~~~i~~~r~ 142 (371)
T KOG3752|consen 107 EHNKANKGYYSSRANASSNYSAERTAKSHKIASARS 142 (371)
T ss_pred hhccccccceeecccccchhhhhcccchhhhhhhhh
Confidence 0000 1 1122356778889999999999887654
No 26
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.84 E-value=28 Score=28.27 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=4.9
Q ss_pred CCCCCCCC
Q psy5302 310 PICVPCGC 317 (333)
Q Consensus 310 ~~C~~Cg~ 317 (333)
..||.||.
T Consensus 108 ~~CP~Cgs 115 (135)
T PRK03824 108 LKCPKCGS 115 (135)
T ss_pred cCCcCCCC
Confidence 34777764
No 27
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=27.09 E-value=45 Score=23.27 Aligned_cols=18 Identities=28% Similarity=0.565 Sum_probs=12.8
Q ss_pred ccCCCCCCCCCCCCCccc
Q psy5302 303 LMKKENPPICVPCGCVMS 320 (333)
Q Consensus 303 r~~~~~~~~C~~Cg~~et 320 (333)
|+-.++...|+.||..+.
T Consensus 12 ~l~~~d~e~CP~Cgs~~~ 29 (64)
T COG2093 12 RLTPEDTEICPVCGSTDL 29 (64)
T ss_pred ccCCCCCccCCCCCCccc
Confidence 455566677999997643
No 28
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.46 E-value=32 Score=27.06 Aligned_cols=7 Identities=29% Similarity=0.762 Sum_probs=3.4
Q ss_pred CCCCCCC
Q psy5302 311 ICVPCGC 317 (333)
Q Consensus 311 ~C~~Cg~ 317 (333)
.|..||.
T Consensus 72 ~C~~Cg~ 78 (114)
T PRK03681 72 WCETCQQ 78 (114)
T ss_pred EcccCCC
Confidence 4544554
No 29
>KOG1812|consensus
Probab=23.51 E-value=2e+02 Score=27.74 Aligned_cols=38 Identities=24% Similarity=0.237 Sum_probs=31.4
Q ss_pred cchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHHH
Q psy5302 131 LSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQT 173 (333)
Q Consensus 131 ~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~~ 173 (333)
.+...||+.|+..+|..+...+.. . +++++|+......
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~---~--~~~~~d~~~~~~~ 84 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLN---H--IVIYCDDELIYES 84 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhccc---c--ceEecccHHHHHH
Confidence 678899999999999999998876 5 9999996544443
No 30
>KOG2212|consensus
Probab=20.40 E-value=71 Score=30.39 Aligned_cols=44 Identities=23% Similarity=0.366 Sum_probs=28.1
Q ss_pred CCCCCCCCCccccccccccCCCCChHHHHHHHHHHHhhCCCCcEEEEecCC
Q psy5302 56 SAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDAS 106 (333)
Q Consensus 56 ~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~~~~~~~~~~~~~~~~iytDGS 106 (333)
+-||+++-..|...+. ++.--.+.|.+++.+-..-++.||+|.-
T Consensus 73 ~rPWWeRYQPvSYKL~-------tRSGNE~eF~dMV~RCN~VGVRiyVDvv 116 (504)
T KOG2212|consen 73 FRPWWERYQPVSYKLC-------TRSGNEDEFRDMVTRCNNVGVRIYVDAV 116 (504)
T ss_pred CCCceeecccceEEee-------ccCCCHHHHHHHHHHhhccceEEEehhh
Confidence 4689885444555432 2222233577777777888999999965
Done!