Query psy5177
Match_columns 213
No_of_seqs 160 out of 1294
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 19:18:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5177.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5177hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03184 DDE_1: DDE superfamil 100.0 1.2E-40 2.7E-45 267.1 8.2 190 8-198 1-206 (217)
2 PF13358 DDE_3: DDE superfamil 99.5 1.4E-14 3E-19 108.3 4.6 129 12-170 1-136 (146)
3 KOG3105|consensus 99.2 6.4E-12 1.4E-16 112.6 3.5 176 3-182 228-411 (488)
4 KOG3105|consensus 98.6 1E-08 2.2E-13 92.0 1.4 157 7-172 155-319 (488)
5 COG3335 Transposase and inacti 94.3 0.3 6.4E-06 34.8 7.4 69 85-157 16-85 (132)
6 PF00665 rve: Integrase core d 91.6 0.47 1E-05 33.5 5.0 37 115-151 68-104 (120)
7 PHA02517 putative transposase 87.3 4.1 8.9E-05 33.6 8.2 82 84-168 141-222 (277)
8 PF07592 DDE_Tnp_ISAZ013: Rhod 77.0 12 0.00026 31.9 7.0 91 78-169 137-245 (311)
9 PRK09409 IS2 transposase TnpB; 70.7 53 0.0012 27.7 9.6 77 92-173 167-245 (301)
10 PRK14702 insertion element IS2 69.4 36 0.00077 28.1 8.1 77 92-173 128-206 (262)
11 PF07905 PucR: Purine cataboli 63.1 26 0.00055 25.3 5.5 61 84-149 46-109 (123)
12 PLN02941 inositol-tetrakisphos 44.6 41 0.00089 28.9 4.5 56 128-183 38-94 (328)
13 PRK13600 putative ribosomal pr 44.5 68 0.0015 21.7 4.7 34 114-147 30-63 (84)
14 PRK08857 para-aminobenzoate sy 42.5 33 0.00071 26.7 3.4 32 117-149 2-33 (193)
15 PF13701 DDE_Tnp_1_4: Transpos 40.3 95 0.0021 27.8 6.4 51 95-147 198-249 (448)
16 PRK12652 putative monovalent c 38.7 28 0.00062 30.2 2.7 35 124-158 98-137 (357)
17 PLN02335 anthranilate synthase 37.7 50 0.0011 26.5 3.8 36 112-148 16-51 (222)
18 PF02603 Hpr_kinase_N: HPr Ser 37.0 25 0.00053 25.6 1.8 40 112-153 80-119 (127)
19 COG5663 Uncharacterized conser 35.7 24 0.00053 27.4 1.6 54 47-102 6-61 (194)
20 PRK13602 putative ribosomal pr 34.2 65 0.0014 21.5 3.4 34 113-146 27-60 (82)
21 PRK08007 para-aminobenzoate sy 33.3 57 0.0012 25.3 3.4 31 117-148 2-32 (187)
22 COG0290 InfC Translation initi 32.5 99 0.0021 24.0 4.5 50 112-161 16-70 (176)
23 KOG3853|consensus 32.1 53 0.0011 27.3 3.1 88 43-151 175-263 (350)
24 TIGR00566 trpG_papA glutamine 31.8 58 0.0012 25.3 3.3 31 117-148 2-32 (188)
25 PRK05670 anthranilate synthase 29.7 69 0.0015 24.8 3.4 32 117-149 2-33 (189)
26 PRK06774 para-aminobenzoate sy 29.4 70 0.0015 24.8 3.4 31 117-148 2-32 (191)
27 PRK07649 para-aminobenzoate/an 29.0 75 0.0016 24.9 3.5 31 117-148 2-32 (195)
28 PRK06683 hypothetical protein; 28.9 93 0.002 20.8 3.5 34 113-146 27-60 (82)
29 cd01473 vWA_CTRP CTRP for CS 28.2 2.7E+02 0.0058 21.6 6.5 61 88-148 81-148 (192)
30 cd01453 vWA_transcription_fact 27.0 2.6E+02 0.0057 21.4 6.2 61 88-148 82-145 (183)
31 CHL00101 trpG anthranilate syn 26.8 81 0.0018 24.5 3.3 32 117-149 2-33 (190)
32 PF12068 DUF3548: Domain of un 26.2 1.6E+02 0.0035 23.7 4.9 30 95-124 157-186 (213)
33 PF07088 GvpD: GvpD gas vesicl 25.7 2.1E+02 0.0045 25.7 5.8 60 92-158 89-164 (484)
34 PF04914 DltD_C: DltD C-termin 25.7 1.8E+02 0.004 21.3 4.8 44 129-179 39-88 (130)
35 PRK05637 anthranilate synthase 25.4 1.1E+02 0.0024 24.3 3.9 33 116-149 3-35 (208)
36 PRK06895 putative anthranilate 25.4 89 0.0019 24.2 3.3 32 116-148 3-34 (190)
37 COG5410 Uncharacterized protei 25.0 1.9E+02 0.004 23.8 5.0 95 12-123 112-209 (305)
38 PF08459 UvrC_HhH_N: UvrC Heli 24.9 3.1E+02 0.0067 20.8 6.0 51 90-141 54-105 (155)
39 cd01450 vWFA_subfamily_ECM Von 24.2 1.3E+02 0.0029 21.6 4.0 37 113-149 104-142 (161)
40 PF02633 Creatininase: Creatin 23.8 2E+02 0.0044 23.0 5.3 56 91-147 78-137 (237)
41 PF09270 BTD: Beta-trefoil DNA 23.3 57 0.0012 24.9 1.7 23 46-68 74-96 (158)
42 PRK01018 50S ribosomal protein 22.2 1.7E+02 0.0036 20.3 3.8 34 113-146 32-65 (99)
43 PF01248 Ribosomal_L7Ae: Ribos 22.1 2.5E+02 0.0055 18.7 5.1 33 114-146 32-65 (95)
44 TIGR00186 rRNA_methyl_3 rRNA m 21.9 4.3E+02 0.0093 21.3 7.6 43 113-155 88-131 (237)
45 COG3914 Spy Predicted O-linked 21.7 5.1E+02 0.011 24.3 7.6 67 77-148 425-497 (620)
46 PF10087 DUF2325: Uncharacteri 21.7 44 0.00096 22.8 0.8 33 114-146 49-82 (97)
47 KOG4233|consensus 20.8 77 0.0017 21.3 1.7 11 93-103 56-66 (90)
48 PRK05428 HPr kinase/phosphoryl 20.5 4.1E+02 0.0089 22.7 6.5 53 112-174 81-133 (308)
49 COG0313 Predicted methyltransf 20.0 3E+02 0.0065 23.1 5.4 49 99-149 65-116 (275)
No 1
>PF03184 DDE_1: DDE superfamily endonuclease; InterPro: IPR004875 These proteins are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere []. ; GO: 0003676 nucleic acid binding
Probab=100.00 E-value=1.2e-40 Score=267.12 Aligned_cols=190 Identities=28% Similarity=0.442 Sum_probs=151.6
Q ss_pred CCCCCeecCCCCCCC-----CceEEeccccccccccc-CCCCceEEEE-eeeccCCcccCCeEEecccccccccc--cCC
Q psy5177 8 TAYTDYWNPDSLVPP-----PKVVAKKRTKKLGQAAS-AERGELVTMI-GIIRASGEAIPPVFVFPRVFMKDEFL--LGA 78 (213)
Q Consensus 8 ~~~~~I~N~DET~~~-----~~~~~~~g~k~v~~~~~-~~~~~~~Tvl-~~~~a~G~~lpP~~I~~~~~~~~~~~--~~~ 78 (213)
|+|++|||+|||++. .+++...+.+....+.. ...++++|++ +|++++|..+||++|++++.....+. ...
T Consensus 1 y~~~~Ifn~DEt~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~t~~l~~~~a~g~~lpP~vI~~~~~~~~~~~~~~~~ 80 (217)
T PF03184_consen 1 YSPSNIFNMDETGFFYGMPPKKTVVGRSKKNKKRVPGQKSDKRRVTTVLCCNSAGGEKLPPLVIFKGKRPRCFWNDVDDK 80 (217)
T ss_pred CCHHHEEEeccceeeecCCCCceEEEEeecccccceeccCCCcccccceeeecccccccccccccccccccccccccccc
Confidence 789999999999974 45533333222222221 1114456555 55667788899999999988776665 456
Q ss_pred CCCceeeecCCCCccHHHHHHHH-HHHHhhhhcCCCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCCCcCccc
Q psy5177 79 PEGSLGFANKSGWSSTEIFFETI-KHIQNQIKASKENPALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTDELQPLD 157 (213)
Q Consensus 79 ~~~~~~~~s~~gw~~~~~f~~wl-~~f~~~~~~~~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~lQPlD 157 (213)
+.++.|..+++||||.++|++|| +.|.++++ ..++++|||+|++++|.+.++.++|++.||.+++||||+|+.+||||
T Consensus 81 ~~~~~~~~~~~g~~t~~~~~~wl~~~f~~~~~-~~~~~~lLllD~~~~h~~~~~~~~~~~~~i~l~~lP~~~t~~lQPld 159 (217)
T PF03184_consen 81 PLGVYYASSENGWMTTELFLEWLKKVFDPRVK-SPGRPVLLLLDSHSSHISPEFKQLCKSNNIILVFLPPNTTHLLQPLD 159 (217)
T ss_pred cCCcccccccccccccccchhhhhhhhccccc-ccccccccccccccccccccchhhhhccccccceecccccccccccc
Confidence 78999999999999999999999 57999887 46899999999999999999999999999999999999999999999
Q ss_pred ccccHHHHHHHHHHHHHHHhcCCCCC------chhhhhhhHhhHHHh
Q psy5177 158 VAVFSPFKNRLKAGFKKWTSDNPGSS------WPLMAMWPKISESSR 198 (213)
Q Consensus 158 ~~v~~~lK~~~~~~~~~~~~~~~~~~------~t~~~~~~~~~~~~~ 198 (213)
+|+|++||..||+.+.+|+.+..+.. +++.+++..+..+|.
T Consensus 160 ~~v~~~~K~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AW~ 206 (217)
T PF03184_consen 160 VGVFGPFKAHYRKKLLQWIIENGNNPKDFLYKPTLLDAIRWISKAWN 206 (217)
T ss_pred hhhhhhhhHHHHHHHHHHHHhcccccccccCCcCHHHHHHHHHHHHH
Confidence 99999999999999999998876543 456666555555554
No 2
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=99.51 E-value=1.4e-14 Score=108.31 Aligned_cols=129 Identities=24% Similarity=0.337 Sum_probs=103.6
Q ss_pred CeecCCCCCCC-----CceEEecccccccccccCCCCceEEEEeeeccCCcccCCeEEecccccccccccCCCCCceeee
Q psy5177 12 DYWNPDSLVPP-----PKVVAKKRTKKLGQAASAERGELVTMIGIIRASGEAIPPVFVFPRVFMKDEFLLGAPEGSLGFA 86 (213)
Q Consensus 12 ~I~N~DET~~~-----~~~~~~~g~k~v~~~~~~~~~~~~Tvl~~~~a~G~~lpP~~I~~~~~~~~~~~~~~~~~~~~~~ 86 (213)
+|+.+||+++. .+.+..+|.+.. ......+.++++++.|++..|.... .
T Consensus 1 ~vv~~DE~~~~~~~~~~~~w~~~g~~~~-~~~~~~~~~~~~~~~ai~~~~~~~~-~------------------------ 54 (146)
T PF13358_consen 1 RVVFSDESGFNLRPRRGRGWSPKGERPR-VRKSYGRGGRVSVWGAISYNGGIVL-F------------------------ 54 (146)
T ss_pred CEEEEeCCCCccCCCCCceEeeCCceeE-EEEeCCCCCEEEEEEEecccccccc-e------------------------
Confidence 68999999875 677888887743 2334444569999999999985433 1
Q ss_pred cCCCCccHHHHHHHHHHHHhhhhcCCCCCeEEeccCCCcccchHHHHHHHH--cCcEEEeeCCCCCCCcCcccccccHHH
Q psy5177 87 NKSGWSSTEIFFETIKHIQNQIKASKENPALILMDNHETHQSMEAIEYCRA--SGITLLTFPPHKTDELQPLDVAVFSPF 164 (213)
Q Consensus 87 s~~gw~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~~~~H~~~~~~~~~~~--~~i~l~~lP~~~t~~lQPlD~~v~~~l 164 (213)
...|.+|++.|.+||+.+...... ..+++|++||++.|.+..+.+.+++ .++.++++||++.. |+|++ .+++.+
T Consensus 55 ~~~~~~~~~~~~~~l~~~~~~~~~--~~~~~li~DNa~~H~~~~~~~~l~~~~~~~~~~~~P~~sPd-LNpiE-~~w~~l 130 (146)
T PF13358_consen 55 VVEGTMNSEDFIEFLEQLLRPYPR--KGRIVLIMDNASIHKSKKVQEWLEEHERGIELLFLPPYSPD-LNPIE-NVWGYL 130 (146)
T ss_pred eeeeeecccccccccccccccccc--ceEEEEecccccccccccccceeeccccccccccccCcCCc-cCHHH-HHHHHH
Confidence 125688899999999876654432 1189999999999999999999988 99999999999988 78999 899999
Q ss_pred HHHHHH
Q psy5177 165 KNRLKA 170 (213)
Q Consensus 165 K~~~~~ 170 (213)
|..+++
T Consensus 131 k~~~~~ 136 (146)
T PF13358_consen 131 KRRIRR 136 (146)
T ss_pred HHHHHh
Confidence 998887
No 3
>KOG3105|consensus
Probab=99.21 E-value=6.4e-12 Score=112.64 Aligned_cols=176 Identities=16% Similarity=0.173 Sum_probs=130.3
Q ss_pred cccccCCCCCeecCCCCCCC-----CceEEeccccccc-ccccCCCCceEEEEeeeccCCcccCCeEEeccccccccccc
Q psy5177 3 GTACLTAYTDYWNPDSLVPP-----PKVVAKKRTKKLG-QAASAERGELVTMIGIIRASGEAIPPVFVFPRVFMKDEFLL 76 (213)
Q Consensus 3 ~~~~~~~~~~I~N~DET~~~-----~~~~~~~g~k~v~-~~~~~~~~~~~Tvl~~~~a~G~~lpP~~I~~~~~~~~~~~~ 76 (213)
.....|++..++++|||++. ..+.+..|.+.+. ....+....+.|++.++.++|..+||+++++++..+..
T Consensus 228 ~~~~~~~~~~~~~a~~t~~~~~~~~~~~~~~~~~~~v~~V~~~~s~~~h~~~~~~i~~~g~~~p~~~~l~~~~~p~~--- 304 (488)
T KOG3105|consen 228 PELSNYHPSMIFNADETGFQKEFWLRRTLAEMGEKEVELVQSLDSLTHHPTVLPMIRADGSKGPAYIVLPEKKFPPD--- 304 (488)
T ss_pred cccccCChhhccccccchhhhhhhhhcccccccceEEEEEEecCCCCcchHHHHHHhhccCcCcceeeccccCCCCc---
Confidence 34567999999999999864 6778888888874 33334446799999999999999999999987733221
Q ss_pred CCCCCceeeecCCCCccHHHHHHHHH-HHHhhhh-cCCCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCCCcC
Q psy5177 77 GAPEGSLGFANKSGWSSTEIFFETIK-HIQNQIK-ASKENPALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTDELQ 154 (213)
Q Consensus 77 ~~~~~~~~~~s~~gw~~~~~f~~wl~-~f~~~~~-~~~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~lQ 154 (213)
..+....-..-..|| +..++..|+. .+...+. .......+|.+|++++|........+...++....+|+|+|..+|
T Consensus 305 ~~i~~~~k~~~r~~~-~~~l~~~~~~~d~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~s~~~~~~~~~~ip~~~ts~iq 383 (488)
T KOG3105|consen 305 QGIINRFKLEYRAGW-KEHLMEKELMRDWLESCVGLPAVPKKLLAWDSWPEHKEDATKQSLKLLDVDIRVIPGGTTSFIQ 383 (488)
T ss_pred CCcchHHHHHHHhhh-hhhhhhhhhhhhhhhhcccccccccceeeecccHHHHHHHHHHhhhhccccccccCCccceeec
Confidence 111111111223466 6666666653 3444332 122345677779999999999999888789999999999999999
Q ss_pred cccccccHHHHHHHHHHHHHHHhcCCCC
Q psy5177 155 PLDVAVFSPFKNRLKAGFKKWTSDNPGS 182 (213)
Q Consensus 155 PlD~~v~~~lK~~~~~~~~~~~~~~~~~ 182 (213)
|+|+.++.++|...++....+.....+.
T Consensus 384 ~~d~~~~~~~~~~~~~~~~~~~~~~~~~ 411 (488)
T KOG3105|consen 384 PLDVYWNSPWKNLIKKFTADELRAQIDD 411 (488)
T ss_pred ccceeecccchhhhhhhHHHHHHhcccc
Confidence 9999999999999999998888876554
No 4
>KOG3105|consensus
Probab=98.62 E-value=1e-08 Score=92.04 Aligned_cols=157 Identities=13% Similarity=0.045 Sum_probs=105.0
Q ss_pred cCCCCCeecCCCCCCCCceEEecc-cccccccccCCCCceEEEEeeeccCCcc-cCCeEEeccccccccccc---CCCCC
Q psy5177 7 LTAYTDYWNPDSLVPPPKVVAKKR-TKKLGQAASAERGELVTMIGIIRASGEA-IPPVFVFPRVFMKDEFLL---GAPEG 81 (213)
Q Consensus 7 ~~~~~~I~N~DET~~~~~~~~~~g-~k~v~~~~~~~~~~~~Tvl~~~~a~G~~-lpP~~I~~~~~~~~~~~~---~~~~~ 81 (213)
.+.++++|++|||++..+.+...+ ....... ...++++|+++|.+++|.. +|+.++.+...+.+.... ..+..
T Consensus 155 ~~~~~~~~~~~et~l~~~~~~~~~~~as~~~~--~r~k~r~~L~~~~~a~g~~kl~~~~~~k~~~p~~~~~~~~~~~~~~ 232 (488)
T KOG3105|consen 155 DPIPDDILRQKATGLNWKLLPLEGFKASLGWL--KRWKRRHTLVLRRNADGVTKLPLDLKGKKVLPASFFEANNRPELSN 232 (488)
T ss_pred CCchHHHHHHHHHHHHHhhCcccccceecchH--HhhhhhheeeeeeccCccccCcHHHHHHhhchHHHHhhcccccccc
Confidence 456788999999987622222111 0001001 1125789999999999999 777777655544322222 22334
Q ss_pred ceeeecCCCCccHHHHHHHHHHHHhhhhcCCCCCe--EEeccCCCcccchHHHHHHHHcCcE-EEeeCCCCCCCcCcccc
Q psy5177 82 SLGFANKSGWSSTEIFFETIKHIQNQIKASKENPA--LILMDNHETHQSMEAIEYCRASGIT-LLTFPPHKTDELQPLDV 158 (213)
Q Consensus 82 ~~~~~s~~gw~~~~~f~~wl~~f~~~~~~~~~~~~--lLllD~~~~H~~~~~~~~~~~~~i~-l~~lP~~~t~~lQPlD~ 158 (213)
+.+......|++...+..|...+..... .+.+ |+.+|+.+.|.+....-......+. .+++|.. .||+++
T Consensus 233 ~~~~~~~~a~~t~~~~~~~~~~~~~~~~---~~~v~~V~~~~s~~~h~~~~~~i~~~g~~~p~~~~l~~~----~~p~~~ 305 (488)
T KOG3105|consen 233 YHPSMIFNADETGFQKEFWLRRTLAEMG---EKEVELVQSLDSLTHHPTVLPMIRADGSKGPAYIVLPEK----KFPPDQ 305 (488)
T ss_pred CChhhccccccchhhhhhhhhccccccc---ceEEEEEEecCCCCcchHHHHHHhhccCcCcceeecccc----CCCCcC
Confidence 5556667888888888888876544332 3334 8999999999887655554444444 4667766 899999
Q ss_pred cccHHHHHHHHHHH
Q psy5177 159 AVFSPFKNRLKAGF 172 (213)
Q Consensus 159 ~v~~~lK~~~~~~~ 172 (213)
++...+|..||..+
T Consensus 306 ~i~~~~k~~~r~~~ 319 (488)
T KOG3105|consen 306 GIINRFKLEYRAGW 319 (488)
T ss_pred CcchHHHHHHHhhh
Confidence 99999999999987
No 5
>COG3335 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=94.30 E-value=0.3 Score=34.81 Aligned_cols=69 Identities=22% Similarity=0.352 Sum_probs=54.4
Q ss_pred eecCCCCccHHHHHHHHHHHHhhhhcCCCCCeEEeccC-CCcccchHHHHHHHHcCcEEEeeCCCCCCCcCccc
Q psy5177 85 FANKSGWSSTEIFFETIKHIQNQIKASKENPALILMDN-HETHQSMEAIEYCRASGITLLTFPPHKTDELQPLD 157 (213)
Q Consensus 85 ~~s~~gw~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~-~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~lQPlD 157 (213)
.....+.++.+.+..|++.+..... . .+..+++|+ ...|....+...++..+..++++||+++.. .|..
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~flp~y~p~~-n~ie 85 (132)
T COG3335 16 RMGLITEANKKFFIGFLRIYLWLVL--K-KPIVLILDNVASFHRKKALKEDAEENGIHLLFLPPYSPDL-NPIE 85 (132)
T ss_pred EeeeccccCHHHHHHHHHHHhhhhc--c-CceEEEecCCcccchHHHHHHHHHhCCccEEEcCCCCCCc-cHHH
Confidence 3445677889999999987655432 3 678999999 888888889999999999999999999874 3544
No 6
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase 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. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=91.61 E-value=0.47 Score=33.54 Aligned_cols=37 Identities=27% Similarity=0.440 Sum_probs=33.0
Q ss_pred CeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCC
Q psy5177 115 PALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTD 151 (213)
Q Consensus 115 ~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~ 151 (213)
|..|..|+.+...+..+.++|+..+|.+.+.||+..+
T Consensus 68 p~~i~tD~g~~f~~~~~~~~~~~~~i~~~~~~~~~p~ 104 (120)
T PF00665_consen 68 PRVIRTDNGSEFTSHAFEAWCKHLGIKHVFTPPYTPQ 104 (120)
T ss_dssp -SEEEEESCHHHHSHHHHHHHHHHT-EEEESSTSSTH
T ss_pred ceecccccccccccchhhhHHHHcCceEeeCCCCChh
Confidence 8999999999999999999999999999999999854
No 7
>PHA02517 putative transposase OrfB; Reviewed
Probab=87.29 E-value=4.1 Score=33.60 Aligned_cols=82 Identities=11% Similarity=0.058 Sum_probs=54.4
Q ss_pred eeecCCCCccHHHHHHHHHHHHhhhhcCCCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCCCcCcccccccHH
Q psy5177 84 GFANKSGWSSTEIFFETIKHIQNQIKASKENPALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTDELQPLDVAVFSP 163 (213)
Q Consensus 84 ~~~s~~gw~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~lQPlD~~v~~~ 163 (213)
+.+.-+.-++.+...+.|+....... ....+++..|+-+...+..+..+|.+.||...+.+|++..---+++ .+|+.
T Consensus 141 ~~~~~~~~~~~~~~~~~l~~a~~~~~--~~~~~i~~sD~G~~y~s~~~~~~~~~~gi~~~~~~~~~P~~N~~iE-r~~~t 217 (277)
T PHA02517 141 VGWRVSSSMDTDFVLDALEQALWARG--RPGGLIHHSDKGSQYVSLAYTQRLKEAGIRASTGSRGDSYDNAPAE-SINGL 217 (277)
T ss_pred eecccCCCCChHHHHHHHHHHHHhcC--CCcCcEeecccccccchHHHHHHHHHcCcccccCCCCCCCCccccc-hhHhh
Confidence 33444556788888888876433211 1233566688887778889999999999999999999844332333 34555
Q ss_pred HHHHH
Q psy5177 164 FKNRL 168 (213)
Q Consensus 164 lK~~~ 168 (213)
||..+
T Consensus 218 lK~e~ 222 (277)
T PHA02517 218 YKAEV 222 (277)
T ss_pred hhhhh
Confidence 56544
No 8
>PF07592 DDE_Tnp_ISAZ013: Rhodopirellula transposase DDE domain; InterPro: IPR011518 These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=77.01 E-value=12 Score=31.85 Aligned_cols=91 Identities=21% Similarity=0.402 Sum_probs=55.1
Q ss_pred CCCCceeeecCCCCc-------cHHHHHHHHHHHHhhh-hcC--CCCCeEEeccCCCccc------chHHHHHHHHc--C
Q psy5177 78 APEGSLGFANKSGWS-------STEIFFETIKHIQNQI-KAS--KENPALILMDNHETHQ------SMEAIEYCRAS--G 139 (213)
Q Consensus 78 ~~~~~~~~~s~~gw~-------~~~~f~~wl~~f~~~~-~~~--~~~~~lLllD~~~~H~------~~~~~~~~~~~--~ 139 (213)
.|.|+.-.....||+ |++...+=|+.+...+ +.. .-+..|+..|+-.+.- ..++.+++.+. .
T Consensus 137 ~PyGiyd~~~n~g~v~vg~s~dTa~Fav~~i~~WW~~~g~~~yp~a~~lli~~D~GgsN~~r~r~wk~~L~~la~~~gl~ 216 (311)
T PF07592_consen 137 IPYGIYDPAANEGWVSVGTSHDTADFAVDSIRRWWEEMGKARYPHAKRLLITADNGGSNGSRRRLWKKRLQELADETGLS 216 (311)
T ss_pred ccceeEeccCCeEEEEEecCcccHHHHHHHHHHHHHHhChhhcCchheEEEeccCCCCccchhHHHHHHHHHHHHHhCCE
Confidence 344554445555555 3455555555444333 111 2455788889765443 35667777765 4
Q ss_pred cEEEeeCCCCCCCcCcccccccHHHHHHHH
Q psy5177 140 ITLLTFPPHKTDELQPLDVAVFSPFKNRLK 169 (213)
Q Consensus 140 i~l~~lP~~~t~~lQPlD~~v~~~lK~~~~ 169 (213)
|.+..+|||++.. .|++--.|.-+-..|+
T Consensus 217 I~v~hyPP~tSKw-N~IEHRlfs~is~~w~ 245 (311)
T PF07592_consen 217 IRVCHYPPGTSKW-NPIEHRLFSHISRNWR 245 (311)
T ss_pred EEEEEcCCCcccc-cchhhhHhHhhhhhcC
Confidence 8899999999874 5777666666655554
No 9
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=70.69 E-value=53 Score=27.66 Aligned_cols=77 Identities=14% Similarity=0.221 Sum_probs=56.6
Q ss_pred ccHHHHHHHHHH-HHhhhhc-CCCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCCCcCcccccccHHHHHHHH
Q psy5177 92 SSTEIFFETIKH-IQNQIKA-SKENPALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTDELQPLDVAVFSPFKNRLK 169 (213)
Q Consensus 92 ~~~~~f~~wl~~-f~~~~~~-~~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~lQPlD~~v~~~lK~~~~ 169 (213)
++.++..+-|+. +...... .+..+.++.-|+-+...+.++.+++.++||...+..+|+ |.|.++...|=..+|
T Consensus 167 ~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy~s~~~~~~l~~~gI~~Smsr~g~-----p~dNa~~Erf~~tlK 241 (301)
T PRK09409 167 FNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCYRANETRQFARMLGLEPKNTAVRS-----PESNGIAESFVKTIK 241 (301)
T ss_pred CCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCcccccHHHHHHHHHcCCeEeeCCCCC-----CCccchhHHHHHHHH
Confidence 566666666653 3332111 134578999999999999999999999999999988887 778777777777777
Q ss_pred HHHH
Q psy5177 170 AGFK 173 (213)
Q Consensus 170 ~~~~ 173 (213)
.++.
T Consensus 242 ~E~l 245 (301)
T PRK09409 242 RDYI 245 (301)
T ss_pred HHHH
Confidence 6654
No 10
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=69.39 E-value=36 Score=28.10 Aligned_cols=77 Identities=14% Similarity=0.221 Sum_probs=54.8
Q ss_pred ccHHHHHHHHHH-HHhhhhc-CCCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCCCcCcccccccHHHHHHHH
Q psy5177 92 SSTEIFFETIKH-IQNQIKA-SKENPALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTDELQPLDVAVFSPFKNRLK 169 (213)
Q Consensus 92 ~~~~~f~~wl~~-f~~~~~~-~~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~lQPlD~~v~~~lK~~~~ 169 (213)
++.++..+-|+. +...... .+..|.++.-|+-+...+..+.++|.+.||...+..||. |.|.++...|-..+|
T Consensus 128 ~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy~s~~~~~~l~~~gI~~Smsr~g~-----p~dNa~~Erf~~tlK 202 (262)
T PRK14702 128 FNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCYRANETRQFARMLGLEPKNTAVRS-----PESNGIAESFVKTIK 202 (262)
T ss_pred CCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcccchHHHHHHHHHcCCeeccCCCCC-----CCcchHHHHHHHHHH
Confidence 455555555543 3222111 134578899999999999999999999999999988887 778777777777776
Q ss_pred HHHH
Q psy5177 170 AGFK 173 (213)
Q Consensus 170 ~~~~ 173 (213)
.++.
T Consensus 203 ~E~l 206 (262)
T PRK14702 203 RDYI 206 (262)
T ss_pred HHHH
Confidence 6643
No 11
>PF07905 PucR: Purine catabolism regulatory protein-like family; InterPro: IPR012914 This domain is found in the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138 from SWISSPROT). PucR is thought to be a transcriptional regulator of genes involved in the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression []. The other members of this family are also putative regulatory proteins.
Probab=63.11 E-value=26 Score=25.26 Aligned_cols=61 Identities=16% Similarity=0.170 Sum_probs=38.8
Q ss_pred eeecCCCCcc--HHHHHHHHHHHHhhhhcCCCCCeEEe-ccCCCcccchHHHHHHHHcCcEEEeeCCCC
Q psy5177 84 GFANKSGWSS--TEIFFETIKHIQNQIKASKENPALIL-MDNHETHQSMEAIEYCRASGITLLTFPPHK 149 (213)
Q Consensus 84 ~~~s~~gw~~--~~~f~~wl~~f~~~~~~~~~~~~lLl-lD~~~~H~~~~~~~~~~~~~i~l~~lP~~~ 149 (213)
+..+-.++-+ .+.+.+|++.+... +--.|.+ .+.+-.++..+++++|+++++-++.+|.+.
T Consensus 46 vlttg~~~~~~~~~~~~~~i~~L~~~-----~~agL~i~~~~~~~~iP~~~i~~A~~~~lPli~ip~~~ 109 (123)
T PF07905_consen 46 VLTTGYALRDDDEEELREFIRELAEK-----GAAGLGIKTGRYLDEIPEEIIELADELGLPLIEIPWEV 109 (123)
T ss_pred EEECCcccCCCCHHHHHHHHHHHHHC-----CCeEEEEeccCccccCCHHHHHHHHHcCCCEEEeCCCC
Confidence 3333334444 23456666554321 2223444 454777999999999999999999999855
No 12
>PLN02941 inositol-tetrakisphosphate 1-kinase
Probab=44.59 E-value=41 Score=28.89 Aligned_cols=56 Identities=16% Similarity=0.366 Sum_probs=43.4
Q ss_pred chHHHHHHHHcCcEEEeeCCCCCCCc-CcccccccHHHHHHHHHHHHHHHhcCCCCC
Q psy5177 128 SMEAIEYCRASGITLLTFPPHKTDEL-QPLDVAVFSPFKNRLKAGFKKWTSDNPGSS 183 (213)
Q Consensus 128 ~~~~~~~~~~~~i~l~~lP~~~t~~l-QPlD~~v~~~lK~~~~~~~~~~~~~~~~~~ 183 (213)
...+.+.|++.||.++.|=+...-.- .|.|+.+-+..-..++..+.++..++++-.
T Consensus 38 ~~~l~~~~~~~Gi~~v~Id~~~pl~~qgpfDvilhK~~~~~~~~~~~~~~~e~pgv~ 94 (328)
T PLN02941 38 QPSLEALARSKGIDLVAIDPSRPLSEQGPFDVILHKLYGKEWRQQLEEYREKHPDVT 94 (328)
T ss_pred hHHHHHHHHHCCCeEEEecCCCCccccCCcCEEEEecCCHHHHHHHHHHHHHCCCcE
Confidence 34577888889999998866532222 388998888888888999999999988753
No 13
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=44.48 E-value=68 Score=21.71 Aligned_cols=34 Identities=15% Similarity=0.193 Sum_probs=27.6
Q ss_pred CCeEEeccCCCcccchHHHHHHHHcCcEEEeeCC
Q psy5177 114 NPALILMDNHETHQSMEAIEYCRASGITLLTFPP 147 (213)
Q Consensus 114 ~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~ 147 (213)
-..+.|-.....+....+..+|+++||.+.++|.
T Consensus 30 ~~~v~iA~Da~~~vv~~l~~lceek~Ip~v~V~s 63 (84)
T PRK13600 30 VTSLIIAEDVEVYLMTRVLSQINQKNIPVSFFKS 63 (84)
T ss_pred ceEEEEeCCCCHHHHHHHHHHHHHcCCCEEEECC
Confidence 3456666666788888999999999999999975
No 14
>PRK08857 para-aminobenzoate synthase component II; Provisional
Probab=42.48 E-value=33 Score=26.74 Aligned_cols=32 Identities=16% Similarity=0.325 Sum_probs=25.6
Q ss_pred EEeccCCCcccchHHHHHHHHcCcEEEeeCCCC
Q psy5177 117 LILMDNHETHQSMEAIEYCRASGITLLTFPPHK 149 (213)
Q Consensus 117 lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~ 149 (213)
+|++|++.+.. ..+.+++++.|+.+.++|.+.
T Consensus 2 il~id~~dsft-~~~~~~l~~~g~~~~~~~~~~ 33 (193)
T PRK08857 2 LLMIDNYDSFT-YNLYQYFCELGAQVKVVRNDE 33 (193)
T ss_pred EEEEECCCCcH-HHHHHHHHHCCCcEEEEECCC
Confidence 78999999884 456777788899999888774
No 15
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=40.26 E-value=95 Score=27.85 Aligned_cols=51 Identities=18% Similarity=0.286 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhhhhcC-CCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCC
Q psy5177 95 EIFFETIKHIQNQIKAS-KENPALILMDNHETHQSMEAIEYCRASGITLLTFPP 147 (213)
Q Consensus 95 ~~f~~wl~~f~~~~~~~-~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~ 147 (213)
.-..++|+..++.+++. ++.++|+=.|++ +.++++.++|++.++.-++.-+
T Consensus 198 ~g~~~fL~~~l~~lr~~~~~~~ILvR~DSg--F~~~el~~~ce~~g~~yvi~l~ 249 (448)
T PF13701_consen 198 KGAAEFLKRVLRRLRQRWPDTRILVRGDSG--FASPELMDWCEAEGVDYVIGLK 249 (448)
T ss_pred HHHHHHHHHHHHHHhhhCccceEEEEecCc--cCcHHHHHHHHhCCCeEEEEec
Confidence 34677788777777653 456788888854 4679999999999998776533
No 16
>PRK12652 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=38.67 E-value=28 Score=30.23 Aligned_cols=35 Identities=26% Similarity=0.376 Sum_probs=29.6
Q ss_pred CcccchHHHHHHHHcCcEEEee-----CCCCCCCcCcccc
Q psy5177 124 ETHQSMEAIEYCRASGITLLTF-----PPHKTDELQPLDV 158 (213)
Q Consensus 124 ~~H~~~~~~~~~~~~~i~l~~l-----P~~~t~~lQPlD~ 158 (213)
.++....+.++++++++.++.+ |.+++..||||+.
T Consensus 98 ~G~pae~Iv~~Aee~~aDLIVm~~~~~~~~~~~~~~~~~~ 137 (357)
T PRK12652 98 PGDYAEVLIAYAEEHGIDRVVLDPEYNPGGTAPMLQPLER 137 (357)
T ss_pred CCCHHHHHHHHHHHcCCCEEEECCCCCCCCCCcccchHHH
Confidence 4788889999999999999887 5578888999865
No 17
>PLN02335 anthranilate synthase
Probab=37.70 E-value=50 Score=26.52 Aligned_cols=36 Identities=19% Similarity=0.364 Sum_probs=25.1
Q ss_pred CCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCC
Q psy5177 112 KENPALILMDNHETHQSMEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 112 ~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~ 148 (213)
...+.+|++|++.+... .+.+++++.|+.+.++|..
T Consensus 16 ~~~~~ilviD~~dsft~-~i~~~L~~~g~~~~v~~~~ 51 (222)
T PLN02335 16 KQNGPIIVIDNYDSFTY-NLCQYMGELGCHFEVYRND 51 (222)
T ss_pred CccCcEEEEECCCCHHH-HHHHHHHHCCCcEEEEECC
Confidence 45667888898877743 4566666778877777764
No 18
>PF02603 Hpr_kinase_N: HPr Serine kinase N terminus; InterPro: IPR011126 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria []. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes []. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains []. ; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1KNX_B 1KO7_A.
Probab=36.98 E-value=25 Score=25.63 Aligned_cols=40 Identities=23% Similarity=0.322 Sum_probs=26.7
Q ss_pred CCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCCCc
Q psy5177 112 KENPALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTDEL 153 (213)
Q Consensus 112 ~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~l 153 (213)
.+-|++++-+|. .+.+++++.|++.++-++.-+-.++.+.
T Consensus 80 ~~~P~iIvt~~~--~~p~~l~e~a~~~~ipll~t~~~ts~~i 119 (127)
T PF02603_consen 80 YNPPCIIVTRGL--EPPPELIELAEKYNIPLLRTPLSTSELI 119 (127)
T ss_dssp TT-S-EEEETTT-----HHHHHHHHHCT--EEEESS-HHHHH
T ss_pred CCCCEEEEECcC--CCCHHHHHHHHHhCCcEEEcCCcHHHHH
Confidence 367899999998 4568899999999999999887665543
No 19
>COG5663 Uncharacterized conserved protein [Function unknown]
Probab=35.66 E-value=24 Score=27.37 Aligned_cols=54 Identities=15% Similarity=0.041 Sum_probs=35.4
Q ss_pred EEEeeeccCCcc-cCCeEEe-cccccccccccCCCCCceeeecCCCCccHHHHHHHHH
Q psy5177 47 TMIGIIRASGEA-IPPVFVF-PRVFMKDEFLLGAPEGSLGFANKSGWSSTEIFFETIK 102 (213)
Q Consensus 47 Tvl~~~~a~G~~-lpP~~I~-~~~~~~~~~~~~~~~~~~~~~s~~gw~~~~~f~~wl~ 102 (213)
-.-+|+.-||+. .+|.++= -+..+...... .....|...+.+|++.+-|.+|.+
T Consensus 6 ~~~~ciDIDGtit~~~t~~~~~n~~f~kslse--~d~t~y~lhkil~i~~ee~~k~~e 61 (194)
T COG5663 6 QLRCCIDIDGTITDDPTFAPYLNPAFEKSLSE--ADPTDYDLHKILNITTEEFWKWME 61 (194)
T ss_pred HhheeeccCCceecCcccchhccHHHHhhhhh--cccccccHHHHhCccHHHHHHHHH
Confidence 345789999999 8887772 22222211111 123556678999999999999975
No 20
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=34.16 E-value=65 Score=21.52 Aligned_cols=34 Identities=3% Similarity=0.172 Sum_probs=28.0
Q ss_pred CCCeEEeccCCCcccchHHHHHHHHcCcEEEeeC
Q psy5177 113 ENPALILMDNHETHQSMEAIEYCRASGITLLTFP 146 (213)
Q Consensus 113 ~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP 146 (213)
.-..++|-.+.+.+....+..+|++.+|.+++++
T Consensus 27 kaklViiA~D~~~~~~~~i~~~c~~~~Vp~~~~~ 60 (82)
T PRK13602 27 SVKEVVVAEDADPRLTEKVEALANEKGVPVSKVD 60 (82)
T ss_pred CeeEEEEECCCCHHHHHHHHHHHHHcCCCEEEEC
Confidence 3446667777777888899999999999999987
No 21
>PRK08007 para-aminobenzoate synthase component II; Provisional
Probab=33.31 E-value=57 Score=25.32 Aligned_cols=31 Identities=19% Similarity=0.319 Sum_probs=20.5
Q ss_pred EEeccCCCcccchHHHHHHHHcCcEEEeeCCC
Q psy5177 117 LILMDNHETHQSMEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 117 lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~ 148 (213)
+|++||+.|... .+.+++++.+..+..++..
T Consensus 2 il~idn~Dsft~-nl~~~l~~~g~~v~v~~~~ 32 (187)
T PRK08007 2 ILLIDNYDSFTW-NLYQYFCELGADVLVKRND 32 (187)
T ss_pred EEEEECCCccHH-HHHHHHHHCCCcEEEEeCC
Confidence 677888877743 3555566667777776665
No 22
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=32.54 E-value=99 Score=23.99 Aligned_cols=50 Identities=16% Similarity=0.290 Sum_probs=37.9
Q ss_pred CCCCeEEeccCCCccc----chHHHHHHHHcCcEEEeeCCCC-CCCcCccccccc
Q psy5177 112 KENPALILMDNHETHQ----SMEAIEYCRASGITLLTFPPHK-TDELQPLDVAVF 161 (213)
Q Consensus 112 ~~~~~lLllD~~~~H~----~~~~~~~~~~~~i~l~~lP~~~-t~~lQPlD~~v~ 161 (213)
...+-+-++|...... ..+.++.+++.|..|+.+.|+. +..+.=||.|-|
T Consensus 16 Ir~~evrlIg~~GeqlGiv~~~eAL~lA~e~~LDLV~Ispna~PPVcKImDYGKf 70 (176)
T COG0290 16 IRAREVRLIGEDGEQLGIVSIEEALKLAEEAGLDLVEISPNAKPPVCKIMDYGKF 70 (176)
T ss_pred ccccEEEEECCCCcEEcceeHHHHHHHHHHcCCCEEEECCCCCCCeeEeeeccch
Confidence 3455677777776665 5788999999999999999994 556777886643
No 23
>KOG3853|consensus
Probab=32.06 E-value=53 Score=27.34 Aligned_cols=88 Identities=17% Similarity=0.270 Sum_probs=48.3
Q ss_pred CceEEEEeeeccCCcccCCeEEecccccccccccCCCCCceeeecCCCCccHH-HHHHHHHHHHhhhhcCCCCCeEEecc
Q psy5177 43 GELVTMIGIIRASGEAIPPVFVFPRVFMKDEFLLGAPEGSLGFANKSGWSSTE-IFFETIKHIQNQIKASKENPALILMD 121 (213)
Q Consensus 43 ~~~~Tvl~~~~a~G~~lpP~~I~~~~~~~~~~~~~~~~~~~~~~s~~gw~~~~-~f~~wl~~f~~~~~~~~~~~~lLllD 121 (213)
.+-+|.|+|+..+|+-+-- +|.+. ..++++|-+-. -+.+++..|.|.-..+...|++.+--
T Consensus 175 ~eYVTtMvCvav~g~Pi~G-vIh~P-----------------F~~~Tawa~v~~s~~~~~SN~~p~~s~Neq~PiivVSR 236 (350)
T KOG3853|consen 175 TEYVTTMVCVAVDGEPIFG-VIHRP-----------------FFNETAWANVTISLEKSFSNFRPKNSENEQNPIIVVSR 236 (350)
T ss_pred HHhhheEEEEEecCceeEE-Eeecc-----------------ccccchhhhcccchhhhhhcCCccCCcccCCCEEEEec
Confidence 4689999999999964221 11111 12333343322 23445555666544445688888877
Q ss_pred CCCcccchHHHHHHHHcCcEEEeeCCCCCC
Q psy5177 122 NHETHQSMEAIEYCRASGITLLTFPPHKTD 151 (213)
Q Consensus 122 ~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~ 151 (213)
+|.+-...-..+. .|=..-.+|++-..
T Consensus 237 SH~g~vK~ia~~v---fG~~~~i~pAgGaG 263 (350)
T KOG3853|consen 237 SHAGKVKEIAEKV---FGDKMNIEPAGGAG 263 (350)
T ss_pred cccchHHHHHHHH---hcCcceeeecCCCc
Confidence 7776654433332 44455556665544
No 24
>TIGR00566 trpG_papA glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase. This model describes the glutamine amidotransferase domain or peptide of the tryptophan-biosynthetic pathway enzyme anthranilate synthase or of the folate biosynthetic pathway enzyme para-aminobenzoate synthase. In at least one case, a single polypeptide from Bacillus subtilis was shown to have both functions. This model covers a subset of the sequences described by the pfam model GATase.
Probab=31.80 E-value=58 Score=25.28 Aligned_cols=31 Identities=13% Similarity=0.344 Sum_probs=15.1
Q ss_pred EEeccCCCcccchHHHHHHHHcCcEEEeeCCC
Q psy5177 117 LILMDNHETHQSMEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 117 lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~ 148 (213)
+|++|++.|.. ..+.++.++.|..+.++|.+
T Consensus 2 il~id~~dsft-~~~~~~l~~~g~~v~v~~~~ 32 (188)
T TIGR00566 2 VLMIDNYDSFT-YNLVQYFCELGAEVVVKRND 32 (188)
T ss_pred EEEEECCcCHH-HHHHHHHHHcCCceEEEECC
Confidence 45556655552 23334444445555555543
No 25
>PRK05670 anthranilate synthase component II; Provisional
Probab=29.68 E-value=69 Score=24.76 Aligned_cols=32 Identities=16% Similarity=0.477 Sum_probs=23.4
Q ss_pred EEeccCCCcccchHHHHHHHHcCcEEEeeCCCC
Q psy5177 117 LILMDNHETHQSMEAIEYCRASGITLLTFPPHK 149 (213)
Q Consensus 117 lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~ 149 (213)
+||+|++.+. +..+.+++++.|+.+..+|...
T Consensus 2 iliid~~d~f-~~~i~~~l~~~g~~~~v~~~~~ 33 (189)
T PRK05670 2 ILLIDNYDSF-TYNLVQYLGELGAEVVVYRNDE 33 (189)
T ss_pred EEEEECCCch-HHHHHHHHHHCCCcEEEEECCC
Confidence 6888888666 4456667777788888887764
No 26
>PRK06774 para-aminobenzoate synthase component II; Provisional
Probab=29.41 E-value=70 Score=24.76 Aligned_cols=31 Identities=19% Similarity=0.335 Sum_probs=18.7
Q ss_pred EEeccCCCcccchHHHHHHHHcCcEEEeeCCC
Q psy5177 117 LILMDNHETHQSMEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 117 lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~ 148 (213)
+|++|++.|... .+.+++++.+..+.+++.+
T Consensus 2 il~id~~dsf~~-nl~~~l~~~~~~~~v~~~~ 32 (191)
T PRK06774 2 LLLIDNYDSFTY-NLYQYFCELGTEVMVKRND 32 (191)
T ss_pred EEEEECCCchHH-HHHHHHHHCCCcEEEEeCC
Confidence 577777777633 3444555566666666654
No 27
>PRK07649 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II; Validated
Probab=29.02 E-value=75 Score=24.89 Aligned_cols=31 Identities=13% Similarity=0.315 Sum_probs=18.8
Q ss_pred EEeccCCCcccchHHHHHHHHcCcEEEeeCCC
Q psy5177 117 LILMDNHETHQSMEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 117 lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~ 148 (213)
+||+|++.+... .+.+++++.++.+.+++..
T Consensus 2 il~idn~dsft~-nl~~~l~~~g~~v~v~~~~ 32 (195)
T PRK07649 2 ILMIDNYDSFTF-NLVQFLGELGQELVVKRND 32 (195)
T ss_pred EEEEeCCCccHH-HHHHHHHHCCCcEEEEeCC
Confidence 577777777643 3555555566666666544
No 28
>PRK06683 hypothetical protein; Provisional
Probab=28.92 E-value=93 Score=20.80 Aligned_cols=34 Identities=6% Similarity=0.103 Sum_probs=29.1
Q ss_pred CCCeEEeccCCCcccchHHHHHHHHcCcEEEeeC
Q psy5177 113 ENPALILMDNHETHQSMEAIEYCRASGITLLTFP 146 (213)
Q Consensus 113 ~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP 146 (213)
.-+.++|-.+.+.+....+.++|+..+|.+..++
T Consensus 27 kaklViiA~Da~~~~~~~i~~~~~~~~Vpv~~~~ 60 (82)
T PRK06683 27 IVKEVVIAEDADMRLTHVIIRTALQHNIPITKVE 60 (82)
T ss_pred CeeEEEEECCCCHHHHHHHHHHHHhcCCCEEEEC
Confidence 4556777788888889999999999999999887
No 29
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=28.24 E-value=2.7e+02 Score=21.55 Aligned_cols=61 Identities=13% Similarity=0.117 Sum_probs=36.7
Q ss_pred CCCCccHHHHHHHH-HHHHhhhhcCC--CCCeEEeccCCCcccc----hHHHHHHHHcCcEEEeeCCC
Q psy5177 88 KSGWSSTEIFFETI-KHIQNQIKASK--ENPALILMDNHETHQS----MEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 88 ~~gw~~~~~f~~wl-~~f~~~~~~~~--~~~~lLllD~~~~H~~----~~~~~~~~~~~i~l~~lP~~ 148 (213)
..|..+....+++. +.|...-..+. .+=++||-||.+.... .+..+.+++.||.++.+=-|
T Consensus 81 ~~g~T~~~~AL~~a~~~~~~~~~~r~~~~kv~IllTDG~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG 148 (192)
T cd01473 81 SGGETYIVEALKYGLKNYTKHGNRRKDAPKVTMLFTDGNDTSASKKELQDISLLYKEENVKLLVVGVG 148 (192)
T ss_pred CCCcCcHHHHHHHHHHHhccCCCCcccCCeEEEEEecCCCCCcchhhHHHHHHHHHHCCCEEEEEEec
Confidence 34667777777775 45543211111 2336788888876532 24455678899999988333
No 30
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=26.95 E-value=2.6e+02 Score=21.43 Aligned_cols=61 Identities=16% Similarity=0.125 Sum_probs=33.2
Q ss_pred CCCCccHHHHHHHHHHHHhhhhcCCCCCeEEeccCCCccc---chHHHHHHHHcCcEEEeeCCC
Q psy5177 88 KSGWSSTEIFFETIKHIQNQIKASKENPALILMDNHETHQ---SMEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 88 ~~gw~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~~~~H~---~~~~~~~~~~~~i~l~~lP~~ 148 (213)
..|+.+-..-++--...+.+......+.+++|+++-..+- ..++.+.+++.+|.+..+--+
T Consensus 82 ~~G~t~l~~aL~~A~~~l~~~~~~~~~~iiil~sd~~~~~~~~~~~~~~~l~~~~I~v~~IgiG 145 (183)
T cd01453 82 CSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLS 145 (183)
T ss_pred CCCchhHHHHHHHHHHHHhcCCccCceEEEEEEcCCCcCChhhHHHHHHHHHHcCcEEEEEEec
Confidence 3566655555554322222211112345677766544332 235677788899999888554
No 31
>CHL00101 trpG anthranilate synthase component 2
Probab=26.82 E-value=81 Score=24.45 Aligned_cols=32 Identities=9% Similarity=0.236 Sum_probs=21.8
Q ss_pred EEeccCCCcccchHHHHHHHHcCcEEEeeCCCC
Q psy5177 117 LILMDNHETHQSMEAIEYCRASGITLLTFPPHK 149 (213)
Q Consensus 117 lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~ 149 (213)
+||+|++.+.. ..+.+.+++.|+.+..+|.+.
T Consensus 2 iliid~~dsft-~~l~~~l~~~g~~~~v~~~~~ 33 (190)
T CHL00101 2 ILIIDNYDSFT-YNLVQSLGELNSDVLVCRNDE 33 (190)
T ss_pred EEEEECCCchH-HHHHHHHHhcCCCEEEEECCC
Confidence 67788877764 345666667777777777653
No 32
>PF12068 DUF3548: Domain of unknown function (DUF3548); InterPro: IPR021935 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes and is typically between 184 to 216 amino acids in length. The domain is found associated with PF00566 from PFAM and at the N terminus of GYP7 proteins.
Probab=26.17 E-value=1.6e+02 Score=23.65 Aligned_cols=30 Identities=7% Similarity=0.325 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHhhhhcCCCCCeEEeccCCC
Q psy5177 95 EIFFETIKHIQNQIKASKENPALILMDNHE 124 (213)
Q Consensus 95 ~~f~~wl~~f~~~~~~~~~~~~lLllD~~~ 124 (213)
..|++-|+.+..-.+...+..++|+.|..+
T Consensus 157 ~~fl~~L~~~v~l~~S~~D~~~~lv~~~~s 186 (213)
T PF12068_consen 157 KEFLKSLQRYVTLARSPRDSNLYLVNDHNS 186 (213)
T ss_pred HHHHHHHHhhEEEeecCCCCcEEEEECCCc
Confidence 356666665554444445677778887764
No 33
>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins. GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding
Probab=25.72 E-value=2.1e+02 Score=25.72 Aligned_cols=60 Identities=23% Similarity=0.442 Sum_probs=39.2
Q ss_pred ccHHHHHHHHHHHHhhhhcCCCCCeEEeccCC--------Ccccc--------hHHHHHHHHcCcEEEeeCCCCCCCcCc
Q psy5177 92 SSTEIFFETIKHIQNQIKASKENPALILMDNH--------ETHQS--------MEAIEYCRASGITLLTFPPHKTDELQP 155 (213)
Q Consensus 92 ~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~~--------~~H~~--------~~~~~~~~~~~i~l~~lP~~~t~~lQP 155 (213)
.+-+.|.+|++.+... .++-++++|++ .-|-. .++.++|++.+++++++-..+.. -|
T Consensus 89 l~~ds~~~f~~~i~~~-----~k~~iI~~DSWdaiieyla~~~~~~ed~e~l~~dLv~lard~g~~LIlVsEsa~~--~~ 161 (484)
T PF07088_consen 89 LDIDSFRDFVDKINEA-----GKKPIIAFDSWDAIIEYLAEEHDEPEDIETLTNDLVELARDMGINLILVSESAEN--EP 161 (484)
T ss_pred cCHHHHHHHHHHhhhc-----ccCcEEEEecHHHHHHHhhhhhcCcHHHHHHHHHHHHHHhhcCceEEEEEecCCC--Cc
Confidence 4567788888865321 45568899992 22321 23445668999999999776654 37
Q ss_pred ccc
Q psy5177 156 LDV 158 (213)
Q Consensus 156 lD~ 158 (213)
||.
T Consensus 162 LdY 164 (484)
T PF07088_consen 162 LDY 164 (484)
T ss_pred chh
Confidence 875
No 34
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=25.69 E-value=1.8e+02 Score=21.30 Aligned_cols=44 Identities=16% Similarity=0.264 Sum_probs=23.9
Q ss_pred hHHHHHHHHcCcEEEeeCCCCCCCcCcccccc------cHHHHHHHHHHHHHHHhcC
Q psy5177 129 MEAIEYCRASGITLLTFPPHKTDELQPLDVAV------FSPFKNRLKAGFKKWTSDN 179 (213)
Q Consensus 129 ~~~~~~~~~~~i~l~~lP~~~t~~lQPlD~~v------~~~lK~~~~~~~~~~~~~~ 179 (213)
.-+++.|++.|+.++++ +||+..-+ -..-...|-+++...+.+.
T Consensus 39 ~l~L~~~k~~g~~~lfV-------i~PvNg~wydytG~~~~~r~~~y~kI~~~~~~~ 88 (130)
T PF04914_consen 39 QLLLDVCKELGIDVLFV-------IQPVNGKWYDYTGLSKEMRQEYYKKIKYQLKSQ 88 (130)
T ss_dssp HHHHHHHHHTT-EEEEE-------E----HHHHHHTT--HHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCceEEE-------ecCCcHHHHHHhCCCHHHHHHHHHHHHHHHHHC
Confidence 34788999999999998 78886533 3344444444444444443
No 35
>PRK05637 anthranilate synthase component II; Provisional
Probab=25.44 E-value=1.1e+02 Score=24.29 Aligned_cols=33 Identities=18% Similarity=0.358 Sum_probs=22.7
Q ss_pred eEEeccCCCcccchHHHHHHHHcCcEEEeeCCCC
Q psy5177 116 ALILMDNHETHQSMEAIEYCRASGITLLTFPPHK 149 (213)
Q Consensus 116 ~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~ 149 (213)
.+|++|++.+... .+.+++++.|+.+.++|.+.
T Consensus 3 ~il~iD~~dsf~~-nl~~~l~~~g~~~~v~~~~~ 35 (208)
T PRK05637 3 HVVLIDNHDSFVY-NLVDAFAVAGYKCTVFRNTV 35 (208)
T ss_pred EEEEEECCcCHHH-HHHHHHHHCCCcEEEEeCCC
Confidence 4788888777743 35556666777777777654
No 36
>PRK06895 putative anthranilate synthase component II; Provisional
Probab=25.36 E-value=89 Score=24.16 Aligned_cols=32 Identities=16% Similarity=0.390 Sum_probs=23.4
Q ss_pred eEEeccCCCcccchHHHHHHHHcCcEEEeeCCC
Q psy5177 116 ALILMDNHETHQSMEAIEYCRASGITLLTFPPH 148 (213)
Q Consensus 116 ~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~ 148 (213)
.+||+|++.+.... +.+++++.|+.+..++..
T Consensus 3 ~iliid~~dsf~~~-i~~~l~~~g~~~~v~~~~ 34 (190)
T PRK06895 3 KLLIINNHDSFTFN-LVDLIRKLGVPMQVVNVE 34 (190)
T ss_pred EEEEEeCCCchHHH-HHHHHHHcCCcEEEEECC
Confidence 57888888888655 777777777777766643
No 37
>COG5410 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.98 E-value=1.9e+02 Score=23.85 Aligned_cols=95 Identities=14% Similarity=0.136 Sum_probs=50.1
Q ss_pred CeecCCC-CCCCCceEEe--cccccccccccCCCCceEEEEeeeccCCcccCCeEEecccccccccccCCCCCceeeecC
Q psy5177 12 DYWNPDS-LVPPPKVVAK--KRTKKLGQAASAERGELVTMIGIIRASGEAIPPVFVFPRVFMKDEFLLGAPEGSLGFANK 88 (213)
Q Consensus 12 ~I~N~DE-T~~~~~~~~~--~g~k~v~~~~~~~~~~~~Tvl~~~~a~G~~lpP~~I~~~~~~~~~~~~~~~~~~~~~~s~ 88 (213)
.|.|+|+ +.++.-.+.. +|.+. +.+.... +-+..-.+..+|+|.-.--++|-. |.+..= -.
T Consensus 112 ~ii~sd~y~~LFp~~I~~~~~~~k~-w~i~~~g-Gg~yaTs~gG~ATG~GaD~LIIDD------------P~k~e~--a~ 175 (305)
T COG5410 112 EIVQSDEYRALFPLEIADDAKSKKR-WNVVVDG-GGVYATSLGGQATGFGADALIIDD------------PLKVED--AY 175 (305)
T ss_pred HHHhccchhhcCceeeccCccCccc-eEEEeeC-CEEEEEeecCccccCCCCeEEecC------------CCCHHH--hh
Confidence 4788998 5554333332 23222 2222222 235556666788888777777732 221111 11
Q ss_pred CCCccHHHHHHHHHHHHhhhhcCCCCCeEEeccCC
Q psy5177 89 SGWSSTEIFFETIKHIQNQIKASKENPALILMDNH 123 (213)
Q Consensus 89 ~gw~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~~ 123 (213)
+--+.+.+..+|...|..... ++..++++++--+
T Consensus 176 SktIR~K~Yr~~~st~~sr~~-~~~s~iii~~~~~ 209 (305)
T COG5410 176 SKTIRSKAYRKLVSTVKSRKA-SPDTPIIVIMQRL 209 (305)
T ss_pred hhHHHHHHHHHHHHHHHhhcc-CCCCcEEEEehhh
Confidence 223566788888887765543 2456666665433
No 38
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=24.89 E-value=3.1e+02 Score=20.80 Aligned_cols=51 Identities=18% Similarity=0.259 Sum_probs=28.5
Q ss_pred CCccHHHHHHHHHH-HHhhhhcCCCCCeEEeccCCCcccchHHHHHHHHcCcE
Q psy5177 90 GWSSTEIFFETIKH-IQNQIKASKENPALILMDNHETHQSMEAIEYCRASGIT 141 (213)
Q Consensus 90 gw~~~~~f~~wl~~-f~~~~~~~~~~~~lLllD~~~~H~~~~~~~~~~~~~i~ 141 (213)
|--|-..|.+.+.. |.........-|=|+|+||-.+|.+.. .+.+++.|+.
T Consensus 54 ~~dDy~~M~Evl~RR~~~~~~~~~~lPDLilIDGG~gQl~aa-~~~l~~lgl~ 105 (155)
T PF08459_consen 54 GGDDYAAMREVLTRRFKRLKEEKEPLPDLILIDGGKGQLNAA-KEVLKELGLN 105 (155)
T ss_dssp TT-HHHHHHHHHHHHHCCCHHHT----SEEEESSSHHHHHHH-HHHHHCTT--
T ss_pred CCcHHHHHHHHHHHHHhcccccCCCCCCEEEEcCCHHHHHHH-HHHHHHcCCC
Confidence 33455677888765 433333323567899999999998764 3344455543
No 39
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=24.21 E-value=1.3e+02 Score=21.56 Aligned_cols=37 Identities=16% Similarity=0.224 Sum_probs=26.9
Q ss_pred CCCeEEeccCCCccc--chHHHHHHHHcCcEEEeeCCCC
Q psy5177 113 ENPALILMDNHETHQ--SMEAIEYCRASGITLLTFPPHK 149 (213)
Q Consensus 113 ~~~~lLllD~~~~H~--~~~~~~~~~~~~i~l~~lP~~~ 149 (213)
.+.++|+-||..... ..+..+.+++.++.++.+--+.
T Consensus 104 ~~~iiliTDG~~~~~~~~~~~~~~~~~~~v~v~~i~~g~ 142 (161)
T cd01450 104 PKVIIVLTDGRSDDGGDPKEAAAKLKDEGIKVFVVGVGP 142 (161)
T ss_pred CeEEEEECCCCCCCCcchHHHHHHHHHCCCEEEEEeccc
Confidence 344778889877664 5677888888899998884443
No 40
>PF02633 Creatininase: Creatinine amidohydrolase; InterPro: IPR003785 This family includes the enzymes creatininase and 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase, also known as formamide hydrolase. Creatinase or creatinine amidohydrolase (3.5.2.10 from EC) catalyses the hydrolysis of creatinine to creatine, which can then be metabolised to urea and sarcosine by creatinase (3.5.3.3 from EC). Creatininase is a member of the urease-related amidohydrolase superfamily []. Formamide hydrolase catalyzes the hydrolysis of the formamide of 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-monophosphate (FAPy) to form 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (APy) (3.5.1.102 from EC). ; PDB: 3A6K_F 3A6F_A 3A6D_B 1J2U_B 3A6J_C 1J2T_A 3A6G_C 3A6H_F 1Q3K_E 3A6L_C ....
Probab=23.82 E-value=2e+02 Score=23.04 Aligned_cols=56 Identities=11% Similarity=0.188 Sum_probs=35.6
Q ss_pred CccHHHHHHHHHHHHhhhhcCCCCCeEEeccCCCcccc--hHHHHHH-HH-cCcEEEeeCC
Q psy5177 91 WSSTEIFFETIKHIQNQIKASKENPALILMDNHETHQS--MEAIEYC-RA-SGITLLTFPP 147 (213)
Q Consensus 91 w~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~~~~H~~--~~~~~~~-~~-~~i~l~~lP~ 147 (213)
++..++|...|......+.. .+.+.++|+.+|.+|.. ..+.+.+ .+ .++.+.++..
T Consensus 78 sl~~~t~~~~l~di~~sl~~-~Gf~~ivivngHgGN~~~l~~~~~~l~~~~~~~~v~~~~~ 137 (237)
T PF02633_consen 78 SLSPETLIALLRDILRSLAR-HGFRRIVIVNGHGGNIAALEAAARELRQEYPGVKVFVINW 137 (237)
T ss_dssp BB-HHHHHHHHHHHHHHHHH-HT--EEEEEESSTTHHHHHHHHHHHHHHHGCC-EEEEEEG
T ss_pred EeCHHHHHHHHHHHHHHHHH-cCCCEEEEEECCHhHHHHHHHHHHHHHhhCCCcEEEEeec
Confidence 46788999999876666543 36778999999999862 2333333 34 5777777644
No 41
>PF09270 BTD: Beta-trefoil DNA-binding domain; InterPro: IPR015350 This DNA-binding domain adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and corepressors (SMRT/N-Cor and CIR) []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2FO1_A 3NBN_A 2F8X_C 3V79_C 3IAG_C 3BRG_C.
Probab=23.33 E-value=57 Score=24.91 Aligned_cols=23 Identities=17% Similarity=0.314 Sum_probs=18.6
Q ss_pred EEEEeeeccCCcccCCeEEeccc
Q psy5177 46 VTMIGIIRASGEAIPPVFVFPRV 68 (213)
Q Consensus 46 ~Tvl~~~~a~G~~lpP~~I~~~~ 68 (213)
-+|++.+..+|-.+||++|-|-.
T Consensus 74 s~V~Lv~~~TGv~sppliIRKVd 96 (158)
T PF09270_consen 74 STVVLVCSVTGVSSPPLIIRKVD 96 (158)
T ss_dssp SEEEEEETTT-EBEEEEEEEEEE
T ss_pred CEEEEEECCCCcccCceEEEEec
Confidence 57888899999999999997643
No 42
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=22.16 E-value=1.7e+02 Score=20.27 Aligned_cols=34 Identities=18% Similarity=0.302 Sum_probs=28.0
Q ss_pred CCCeEEeccCCCcccchHHHHHHHHcCcEEEeeC
Q psy5177 113 ENPALILMDNHETHQSMEAIEYCRASGITLLTFP 146 (213)
Q Consensus 113 ~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP 146 (213)
.-+.++|-++.+.+....+..+|++.+|.++..+
T Consensus 32 kaklViiA~D~~~~~~~~i~~~c~~~~Ip~~~~~ 65 (99)
T PRK01018 32 KAKLVIVASNCPKDIKEDIEYYAKLSGIPVYEYE 65 (99)
T ss_pred CceEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEC
Confidence 4556777777888999999999999999987764
No 43
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=22.05 E-value=2.5e+02 Score=18.71 Aligned_cols=33 Identities=15% Similarity=0.299 Sum_probs=23.9
Q ss_pred CCeEEeccCCCcccchH-HHHHHHHcCcEEEeeC
Q psy5177 114 NPALILMDNHETHQSME-AIEYCRASGITLLTFP 146 (213)
Q Consensus 114 ~~~lLllD~~~~H~~~~-~~~~~~~~~i~l~~lP 146 (213)
...+++-.+.+...... +..+|++++|.+++++
T Consensus 32 ~~lvilA~d~~~~~~~~~l~~~c~~~~Ip~~~~~ 65 (95)
T PF01248_consen 32 AKLVILAEDCSPDSIKKHLPALCEEKNIPYVFVP 65 (95)
T ss_dssp ESEEEEETTSSSGHHHHHHHHHHHHTTEEEEEES
T ss_pred CcEEEEcCCCChhhhcccchhheeccceeEEEEC
Confidence 34455555555555556 8889999999999987
No 44
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=21.90 E-value=4.3e+02 Score=21.29 Aligned_cols=43 Identities=16% Similarity=0.335 Sum_probs=32.8
Q ss_pred CCCeEEeccCCCccc-chHHHHHHHHcCcEEEeeCCCCCCCcCc
Q psy5177 113 ENPALILMDNHETHQ-SMEAIEYCRASGITLLTFPPHKTDELQP 155 (213)
Q Consensus 113 ~~~~lLllD~~~~H~-~~~~~~~~~~~~i~l~~lP~~~t~~lQP 155 (213)
..+.+|++|+-.--- -..++..|...|+.-+++++++.....|
T Consensus 88 ~~~~~lvLd~v~dp~NlGaI~Rta~afG~~~vil~~~~~~~~~~ 131 (237)
T TIGR00186 88 KQPFLLILDEITDPHNLGAILRTAEAFGVDGVILPKRRSAPLNS 131 (237)
T ss_pred CCCEEEEEcCCCCCccHHHHHHHHHHcCCCEEEECCCCcCCCCC
Confidence 457788999876555 4567888899999999999987665444
No 45
>COG3914 Spy Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]
Probab=21.72 E-value=5.1e+02 Score=24.33 Aligned_cols=67 Identities=19% Similarity=0.296 Sum_probs=43.6
Q ss_pred CCCCCcee--eecCCCCccHHHHHHHHHHHHhhhhcCCCCCeEEeccCC-CcccchHHHHHHHHcCc---EEEeeCCC
Q psy5177 77 GAPEGSLG--FANKSGWSSTEIFFETIKHIQNQIKASKENPALILMDNH-ETHQSMEAIEYCRASGI---TLLTFPPH 148 (213)
Q Consensus 77 ~~~~~~~~--~~s~~gw~~~~~f~~wl~~f~~~~~~~~~~~~lLllD~~-~~H~~~~~~~~~~~~~i---~l~~lP~~ 148 (213)
+.|.+..+ ..+..--+|.++|..|++.+- .+ ..-+|||.++- ..-+...+.+.+++.|+ .+.|+||-
T Consensus 425 glp~~avVf~c~~n~~K~~pev~~~wmqIL~-~v----P~Svl~L~~~~~~~~~~~~l~~la~~~Gv~~eRL~f~p~~ 497 (620)
T COG3914 425 GLPEDAVVFCCFNNYFKITPEVFALWMQILS-AV----PNSVLLLKAGGDDAEINARLRDLAEREGVDSERLRFLPPA 497 (620)
T ss_pred CCCCCeEEEEecCCcccCCHHHHHHHHHHHH-hC----CCcEEEEecCCCcHHHHHHHHHHHHHcCCChhheeecCCC
Confidence 45666443 346777899999999998652 22 33467777764 23334556667777876 57788763
No 46
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.66 E-value=44 Score=22.84 Aligned_cols=33 Identities=12% Similarity=0.211 Sum_probs=26.6
Q ss_pred CCeEEeccCCCccc-chHHHHHHHHcCcEEEeeC
Q psy5177 114 NPALILMDNHETHQ-SMEAIEYCRASGITLLTFP 146 (213)
Q Consensus 114 ~~~lLllD~~~~H~-~~~~~~~~~~~~i~l~~lP 146 (213)
--+++++=++-+|- ...+.+.|++.++.+++..
T Consensus 49 aD~VIv~t~~vsH~~~~~vk~~akk~~ip~~~~~ 82 (97)
T PF10087_consen 49 ADLVIVFTDYVSHNAMWKVKKAAKKYGIPIIYSR 82 (97)
T ss_pred CCEEEEEeCCcChHHHHHHHHHHHHcCCcEEEEC
Confidence 34677777778886 6788999999999999986
No 47
>KOG4233|consensus
Probab=20.85 E-value=77 Score=21.26 Aligned_cols=11 Identities=27% Similarity=0.510 Sum_probs=9.7
Q ss_pred cHHHHHHHHHH
Q psy5177 93 STEIFFETIKH 103 (213)
Q Consensus 93 ~~~~f~~wl~~ 103 (213)
|.++|.+||+.
T Consensus 56 dE~lF~~Wlk~ 66 (90)
T KOG4233|consen 56 DEDLFQEWLKE 66 (90)
T ss_pred cHHHHHHHHHH
Confidence 68999999985
No 48
>PRK05428 HPr kinase/phosphorylase; Provisional
Probab=20.54 E-value=4.1e+02 Score=22.68 Aligned_cols=53 Identities=28% Similarity=0.400 Sum_probs=39.6
Q ss_pred CCCCeEEeccCCCcccchHHHHHHHHcCcEEEeeCCCCCCCcCcccccccHHHHHHHHHHHHH
Q psy5177 112 KENPALILMDNHETHQSMEAIEYCRASGITLLTFPPHKTDELQPLDVAVFSPFKNRLKAGFKK 174 (213)
Q Consensus 112 ~~~~~lLllD~~~~H~~~~~~~~~~~~~i~l~~lP~~~t~~lQPlD~~v~~~lK~~~~~~~~~ 174 (213)
.+-|++++-++... .+++.+.|++.+|.++.-|-.++. ++..+..++..++..
T Consensus 81 ~~~P~iIvt~~~~~--p~~l~~~a~~~~ipll~t~~~t~~--------~i~~l~~~L~~~la~ 133 (308)
T PRK05428 81 LEPPCIIVTRGLEP--PPELLEAAKEAGIPLLRTPLSTTR--------LISKLTNYLDRKLAP 133 (308)
T ss_pred CCCCEEEEECcCCC--CHHHHHHHHHcCCcEEEeCCcHHH--------HHHHHHHHHHHHhhh
Confidence 36789999998765 567899999999999998876554 345666666665554
No 49
>COG0313 Predicted methyltransferases [General function prediction only]
Probab=20.03 E-value=3e+02 Score=23.09 Aligned_cols=49 Identities=18% Similarity=0.322 Sum_probs=34.1
Q ss_pred HHHHHHHhhhhcCCCCCeEEeccCCCccc---chHHHHHHHHcCcEEEeeCCCC
Q psy5177 99 ETIKHIQNQIKASKENPALILMDNHETHQ---SMEAIEYCRASGITLLTFPPHK 149 (213)
Q Consensus 99 ~wl~~f~~~~~~~~~~~~lLllD~~~~H~---~~~~~~~~~~~~i~l~~lP~~~ 149 (213)
+++..+.+.++ .++.+.||-|---.=+ -..+.+.|.+.||.+..+|.-|
T Consensus 65 ~~~~~li~~l~--~g~~valVSDAG~P~ISDPG~~LV~~a~~~gi~V~~lPG~s 116 (275)
T COG0313 65 EKLPKLIPLLK--KGKSVALVSDAGTPLISDPGYELVRAAREAGIRVVPLPGPS 116 (275)
T ss_pred HHHHHHHHHHh--cCCeEEEEecCCCCcccCccHHHHHHHHHcCCcEEecCCcc
Confidence 33444555554 2567889999554443 3468899999999999999754
Done!