Query 001181
Match_columns 1131
No_of_seqs 217 out of 336
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 18:02:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001181.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001181hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06087 Tyr-DNA_phospho: Tyro 100.0 2.8E-85 6.1E-90 748.9 5.0 417 414-1058 2-443 (443)
2 KOG2031 Tyrosyl-DNA phosphodie 100.0 1.4E-78 3.1E-83 679.4 24.1 411 414-1071 78-507 (519)
3 PF00498 FHA: FHA domain; Int 99.4 1.5E-12 3.2E-17 112.9 7.4 67 71-174 1-67 (68)
4 cd00060 FHA Forkhead associate 99.0 2.5E-09 5.5E-14 97.3 9.6 83 58-176 11-93 (102)
5 TIGR03354 VI_FHA type VI secre 98.6 7.5E-08 1.6E-12 111.1 7.3 67 69-174 24-94 (396)
6 smart00240 FHA Forkhead associ 98.5 1.4E-07 3.1E-12 77.5 4.6 52 71-158 1-52 (52)
7 PF08797 HIRAN: HIRAN domain; 98.4 5E-08 1.1E-12 92.8 -1.5 88 668-773 1-88 (107)
8 PLN02927 antheraxanthin epoxid 98.1 3.6E-06 7.8E-11 102.9 7.3 79 59-175 545-635 (668)
9 COG1716 FOG: FHA domain [Signa 98.1 7.3E-06 1.6E-10 83.8 7.7 70 69-178 89-158 (191)
10 COG3456 Predicted component of 98.0 4.2E-06 9.1E-11 96.3 4.8 67 69-174 26-95 (430)
11 KOG1882 Transcriptional regula 97.7 4.1E-05 9E-10 83.0 4.9 86 55-175 180-276 (293)
12 KOG0615 Serine/threonine prote 97.1 0.00029 6.2E-09 81.8 3.6 90 61-175 57-146 (475)
13 KOG1880 Nuclear inhibitor of p 94.7 0.023 5.1E-07 63.9 3.4 74 68-176 37-110 (337)
14 PF13091 PLDc_2: PLD-like doma 93.3 0.087 1.9E-06 50.1 3.8 27 954-988 73-99 (126)
15 TIGR01663 PNK-3'Pase polynucle 91.7 0.3 6.5E-06 59.5 6.5 81 61-181 25-105 (526)
16 KOG1881 Anion exchanger adapto 89.9 0.13 2.9E-06 63.5 1.3 81 57-173 165-254 (793)
17 smart00155 PLDc Phospholipase 87.5 0.54 1.2E-05 35.4 2.7 26 953-986 2-27 (28)
18 TIGR02500 type_III_yscD type I 80.4 2.1 4.7E-05 50.5 4.9 37 63-101 15-52 (410)
19 PRK13912 nuclease NucT; Provis 69.3 4 8.7E-05 42.7 3.1 28 953-988 117-144 (177)
20 cd01764 Urm1 Urm1-like ubuitin 67.6 4.1 8.9E-05 39.2 2.5 28 151-178 62-91 (94)
21 PRK01642 cls cardiolipin synth 66.4 4.8 0.0001 48.5 3.3 27 525-554 218-244 (483)
22 smart00155 PLDc Phospholipase 63.9 6.5 0.00014 29.6 2.5 24 525-551 3-26 (28)
23 PF00614 PLDc: Phospholipase D 63.2 5.1 0.00011 31.0 1.8 24 525-551 3-26 (28)
24 PRK11263 cardiolipin synthase 63.0 5.6 0.00012 47.3 3.0 24 525-551 109-132 (411)
25 PF13091 PLDc_2: PLD-like doma 59.1 9.2 0.0002 36.4 3.2 36 526-564 74-110 (126)
26 cd00754 MoaD Ubiquitin domain 57.0 8.5 0.00018 34.6 2.4 26 150-177 51-76 (80)
27 PF02597 ThiS: ThiS family; I 56.5 7.8 0.00017 34.4 2.1 31 143-177 43-73 (77)
28 cd00138 PLDc Phospholipase D. 56.4 14 0.0003 37.4 4.1 37 525-564 112-149 (176)
29 PF09565 RE_NgoFVII: NgoFVII r 55.5 9.8 0.00021 43.7 3.2 33 953-990 78-110 (296)
30 cd00138 PLDc Phospholipase D. 55.1 8.2 0.00018 39.0 2.3 29 953-989 111-139 (176)
31 PRK09428 pssA phosphatidylseri 53.3 14 0.00031 44.6 4.2 43 951-1028 351-393 (451)
32 KOG0245 Kinesin-like protein [ 50.2 35 0.00075 45.0 6.9 75 62-174 470-546 (1221)
33 COG1502 Cls Phosphatidylserine 50.1 11 0.00025 43.7 2.7 34 522-558 160-193 (438)
34 PRK12452 cardiolipin synthetas 48.2 15 0.00032 45.0 3.3 23 526-551 241-263 (509)
35 PRK01777 hypothetical protein; 47.9 17 0.00036 35.4 3.0 32 144-177 45-76 (95)
36 TIGR01687 moaD_arch MoaD famil 46.0 16 0.00034 33.9 2.4 26 151-176 58-83 (88)
37 PRK11130 moaD molybdopterin sy 42.0 25 0.00053 32.5 3.0 27 144-177 51-77 (81)
38 TIGR01682 moaD molybdopterin c 39.9 30 0.00064 31.7 3.2 28 143-177 49-76 (80)
39 smart00363 S4 S4 RNA-binding d 38.4 35 0.00076 27.6 3.1 29 146-175 23-51 (60)
40 PRK06944 sulfur carrier protei 38.2 27 0.00059 30.6 2.6 26 152-177 34-61 (65)
41 TIGR02988 YaaA_near_RecF S4 do 37.8 28 0.00061 30.3 2.6 27 146-174 31-58 (59)
42 cd00565 ThiS ThiaminS ubiquiti 37.8 29 0.00064 30.7 2.7 27 151-177 33-61 (65)
43 PF11012 DUF2850: Protein of u 37.0 47 0.001 31.7 4.0 34 143-176 18-56 (79)
44 PRK13912 nuclease NucT; Provis 36.6 41 0.00089 35.3 4.0 98 451-561 51-152 (177)
45 PF01479 S4: S4 domain; Inter 35.5 26 0.00056 29.0 1.9 25 146-172 23-48 (48)
46 PRK06437 hypothetical protein; 34.1 39 0.00085 30.6 2.9 25 150-176 38-62 (67)
47 PF09138 Urm1: Urm1 (Ubiquitin 27.0 23 0.00051 34.7 0.3 27 151-177 64-92 (96)
48 cd00165 S4 S4/Hsp/ tRNA synthe 26.8 56 0.0012 27.1 2.6 30 146-176 23-52 (70)
49 PRK11507 ribosome-associated p 25.7 25 0.00055 32.8 0.3 35 139-174 27-61 (70)
50 TIGR01683 thiS thiamine biosyn 25.5 60 0.0013 28.7 2.6 29 144-177 30-60 (64)
51 PHA02820 phospholipase-D-like 24.3 46 0.001 40.0 2.1 26 525-556 112-137 (424)
52 PF09565 RE_NgoFVII: NgoFVII r 20.2 83 0.0018 36.5 3.0 26 527-552 81-107 (296)
No 1
>PF06087 Tyr-DNA_phospho: Tyrosyl-DNA phosphodiesterase; InterPro: IPR010347 Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA [].; GO: 0008081 phosphoric diester hydrolase activity, 0006281 DNA repair, 0005634 nucleus; PDB: 3SQ8_A 3SQ5_B 3SQ3_A 1Q32_D 3SQ7_A 1QZQ_A 1RGU_B 1RG2_B 1MU9_B 1RFI_B ....
Probab=100.00 E-value=2.8e-85 Score=748.88 Aligned_cols=417 Identities=33% Similarity=0.535 Sum_probs=268.6
Q ss_pred CceEEEEecccCCC-CCCCCccccccccCCchhHHHHHHhhcccCHHHHhhhcCCCC--CccEEEEecCCccccccCcCC
Q 001181 414 KKFYLNRLEFMDLT-SLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPS--HLPVTIACHNTERCWSTSADK 490 (1131)
Q Consensus 414 spFyLnrI~~l~~~-~nn~~tISL~DLL~p~g~L~~allfnFm~DidWLLs~f~~~r--~vpVtIv~h~~e~~ws~~~~~ 490 (1131)
.+||+|+|.++++. ..+.++|||+|||++ ++|++||+||||+|++|||++|+... ++||+++.+..+... ..
T Consensus 2 ~~~~~~~i~~~~~~~~~~~~~itl~dil~~-~~l~~~~~~nf~~D~~wll~~~~~~~~~~~~i~~v~g~~~~~~----~~ 76 (443)
T PF06087_consen 2 FKLYLTTIYDLPPRSNNNPDTITLEDILGD-PDLEEALLFNFMIDLDWLLSQFPPSTRKNIPITIVHGTKDPPD----KR 76 (443)
T ss_dssp CEEEEBTTTTS-GG--GTTTEE-HHHHCSG-TTEEEEEEE-SSEEHHHHHCCS-CCGTTCEEEEEECTSEEHHH----HH
T ss_pred cceEEeeecCCCccccCCCCcEeHHHHcCC-ccHHHHHhhhheeeHHHHHHhCCHhhcccceEEEEeCCCcchh----hh
Confidence 47899999999987 346899999999998 58999999999999999999999532 358888744222210 11
Q ss_pred cCCCCCCCCCCeEEEcCCCCccccccccccCCCccccccceEEeeeCCc-eEEEEeCCCCChhhhcccccEEEEecC-CC
Q 001181 491 RTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDS-IRVIVTSANLGAKQWNAVTNTVWWQDF-PR 568 (1131)
Q Consensus 491 rl~~~~~~~pNV~li~PpMPe~IpFG~dr~~~g~GcHHSKMMLL~Y~D~-LRVVI~TANLi~~DW~~~TQ~VWiqDF-Pr 568 (1131)
.+......++|+++|.||||. ||| |||||||||+|+|+ ||||||||||+++||+++||+||+||| |+
T Consensus 77 ~~~~~~~~~~nv~~~~~~mp~--~~g---------~hHsKm~ll~y~~~~lRVvI~TaNl~~~Dw~~~~q~vw~~d~lP~ 145 (443)
T PF06087_consen 77 EIRQQAAIYPNVKLIFPPMPI--PFG---------THHSKMMLLFYEDGSLRVVIPTANLTPYDWNNKTQGVWIQDFLPR 145 (443)
T ss_dssp HHHHHHCCHTTEEEEEE---S--TT-----------B--EEEEEEETTCEEEEEEESS-BSHHHHCSSB-EEEE---E-B
T ss_pred hhhhhcccCCCeEEEccCCCc--ccc---------cccceeEEEEeCCccEEEEEECCCCCHHHHCCcceeEEEecccCc
Confidence 111123478999999999994 677 99999999999998 999999999999999999999999998 99
Q ss_pred CCCCCccccccCCCcccccCCCCCcHHHHHHHHHHHhcCCCCchhHHHHhhccccccccceEEEEecCCcccCCCCCCcc
Q 001181 569 RCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSE 648 (1131)
Q Consensus 569 l~~~d~s~~~~~~s~gE~~~~s~sdFk~dL~~YL~Sy~~~~Psl~~wI~~L~kyDFS~akV~LVaSVPG~H~g~~~~~~e 648 (1131)
++..... ....+++|+++|.+||.+|+. +....|++.|++||||.++|+||+||||+|... . .
T Consensus 146 ~~~~~~~-----------~~~~~~~F~~dL~~yL~~y~~--~~~~~~~~~l~~yDFS~~~v~lV~SvPG~h~~~-~---~ 208 (443)
T PF06087_consen 146 LPSSKSS-----------SEESGSRFKKDLVAYLNSYGK--SPLDKLIERLRKYDFSSARVHLVASVPGKHKED-K---D 208 (443)
T ss_dssp -ECTS-S-------------SSTTHHHHHHHHHHHTT----HHHHHCHHHHHTEE-CCGTSEEEEE-SECCCGG-G---G
T ss_pred ccccccc-----------cCCCCCchHHHHHHHHHHhCC--cchhHHHHHHHhcCCccCceEEEeccCccccCC-C---c
Confidence 9863211 135789999999999999984 236789999999999999999999999999821 0 0
Q ss_pred CCCCCCCCCCcccccCCccccceeeeeeccccccccccCCchhHHHHHHHHhccccccchhhhhhhhcCCCCCCCccccc
Q 001181 649 STYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVS 728 (1131)
Q Consensus 649 s~~~~~~~~~~~~~~~~~~~g~~~~s~~G~sH~f~~~~D~ng~~Lk~la~~l~~~~~~~g~~~~~l~rn~~ip~d~nav~ 728 (1131)
+| | |. +|++ +|+++...+
T Consensus 209 -~~-------------------------G--~~----------~L~~-----------------~L~~~~~~~------- 226 (443)
T PF06087_consen 209 -KW-------------------------G--HM----------RLRK-----------------VLKRLGLPS------- 226 (443)
T ss_dssp -GS-------------------------H--HH----------HHHH-----------------HHHHCCTT--------
T ss_pred -ch-------------------------h--HH----------HHHH-----------------HHHhccccc-------
Confidence 22 4 43 4443 233321000
Q ss_pred cccCCCCCCCCCcccccCCCccccccccCCcccccccccccccchHHHHHHHhhccchheeeeecccCCCCcchhhhhHH
Q 001181 729 VLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQ 808 (1131)
Q Consensus 729 ~~v~~~d~~s~~~~~~~gf~~~~~a~~~s~l~d~g~~~~~g~~~p~~~l~~a~g~~~~k~ql~l~v~~g~~~~~~~~~~~ 808 (1131)
T Consensus 227 -------------------------------------------------------------------------------- 226 (443)
T PF06087_consen 227 -------------------------------------------------------------------------------- 226 (443)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHHHHhhhhhHHHHHhhcCchhhhhhhcccCCCCCcccceEEeecccccc---cHHHHHH-HHHhcCCCccccccCCCCC
Q 001181 809 IEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFSYGSSSIGSI---NAQFLAA-FAAASGKKSLRFYDSEESD 884 (1131)
Q Consensus 809 ~~~~~~~csl~~s~~r~~GL~rlq~vl~~~~wp~~~e~DiVyQ~SSIGSL---~~~wL~~-F~aa~G~~~~~~~~s~~s~ 884 (1131)
.-..+.+.+|+||+||||++ ...||.. |+.++...... + ...
T Consensus 227 ------------------------------~~~~~~~~~~~~Q~SSIGs~~~~~~~Wl~~~f~~sl~~~~~~---~-~~~ 272 (443)
T PF06087_consen 227 ------------------------------NKDKDKESDIVCQFSSIGSLGSSPKDWLTSEFLTSLYPASFS---S-PST 272 (443)
T ss_dssp --------------------------------TTCCCCEEEEE-SBB---SSSTTTTTTTHHHHHCCHHCCT--------
T ss_pred ------------------------------cCCcCCCCeEEEEcccccccCcchhhhHHHHHHHHHhhcccc---c-ccc
Confidence 00123567899999999999 3447653 65221110000 0 112
Q ss_pred CcccccccccccCCCCeEEEcCCHHHHhhcCCCCCCCceeeeeccccccccCc----cccccccccC--CCCCCCCCcce
Q 001181 885 PEWGCWSASQELRSPSIRIIFPTIERVRNACDGILPSKRVLCFSEKTWQRLRN----VDILHDAIPH--PHDRVGHPMHV 958 (1131)
Q Consensus 885 pe~~~~t~~~e~~~p~~rIIFPT~e~Vr~S~~G~~gGgsi~Cf~~k~W~~~~p----r~ifhD~~~~--~s~R~galPHi 958 (1131)
+......+..+...++++|||||+++|++|..|+.+||+ +|++.+||+..++ +.+||+|.+. .++|.+++||+
T Consensus 273 ~~~~~~~~~~~~~~~~~~IvfPT~e~Vr~S~~G~~~ggs-i~~~~~~~~~~~~~~~l~~~~~~w~~~~~~~~R~~~~pH~ 351 (443)
T PF06087_consen 273 PSSKSSSSQQENNRPPLKIVFPTVEEVRNSPEGYNGGGS-IPFKYKWWEPNFPQEWLRPYFHKWYASDDPSGRSRAPPHI 351 (443)
T ss_dssp --HHHHHHHCCHHTEEEEEE--BCHHHCTSTTGGGGGGG-SB--HC--GHHCCHHHHHHCCE-EEEC-TGCTTTTS-B--
T ss_pred ccccccccccccCCCCceEECCCHHHHhhCccCCcCcee-EEecchhccccchHHHHHHHHhhhccccccCCCCCcCcce
Confidence 222222333445578999999999999999999998876 4667788874444 4778899877 78999999999
Q ss_pred EEEEeeecCCCCCceeEEEEcccccchhhcCCCccCCCCCCCCCCCccCCCCCCceeEeeeeeeEEEeCCCC--CCCCCC
Q 001181 959 KVAWRRFQSRTDTSLGWVYCGSHNFSAAAWGRPIQTPSTIKPNGSEKTKSSSSQRLHICNYELGIVFVFPPT--EKQSST 1036 (1131)
Q Consensus 959 Kty~Rrf~s~~~~~igWvYVGSANLSkAAWG~l~knr~~~Ks~~~~~~~ss~~~qL~IrNYELGVLfp~P~~--~~~~~~ 1036 (1131)
|+|+|+. .+....++|+|+||||||+||||+..++ +++++|||||||||| +|+. .+.+++
T Consensus 352 K~y~~~~-~~~~~~~~W~~lgShNLS~aAWG~~~~~----------------~~~l~i~nyElGVl~-~P~~~~~~~~~~ 413 (443)
T PF06087_consen 352 KTYMRFS-KNDFKSLGWFYLGSHNLSKAAWGKRSKN----------------GSQLSIRNYELGVLF-LPSSFGVMLPVF 413 (443)
T ss_dssp EEEEEEE--TTTSEECEEEEES--BSHHHH-EEETT----------------TTCCEESSBEEEEEE-EGGGCTSSSSCE
T ss_pred EEEEEec-CCCCCccceEEeCcccCCHHHhcccccC----------------CceeeecceEEEEEE-ecCccccccccc
Confidence 9999974 3445699999999999999999996543 689999999999999 4432 233433
Q ss_pred CC--------CCCCCCceeeecccCCCCCC
Q 001181 1037 GN--------NTSNLDDIVLPFVVPAPKYR 1058 (1131)
Q Consensus 1037 ~~--------~~~~~~~~pvPfdlP~~~Y~ 1058 (1131)
.. .......++|||++|++||+
T Consensus 414 ~~~~~~~~~~~~~~~~~v~vPf~lP~~~Y~ 443 (443)
T PF06087_consen 414 SLDDPVYRSISSTNTVPVPVPFDLPPTPYG 443 (443)
T ss_dssp EEECCG-------GGGCEEESS-SSEEE--
T ss_pred ccccccccccccCCCceEEecCCCCCcCcC
Confidence 21 12234579999999999996
No 2
>KOG2031 consensus Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair]
Probab=100.00 E-value=1.4e-78 Score=679.38 Aligned_cols=411 Identities=26% Similarity=0.391 Sum_probs=315.2
Q ss_pred CceEEEEeccc-CCCCCCCCccccccccCC-chhHHHHHHhhcccCHHHHhhhcC-CCCCccEEEEecCCccccccCcCC
Q 001181 414 KKFYLNRLEFM-DLTSLNYDVISLPELLYP-VESISRMFIATFTSDILWFMSYCE-IPSHLPVTIACHNTERCWSTSADK 490 (1131)
Q Consensus 414 spFyLnrI~~l-~~~~nn~~tISL~DLL~p-~g~L~~allfnFm~DidWLLs~f~-~~r~vpVtIv~h~~e~~ws~~~~~ 490 (1131)
..+||+++++. .+.+.....+++.+||.+ .|++..++|||||+|++||+.+|+ ..+..|++++ |++.. ..
T Consensus 78 ~~~~ft~v~~~s~~~~~s~~s~sl~~il~~i~g~~v~silfsfmvdid~Lv~~y~~~~~~~~i~l~-~G~~d------~~ 150 (519)
T KOG2031|consen 78 KGAVFTTVKGDSVPRYDSMGSVSLMEILADIFGTPVNSILFSFMVDIDWLVGQYPPSVRIKPITLV-HGEPD------EA 150 (519)
T ss_pred ccccccccccccccccCcccchHHHHHHHHhhCCchhheEEEEEeEHHHHHhhCcchhccCceEEE-ecCCc------hH
Confidence 35789999884 344444577888888873 456899999999999999999998 4677787776 55432 12
Q ss_pred cCCCCCCCCCCeEEEcCCCCccccccccccCCCccccccceEEeeeCCceEEEEeCCCCChhhhcccccEEEEecCCCCC
Q 001181 491 RTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRC 570 (1131)
Q Consensus 491 rl~~~~~~~pNV~li~PpMPe~IpFG~dr~~~g~GcHHSKMMLL~Y~D~LRVVI~TANLi~~DW~~~TQ~VWiqDFPrl~ 570 (1131)
++.......-+++++.+.|| |||| |||+|||+|+|++++|||||||||++.||+++||++|++++++..
T Consensus 151 ~~~~~~K~~~l~~~~~~~Lp--ipF~---------thHtKm~~l~y~~G~rvvv~taNl~~~Dw~~ktQ~~w~sp~~~~~ 219 (519)
T KOG2031|consen 151 RLLAQTKAPILVTVKLASLP--IPFG---------THHTKMIILFYEEGCRVVVHTANLIHDDWNNKTQGFWCSPLLKIG 219 (519)
T ss_pred HHHhhhhccceeeeeccccc--cccc---------ccccceEEEeccCccEEEEecCCcceecccccccceeecCCcccc
Confidence 33333444569999999999 7999 999999999999999999999999999999999999999876665
Q ss_pred CCCccccccCCCcccccCCCCCcHHHHHHHHHHHhcCCCCchhHHHHhhccccccccceEEEEecCCcccCCCCCCccCC
Q 001181 571 APDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSEST 650 (1131)
Q Consensus 571 ~~d~s~~~~~~s~gE~~~~s~sdFk~dL~~YL~Sy~~~~Psl~~wI~~L~kyDFS~akV~LVaSVPG~H~g~~~~~~es~ 650 (1131)
... ....+.|++||++||.+|. .|+++.|++.|++||||.++|+||+||||++.+..
T Consensus 220 ~~~--------------g~~~~~Fk~DLi~YL~~Y~--~~~l~~~i~~lkk~DfS~i~v~fIgStPG~f~gs~------- 276 (519)
T KOG2031|consen 220 DKK--------------GVSPTGFKQDLIEYLNSYR--LPQLKEWIASLKKVDFSAINVRFIGSTPGKFQGSG------- 276 (519)
T ss_pred cCC--------------CCCCCchHHHHHHHHHHhc--cchhHHHHHHHHhcchhhceEEEEeecCCcccCcc-------
Confidence 211 3577999999999999996 46889999999999999999999999999976643
Q ss_pred CCCCCCCCcccccCCccccceeeeeeccccccccccCCchhHHHHHHHHhccccccchhhhhhhhcCCCCCCCccccccc
Q 001181 651 YSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVL 730 (1131)
Q Consensus 651 ~~~~~~~~~~~~~~~~~~g~~~~s~~G~sH~f~~~~D~ng~~Lk~la~~l~~~~~~~g~~~~~l~rn~~ip~d~nav~~~ 730 (1131)
+-+ || |. +|++| |+.+
T Consensus 277 ---------------------~~~-WG--h~----------kL~ki-----------------L~~~------------- 292 (519)
T KOG2031|consen 277 ---------------------LLS-WG--HN----------KLKKI-----------------LKEH------------- 292 (519)
T ss_pred ---------------------ccc-cc--HH----------HHHHH-----------------HHhh-------------
Confidence 122 35 66 77774 2221
Q ss_pred cCCCCCCCCCcccccCCCccccccccCCcccccccccccccchHHHHHHHhhccchheeeeecccCCCCcchhhhhHHHH
Q 001181 731 VPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIE 810 (1131)
Q Consensus 731 v~~~d~~s~~~~~~~gf~~~~~a~~~s~l~d~g~~~~~g~~~p~~~l~~a~g~~~~k~ql~l~v~~g~~~~~~~~~~~~~ 810 (1131)
T Consensus 293 -------------------------------------------------------------------------------- 292 (519)
T KOG2031|consen 293 -------------------------------------------------------------------------------- 292 (519)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHHhhhhhHHHHHhhcCchhhhhhhcccCC-CCCcccceEEeecccccccHHHHHHHH-HhcCCCccccccCCCCCCccc
Q 001181 811 HVVALSSLIASIQRCRGLWRLQEVLGQYRW-PELQESDFSYGSSSIGSINAQFLAAFA-AASGKKSLRFYDSEESDPEWG 888 (1131)
Q Consensus 811 ~~~~~csl~~s~~r~~GL~rlq~vl~~~~w-p~~~e~DiVyQ~SSIGSL~~~wL~~F~-aa~G~~~~~~~~s~~s~pe~~ 888 (1131)
.- |...+..+|+|+||||||+..|.+-|. .-.+ ++. +.+
T Consensus 293 ----------------------------~~~~~~~r~~~v~q~sS~gsl~~~~~~~~~~~f~~--~l~----kdt----- 333 (519)
T KOG2031|consen 293 ----------------------------AASPYLERTPVVGQSSSIGSLGSLWSAWFIGDFVE--SLA----KDT----- 333 (519)
T ss_pred ----------------------------ccCcccccCceeeeeeccccccchhhhhhhhhhcc--chh----hcc-----
Confidence 00 111234489999999999988877643 1111 110 000
Q ss_pred ccccccccCCCCeEEEcCCHHHHhhcCCCCCCCceeeeec----cccccccCccccccccccCCCCCCCCCcceEEEEee
Q 001181 889 CWSASQELRSPSIRIIFPTIERVRNACDGILPSKRVLCFS----EKTWQRLRNVDILHDAIPHPHDRVGHPMHVKVAWRR 964 (1131)
Q Consensus 889 ~~t~~~e~~~p~~rIIFPT~e~Vr~S~~G~~gGgsi~Cf~----~k~W~~~~pr~ifhD~~~~~s~R~galPHiKty~Rr 964 (1131)
+......+++.|||||+++||+|+.||.+||++..-. ++.|. +.++++|.+..++|.|+|||||||||.
T Consensus 334 ---~~~gk~~~~~yiIfPTveeVrtS~~G~~~Ggsipy~~~~~~kq~~l----k~y~~kW~A~~s~R~ramPHiKtYmr~ 406 (519)
T KOG2031|consen 334 ---TPPGKLRPPFYIIFPTVEEVRTSLLGYAGGGSLPYGKNTNEKQPWL----KKYLCKWKAMDSRRSRAMPHIKTYMRF 406 (519)
T ss_pred ---CCCCCCCCCeeEEcccHHHhhccccccccCceecccchhhhhhHHH----HHHHHhhhhhhhhccccCCcceeeeee
Confidence 1111223789999999999999999999999775421 33455 578999999999999999999999984
Q ss_pred ecCCCCCceeEEEEcccccchhhcCCCccCCCCCCCCCCCccCCCCCCceeEeeeeeeEEEeCCCC-CCCCC-------C
Q 001181 965 FQSRTDTSLGWVYCGSHNFSAAAWGRPIQTPSTIKPNGSEKTKSSSSQRLHICNYELGIVFVFPPT-EKQSS-------T 1036 (1131)
Q Consensus 965 f~s~~~~~igWvYVGSANLSkAAWG~l~knr~~~Ks~~~~~~~ss~~~qL~IrNYELGVLfp~P~~-~~~~~-------~ 1036 (1131)
+++++.+.|+++|||||||||||.+++|+ +++++|+|||||+|||| +|.. ...+. +
T Consensus 407 --~~d~q~l~W~LlTSANLSKaAWG~l~kn~-------------sk~~~LmIRsYEaGVLf-~p~~~~~~kt~k~~~~tf 470 (519)
T KOG2031|consen 407 --NLDDQKLAWFLLTSANLSKAAWGTLSKNK-------------SKQPQLMIRSYEAGVLF-LPRFFANLKTFKVVEDTF 470 (519)
T ss_pred --cCCCCEEEEEEEeccccchhhhhhhccCC-------------CCCchheeeecccceEe-cchhhhccccccccceec
Confidence 56778999999999999999999999872 23488999999999999 6653 20011 1
Q ss_pred C--CCCCCCCceeeecccCCCCCCCCCCCcchhHhHH
Q 001181 1037 G--NNTSNLDDIVLPFVVPAPKYRPKDRPATAQAMRE 1071 (1131)
Q Consensus 1037 ~--~~~~~~~~~pvPfdlP~~~Y~~~D~PW~~~a~~e 1071 (1131)
. ........||||||+|+.+|++.|+||+.+..|+
T Consensus 471 ~~~~~~~~v~~vpvpydlPp~pY~~~d~~~~~~~~~~ 507 (519)
T KOG2031|consen 471 PRDNNGDGVIAVPVPYDLPPVPYSPKDEPFFTDIYRQ 507 (519)
T ss_pred ccccCCCCcceeccccCCCCcCCCccCCceeeccccc
Confidence 1 1123346799999999999999999999996654
No 3
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=99.36 E-value=1.5e-12 Score=112.86 Aligned_cols=67 Identities=40% Similarity=0.680 Sum_probs=60.3
Q ss_pred eeecCCCcccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccccccceeeeeeccc
Q 001181 71 YSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNG 150 (1131)
Q Consensus 71 ~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ng 150 (1131)
|+|||+. .||+++++..||++||.|.++.. .++||.|- -|.||
T Consensus 1 ~~iGR~~-~~di~l~~~~iSr~Ha~i~~~~~-~~~~i~d~-----------------------------------~s~ng 43 (68)
T PF00498_consen 1 VTIGRSP-DCDIVLPDPSISRRHARISFDDD-GQFYIEDL-----------------------------------GSTNG 43 (68)
T ss_dssp EEEESST-TSSEEETSTTSSTTSEEEEEETT-EEEEEEES-----------------------------------SSSS-
T ss_pred CEEcCCC-CCCEEECCHheeeeeeEEEEece-eeEEEEeC-----------------------------------CCCCc
Confidence 7999995 89999999999999999999998 88999980 37999
Q ss_pred eEeeceEecccceEeecCCCeEEE
Q 001181 151 VFVNGIRLKSGIVRELNAGDEVLF 174 (1131)
Q Consensus 151 ~fvng~r~~kg~~~el~~gd~v~~ 174 (1131)
|||||.++.++..++|..||++.|
T Consensus 44 t~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 44 TFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp EEETTEEESSTSEEEE-TTEEEEE
T ss_pred EEECCEEcCCCCEEECCCCCEEEc
Confidence 999999999999999999999976
No 4
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=98.97 E-value=2.5e-09 Score=97.30 Aligned_cols=83 Identities=36% Similarity=0.560 Sum_probs=70.5
Q ss_pred CcceeeeeecCCceeecCCCcccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccc
Q 001181 58 SPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEE 137 (1131)
Q Consensus 58 ~~~~~~~l~~d~~~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 137 (1131)
..-..+.|.++..++|||+...+|++|.+..||++||.|.++... +.++.| .
T Consensus 11 ~~~~~~~l~~~~~~~iGr~~~~~~i~l~~~~iS~~H~~i~~~~~~-~~~~~~------------------------~--- 62 (102)
T cd00060 11 ASGRRYYLDPGGTYTIGRDSDNCDIVLDDPSVSRRHAVIRYDGDG-GVVLID------------------------L--- 62 (102)
T ss_pred CceeEEEECCCCeEEECcCCCcCCEEcCCCCeeCcceEEEEcCCC-CEEEEE------------------------C---
Confidence 456788888889999999993349999999999999999999863 334444 1
Q ss_pred cccceeeeeeccceEeeceEecccceEeecCCCeEEEEe
Q 001181 138 DEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (1131)
Q Consensus 138 ~~~~~~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~~ 176 (1131)
.|.||+||||.++.++..+.|..||++.+..
T Consensus 63 --------~s~~g~~vn~~~~~~~~~~~l~~gd~i~ig~ 93 (102)
T cd00060 63 --------GSTNGTFVNGQRVSPGEPVRLRDGDVIRLGN 93 (102)
T ss_pred --------CCCCCeEECCEECCCCCcEECCCCCEEEECC
Confidence 6889999999999999999999999998864
No 5
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=98.58 E-value=7.5e-08 Score=111.10 Aligned_cols=67 Identities=33% Similarity=0.570 Sum_probs=61.0
Q ss_pred CceeecCCCcccceEEcccc--ccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccccccceeeee
Q 001181 69 RPYSIGRASINCDFTFDNRL--VSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMV 146 (1131)
Q Consensus 69 ~~~~igr~~~~~d~~~~~~~--vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 146 (1131)
..++|||+. .||+++.++. ||++||+|.++.. ..||.| .
T Consensus 24 ~~~~IGR~~-~~d~~l~d~~~~VS~~Ha~I~~~~g--~~~l~D------------------------------------l 64 (396)
T TIGR03354 24 NGGTIGRSE-DCDWVLPDPERHVSGRHARIRYRDG--AYLLTD------------------------------------L 64 (396)
T ss_pred CCEEEecCC-CCCEEeCCCCCCcchhhcEEEEECC--EEEEEE------------------------------------C
Confidence 469999999 8999999998 9999999999863 677888 6
Q ss_pred eccceEee--ceEecccceEeecCCCeEEE
Q 001181 147 SLNGVFVN--GIRLKSGIVRELNAGDEVLF 174 (1131)
Q Consensus 147 s~ng~fvn--g~r~~kg~~~el~~gd~v~~ 174 (1131)
|+|||||| |.+|.+|..+.|+.||+|.+
T Consensus 65 StNGT~VN~sg~~l~~~~~~~L~~GD~I~i 94 (396)
T TIGR03354 65 STNGVFLNGSGSPLGRGNPVRLEQGDRLRL 94 (396)
T ss_pred CCCCeEECCCCCCCCCCCceEcCCCCEEEE
Confidence 89999999 99999999999999999865
No 6
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=98.49 E-value=1.4e-07 Score=77.53 Aligned_cols=52 Identities=40% Similarity=0.771 Sum_probs=46.0
Q ss_pred eeecCCCcccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccccccceeeeeeccc
Q 001181 71 YSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNG 150 (1131)
Q Consensus 71 ~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ng 150 (1131)
++|||.+-.|++++++..||++||.|.+|+.. .++|.|. -|.||
T Consensus 1 ~~iGr~~~~~~i~~~~~~vs~~H~~i~~~~~~-~~~i~d~-----------------------------------~s~~g 44 (52)
T smart00240 1 VTIGRSSEDCDIQLPGPSISRRHAEIVYDGGG-RFYLIDL-----------------------------------GSTNG 44 (52)
T ss_pred CEeCCCCCCCCEEeCCCCcchhHcEEEECCCC-eEEEEEC-----------------------------------CCCCC
Confidence 58999986799999999999999999999875 6888882 46999
Q ss_pred eEeeceEe
Q 001181 151 VFVNGIRL 158 (1131)
Q Consensus 151 ~fvng~r~ 158 (1131)
|||||.+|
T Consensus 45 t~vng~~v 52 (52)
T smart00240 45 TFVNGKRI 52 (52)
T ss_pred eeECCEEC
Confidence 99999986
No 7
>PF08797 HIRAN: HIRAN domain; InterPro: IPR014905 The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. HIRAN is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes []. It has been predicted that this protein functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 2L1I_A 3K2Y_C.
Probab=98.35 E-value=5e-08 Score=92.83 Aligned_cols=88 Identities=33% Similarity=0.526 Sum_probs=58.6
Q ss_pred ccceeeeeeccccccccccCCchhHHHHHHHHhccccccchhhhhhhhcCCCCCCCccccccccCCCCCCCCCcccccCC
Q 001181 668 LGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGF 747 (1131)
Q Consensus 668 ~g~~~~s~~G~sH~f~~~~D~ng~~Lk~la~~l~~~~~~~g~~~~~l~rn~~ip~d~nav~~~v~~~d~~s~~~~~~~gf 747 (1131)
+|++++.++|+.|. |. .+ ..+ ......++.|+|..+.|.|+||+.|...+....+.|. ++|+
T Consensus 1 ~G~~~~~v~g~~~~-----~~-----~~---~~~---~l~~g~~v~L~re~~N~~D~nAi~v~~~~~~~~~~~~--~iGy 62 (107)
T PF08797_consen 1 IGSFYFFVAGTRYY-----DG-----RA---GRG---KLKPGDRVVLVREPDNPYDPNAIKVYTIDRFSNSRGR--EIGY 62 (107)
T ss_dssp --B--EEEE-CCCS-----TT-----HH---CCT---T--TTSEEEEEEETT-TTHCCCCCEEETT------BG--CCCC
T ss_pred CcEEEEEEEEeecc-----cc-----cc---ccc---ccCCCCEEEEEEcCCCCCCcccEEEEEeecccccCCC--EEEE
Confidence 58999999999984 11 00 010 2223567889999999999999999887765555444 8999
Q ss_pred CccccccccCCcccccccccccccch
Q 001181 748 MPRDIAKWVSPLWDIGFIRFSGFISR 773 (1131)
Q Consensus 748 ~~~~~a~~~s~l~d~g~~~~~g~~~p 773 (1131)
||+++|+|++||.|.|.++|.|.+..
T Consensus 63 lp~~~a~~l~~Lld~~~~~~~~~v~~ 88 (107)
T PF08797_consen 63 LPREIAKWLSPLLDSGGVKFEGTVVF 88 (107)
T ss_dssp CHHHHHHHHHHHCCT-TEEEEEEEEC
T ss_pred ecHHHHHHHHHHHhCCCcEEEEEEEE
Confidence 99999999999999999999999654
No 8
>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase
Probab=98.13 E-value=3.6e-06 Score=102.91 Aligned_cols=79 Identities=20% Similarity=0.442 Sum_probs=66.5
Q ss_pred cceeeeeecCC--ceeecCCCcccce-----EEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccc
Q 001181 59 PVDSLTLEPDR--PYSIGRASINCDF-----TFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKS 131 (1131)
Q Consensus 59 ~~~~~~l~~d~--~~~igr~~~~~d~-----~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~ 131 (1131)
-...|.|.+|. ||.|||.+ .||+ ||++.-||++|..|.++.. ..||.|
T Consensus 545 ~~~~~~l~~~~~~p~~iG~~~-~~~~~~~~i~i~~~~vS~~Ha~i~~~~~--~~~~~D---------------------- 599 (668)
T PLN02927 545 VSETLCLTKDEDQPCIVGSEP-DQDFPGMRIVIPSSQVSKMHARVIYKDG--AFFLMD---------------------- 599 (668)
T ss_pred ccceeeeecCCCCCeEecCCC-CcCCCCceEEecCCccChhHeEEEEECC--EEEEEE----------------------
Confidence 34667777776 99999999 8898 9999999999999999854 567777
Q ss_pred cccccccccceeeeeeccceEeeceE-----ecccceEeecCCCeEEEE
Q 001181 132 LEDEEEDEGFSRVMVSLNGVFVNGIR-----LKSGIVRELNAGDEVLFV 175 (1131)
Q Consensus 132 ~~~~~~~~~~~~~~~s~ng~fvng~r-----~~kg~~~el~~gd~v~~~ 175 (1131)
| =|+|||||||.+ +..+....|++||.|.|-
T Consensus 600 ---------l----~S~nGT~v~~~~~~r~~~~p~~~~~l~~~d~I~~g 635 (668)
T PLN02927 600 ---------L----RSEHGTYVTDNEGRRYRATPNFPARFRSSDIIEFG 635 (668)
T ss_pred ---------C----CCCCccEEeCCCCceEecCCCCceEeCCCCEEEeC
Confidence 2 589999997776 557889999999999883
No 9
>COG1716 FOG: FHA domain [Signal transduction mechanisms]
Probab=98.10 E-value=7.3e-06 Score=83.76 Aligned_cols=70 Identities=29% Similarity=0.397 Sum_probs=58.5
Q ss_pred CceeecCCCcccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccccccceeeeeec
Q 001181 69 RPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSL 148 (1131)
Q Consensus 69 ~~~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ 148 (1131)
..+||||+ .++|+++++..||++||.|..++..-- +.| + =|+
T Consensus 89 ~~~tigr~-~~~~i~~~~~~vSR~Ha~l~~~~~~~~--~~d-------------------------------~----~S~ 130 (191)
T COG1716 89 PVTTIGRD-PDNDIVLDDDVVSRRHAELRREGNEVF--LED-------------------------------L----GST 130 (191)
T ss_pred ceEEeccC-CCCCEEcCCCccccceEEEEEeCCceE--EEE-------------------------------C----CCC
Confidence 38999994 599999999999999999999987332 244 3 489
Q ss_pred cceEeeceEecccceEeecCCCeEEEEecC
Q 001181 149 NGVFVNGIRLKSGIVRELNAGDEVLFVCRD 178 (1131)
Q Consensus 149 ng~fvng~r~~kg~~~el~~gd~v~~~~~~ 178 (1131)
|||||||.++.. .+.|..||.+.|-...
T Consensus 131 nGt~vn~~~v~~--~~~l~~gd~i~i~~~~ 158 (191)
T COG1716 131 NGTYVNGEKVRQ--RVLLQDGDVIRLGGTL 158 (191)
T ss_pred cceEECCeEccC--cEEcCCCCEEEECccc
Confidence 999999999998 8889999999875433
No 10
>COG3456 Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=98.02 E-value=4.2e-06 Score=96.31 Aligned_cols=67 Identities=37% Similarity=0.658 Sum_probs=58.8
Q ss_pred CceeecCCCcccceEEccc--cccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccccccceeeee
Q 001181 69 RPYSIGRASINCDFTFDNR--LVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMV 146 (1131)
Q Consensus 69 ~~~~igr~~~~~d~~~~~~--~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 146 (1131)
+--+|||+. +||.+|+|+ .||++||.|..+... .||+| .
T Consensus 26 ~~g~IGrs~-dcdW~i~D~~~~VS~~Hc~I~~~dg~--f~L~D------------------------------------t 66 (430)
T COG3456 26 GGGVIGRSP-DCDWQIDDPERFVSKQHCTISYRDGG--FCLTD------------------------------------T 66 (430)
T ss_pred CCcccccCC-CCCccccCcccccchhheEEEecCCe--EEEEe------------------------------------c
Confidence 367899998 999999998 999999999988663 35556 6
Q ss_pred eccceEeeceEecccce-EeecCCCeEEE
Q 001181 147 SLNGVFVNGIRLKSGIV-RELNAGDEVLF 174 (1131)
Q Consensus 147 s~ng~fvng~r~~kg~~-~el~~gd~v~~ 174 (1131)
|.||+||||-.+..|.- .-|+-||||++
T Consensus 67 S~g~l~VNgs~~~~g~~~~RLqqGd~i~i 95 (430)
T COG3456 67 SNGGLLVNGSDLPLGEGSARLQQGDEILI 95 (430)
T ss_pred CCCceeecccccCCCCCccccccCCEEee
Confidence 78999999999999998 99999999965
No 11
>KOG1882 consensus Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms]
Probab=97.68 E-value=4.1e-05 Score=82.98 Aligned_cols=86 Identities=27% Similarity=0.304 Sum_probs=75.4
Q ss_pred CCCCcceeeeeecCCceeecCCCcccceEEccccccccceeEeeeccc-----------eeEEEEcCcccccccchhhHH
Q 001181 55 ATGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSE-----------RKIYVLDGTFLLPAFSSVVNE 123 (1131)
Q Consensus 55 ~~~~~~~~~~l~~d~~~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~-----------~k~~i~d~~~~~~~~~~~~~~ 123 (1131)
..+.+++.++||.-..|-+||..--.|.-||+..-|||||-|-|-.+. .|.||.|
T Consensus 180 k~~e~l~~l~iHrqs~yL~gRerkIaDi~idhpScSKQHaviQyR~v~~~r~dGt~grrvkpYiiD-------------- 245 (293)
T KOG1882|consen 180 KCYEVLPVLYIHRQSCYLDGRERKIADIPIDHPSCSKQHAVIQYRLVEFTRADGTVGRRVKPYIID-------------- 245 (293)
T ss_pred cCCcccchheeeeeeeeecCceeeeeccCCCCccccccceeeeeeecccccCCCccceeeeeEEEe--------------
Confidence 456688999999999999999888889999999999999999885543 5778888
Q ss_pred HhhhcccccccccccccceeeeeeccceEeeceEecccceEeecCCCeEEEE
Q 001181 124 FRKKRDKSLEDEEEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (1131)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~ 175 (1131)
| =|.||||+|-++|..-.-.||..+|-+.|-
T Consensus 246 -----------------L----gS~NgTfLNnk~IepqRYyEL~ekDvlkfg 276 (293)
T KOG1882|consen 246 -----------------L----GSGNGTFLNNKVIEPQRYYELREKDVLKFG 276 (293)
T ss_pred -----------------c----CCCCcceecCcccCchheeeeecCceeeec
Confidence 1 589999999999999999999999998874
No 12
>KOG0615 consensus Serine/threonine protein kinase Chk2 and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.15 E-value=0.00029 Score=81.77 Aligned_cols=90 Identities=32% Similarity=0.421 Sum_probs=63.7
Q ss_pred eeeeeecCCceeecCCCcccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhccccccccccccc
Q 001181 61 DSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEG 140 (1131)
Q Consensus 61 ~~~~l~~d~~~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (1131)
.++++.-| -|+.||.. .||+..+.-+||.+|=+|++=....++.-+.+.-.. + -.+-++|
T Consensus 57 ~~~d~~nd-~f~fGR~~-~~d~~ln~~~~s~~~~~i~~~~~~~~~~f~~dr~~~---s---------n~~y~~D------ 116 (475)
T KOG0615|consen 57 KSIDLAND-EFTFGRGD-SCDAPLNLNNVSNKHFKILLYNKISKIHFRIDRDKN---S---------NRVYLHD------ 116 (475)
T ss_pred ccceeccc-eEEecCCC-cccccccCccccccchheeeeeeeeeeeecccCCCc---c---------ceEEEEe------
Confidence 55555543 69999998 899999999999999999876433333322210000 0 0001122
Q ss_pred ceeeeeeccceEeeceEecccceEeecCCCeEEEE
Q 001181 141 FSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (1131)
Q Consensus 141 ~~~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~ 175 (1131)
.|.||||||--++.||..++|+.|||+++-
T Consensus 117 -----hS~nGT~VN~e~i~k~~~r~lkN~dei~is 146 (475)
T KOG0615|consen 117 -----HSRNGTFVNDEMIGKGLSRILKNGDEISIS 146 (475)
T ss_pred -----cccCcccccHhHhhccccccccCCCEEEec
Confidence 799999999999999999999999999943
No 13
>KOG1880 consensus Nuclear inhibitor of phosphatase-1 [General function prediction only]
Probab=94.73 E-value=0.023 Score=63.93 Aligned_cols=74 Identities=28% Similarity=0.545 Sum_probs=66.1
Q ss_pred CCceeecCCCcccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccccccceeeeee
Q 001181 68 DRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVS 147 (1131)
Q Consensus 68 d~~~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s 147 (1131)
++-|-.||.+.-|||+||+..+|++|--+++---...+|+.| .=|
T Consensus 37 kr~y~Fgrn~q~~df~idh~scSrvhaa~vyhkhl~~~~lid-----------------------------------l~s 81 (337)
T KOG1880|consen 37 KRRYLFGRNHQTCDFVIDHASCSRVHAALVYHKHLSRIFLID-----------------------------------LGS 81 (337)
T ss_pred hhhhhhccCCCccceEeecchhhhhHhhhhhhhccceEEEEE-----------------------------------ccC
Confidence 448999999999999999999999999998888877788888 146
Q ss_pred ccceEeeceEecccceEeecCCCeEEEEe
Q 001181 148 LNGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (1131)
Q Consensus 148 ~ng~fvng~r~~kg~~~el~~gd~v~~~~ 176 (1131)
+-|||+--.||++.+.++|++|-.+.|-.
T Consensus 82 ~hgtf~g~~rL~~~~p~~l~i~~~~~fga 110 (337)
T KOG1880|consen 82 THGTFLGNERLEPHKPVQLEIGSTFHFGA 110 (337)
T ss_pred CcceeeeeeeeccCCCccccCCceEEEec
Confidence 78999999999999999999999888754
No 14
>PF13091 PLDc_2: PLD-like domain; PDB: 2ZE4_A 2ZE9_A 1BYS_A 1BYR_A 1V0T_A 1V0U_A 1V0V_A 1V0S_A 1V0R_A 1V0W_A ....
Probab=93.30 E-value=0.087 Score=50.14 Aligned_cols=27 Identities=19% Similarity=0.316 Sum_probs=17.5
Q ss_pred CCcceEEEEeeecCCCCCceeEEEEcccccchhhc
Q 001181 954 HPMHVKVAWRRFQSRTDTSLGWVYCGSHNFSAAAW 988 (1131)
Q Consensus 954 alPHiKty~Rrf~s~~~~~igWvYVGSANLSkAAW 988 (1131)
-.+|.|+|+. ++ . .+++||+|||..+|
T Consensus 73 ~~~H~K~~i~--d~---~---~~iiGS~N~t~~~~ 99 (126)
T PF13091_consen 73 NRLHAKFYII--DD---K---VAIIGSANLTSSSF 99 (126)
T ss_dssp S-B--EEEEE--TT---T---EEEEES--CSCCCS
T ss_pred cCCCcceEEe--cC---c---cEEEcCCCCCcchh
Confidence 4899999995 21 1 79999999998888
No 15
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=91.73 E-value=0.3 Score=59.47 Aligned_cols=81 Identities=21% Similarity=0.290 Sum_probs=69.7
Q ss_pred eeeeeecCCceeecCCCcccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhccccccccccccc
Q 001181 61 DSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEG 140 (1131)
Q Consensus 61 ~~~~l~~d~~~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (1131)
..|||. +....|||++ +=.|-|++-||+.=|+-.|-..+-|.+--
T Consensus 25 ~~~~~~-~~~~~~gr~p---et~i~d~~cs~~qv~l~a~~~~~~v~~k~------------------------------- 69 (526)
T TIGR01663 25 HFIHLD-AGALFLGRGP---ETGIRDRKCSKRQIELQADLEKATVALKQ------------------------------- 69 (526)
T ss_pred CeeccC-CCceEEccCc---ccccchhhhchhhheeeecccCceEEEEE-------------------------------
Confidence 667777 6788899999 88999999999999999999877666554
Q ss_pred ceeeeeeccceEeeceEecccceEeecCCCeEEEEecCCcc
Q 001181 141 FSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESL 181 (1131)
Q Consensus 141 ~~~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~~~~~~~ 181 (1131)
+-.|=.-|||+.+.||+..||..||-+.+|.|-...
T Consensus 70 -----lg~np~~~~~~~~~~~~~~~l~~g~~l~~v~~~~~~ 105 (526)
T TIGR01663 70 -----LGVNPCGTGGLELKPGGEGELGHGDLLEIVNGLHPL 105 (526)
T ss_pred -----ccCCCcccCceEecCCCeeeecCCCEEEEeccccce
Confidence 556888899999999999999999999999876543
No 16
>KOG1881 consensus Anion exchanger adaptor protein Kanadaptin, contains FHA domain [General function prediction only]
Probab=89.89 E-value=0.13 Score=63.48 Aligned_cols=81 Identities=22% Similarity=0.402 Sum_probs=65.6
Q ss_pred CCcceeeeeecCCceeecCCCcccceEEccccccccceeEeeecccee---------EEEEcCcccccccchhhHHHhhh
Q 001181 57 GSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERK---------IYVLDGTFLLPAFSSVVNEFRKK 127 (1131)
Q Consensus 57 ~~~~~~~~l~~d~~~~igr~~~~~d~~~~~~~vs~~hcqi~~d~~~~k---------~~i~d~~~~~~~~~~~~~~~~~~ 127 (1131)
|..|.+.+|+--.-|++||-. .||+-+.+..||+-||-|-+=+.--- -||+|
T Consensus 165 g~iiet~~l~~~~~~~fgr~~-~cD~~~eHpsISr~h~vlQy~~~~~~~p~~s~~~g~~i~d------------------ 225 (793)
T KOG1881|consen 165 GAIIETEDLKGAAACLFGRLG-GCDVALEHPSISRFHAVLQYKASGPDDPCASNGEGWYIYD------------------ 225 (793)
T ss_pred CceeeeeecccceeEEecccC-CCccccccCcccccceeeeccCCCCCccccCCCCceEEee------------------
Confidence 557788999999999999999 99999999999999999988655322 33333
Q ss_pred cccccccccccccceeeeeeccceEeeceEecccceEeecCCCeEE
Q 001181 128 RDKSLEDEEEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVL 173 (1131)
Q Consensus 128 ~~~~~~~~~~~~~~~~~~~s~ng~fvng~r~~kg~~~el~~gd~v~ 173 (1131)
+.|+-|+|+|-.||.+-.-+-+.+|+-+-
T Consensus 226 -----------------lgsThgt~~NK~rvppk~yir~~Vg~v~~ 254 (793)
T KOG1881|consen 226 -----------------LGSTHGTFLNKDRVPPKVYIRDRVGHVAR 254 (793)
T ss_pred -----------------ccccccceeccccCCCcchhhhhHHHHHH
Confidence 27999999999999998777766666544
No 17
>smart00155 PLDc Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not be
Probab=87.55 E-value=0.54 Score=35.40 Aligned_cols=26 Identities=23% Similarity=0.272 Sum_probs=20.2
Q ss_pred CCCcceEEEEeeecCCCCCceeEEEEcccccchh
Q 001181 953 GHPMHVKVAWRRFQSRTDTSLGWVYCGSHNFSAA 986 (1131)
Q Consensus 953 galPHiKty~Rrf~s~~~~~igWvYVGSANLSkA 986 (1131)
...+|.|+++. | -.|+++||+||+..
T Consensus 2 ~~~~H~K~~v~---D-----~~~~~iGs~N~~~~ 27 (28)
T smart00155 2 DGVLHTKLMIV---D-----DEIAYIGSANLDGR 27 (28)
T ss_pred CCcEEeEEEEE---c-----CCEEEEeCccCCCC
Confidence 35689999985 2 13899999999864
No 18
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=80.36 E-value=2.1 Score=50.49 Aligned_cols=37 Identities=19% Similarity=0.406 Sum_probs=31.1
Q ss_pred eeeecCCceeec-CCCcccceEEccccccccceeEeeecc
Q 001181 63 LTLEPDRPYSIG-RASINCDFTFDNRLVSRQHCQILFDSS 101 (1131)
Q Consensus 63 ~~l~~d~~~~ig-r~~~~~d~~~~~~~vs~~hcqi~~d~~ 101 (1131)
+.|.+.+ ++|| |.. .||.++.|..||++|+.|.++..
T Consensus 15 ~~L~~g~-~~iG~~~~-~~di~L~d~~~~~~h~~l~v~~~ 52 (410)
T TIGR02500 15 LPLPEGN-LVLGTDAA-DCDIVLSDGGIAAVHVSLHVRLE 52 (410)
T ss_pred EECCCCc-eEeccCCC-CcEEEeCCCCccchheEEEEcCc
Confidence 4455555 9999 665 99999999999999999999864
No 19
>PRK13912 nuclease NucT; Provisional
Probab=69.28 E-value=4 Score=42.73 Aligned_cols=28 Identities=39% Similarity=0.274 Sum_probs=21.5
Q ss_pred CCCcceEEEEeeecCCCCCceeEEEEcccccchhhc
Q 001181 953 GHPMHVKVAWRRFQSRTDTSLGWVYCGSHNFSAAAW 988 (1131)
Q Consensus 953 galPHiKty~Rrf~s~~~~~igWvYVGSANLSkAAW 988 (1131)
...||.|+++. | -.|+++||+|++..++
T Consensus 117 ~~~~H~K~~vi---D-----~~~~~iGS~N~t~~s~ 144 (177)
T PRK13912 117 YGIMHQKVAII---D-----DKIVVLGSANWSKNAF 144 (177)
T ss_pred ccccceeEEEE---c-----CCEEEEeCCCCChhHh
Confidence 34699999985 2 1589999999987544
No 20
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=67.60 E-value=4.1 Score=39.15 Aligned_cols=28 Identities=25% Similarity=0.347 Sum_probs=24.7
Q ss_pred eEeeceEec--ccceEeecCCCeEEEEecC
Q 001181 151 VFVNGIRLK--SGIVRELNAGDEVLFVCRD 178 (1131)
Q Consensus 151 ~fvng~r~~--kg~~~el~~gd~v~~~~~~ 178 (1131)
++|||..++ .|+..+|+.||+|+|+.+-
T Consensus 62 VlvN~~di~~l~g~~t~L~dgD~v~i~P~v 91 (94)
T cd01764 62 VLINDTDWELLGEEDYILEDGDHVVFISTL 91 (94)
T ss_pred EEECCccccccCCcccCCCCcCEEEEECCC
Confidence 789998886 7999999999999998753
No 21
>PRK01642 cls cardiolipin synthetase; Reviewed
Probab=66.42 E-value=4.8 Score=48.54 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=22.1
Q ss_pred cccccceEEeeeCCceEEEEeCCCCChhhh
Q 001181 525 ACHHPKLFVLQREDSIRVIVTSANLGAKQW 554 (1131)
Q Consensus 525 GcHHSKMMLL~Y~D~LRVVI~TANLi~~DW 554 (1131)
..+|.|+++. |+-..++.+.|+...+|
T Consensus 218 ~RnHrKi~VI---Dg~ia~~Gg~Ni~d~~y 244 (483)
T PRK01642 218 LRNHRKIVVI---DGYIAYTGSMNVVDPEY 244 (483)
T ss_pred cccCceEEEE---cCCEEEeCCcccCCHHH
Confidence 3699999999 67778999999987444
No 22
>smart00155 PLDc Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not be
Probab=63.91 E-value=6.5 Score=29.60 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=19.8
Q ss_pred cccccceEEeeeCCceEEEEeCCCCCh
Q 001181 525 ACHHPKLFVLQREDSIRVIVTSANLGA 551 (1131)
Q Consensus 525 GcHHSKMMLL~Y~D~LRVVI~TANLi~ 551 (1131)
+.+|+|+|+. |.-.++|.|+||..
T Consensus 3 ~~~H~K~~v~---D~~~~~iGs~N~~~ 26 (28)
T smart00155 3 GVLHTKLMIV---DDEIAYIGSANLDG 26 (28)
T ss_pred CcEEeEEEEE---cCCEEEEeCccCCC
Confidence 3799999998 44489999999975
No 23
>PF00614 PLDc: Phospholipase D Active site motif; InterPro: IPR001736 Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site aspartic acid. An Escherichia coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs [, , , ].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3HSI_C.
Probab=63.23 E-value=5.1 Score=30.99 Aligned_cols=24 Identities=38% Similarity=0.493 Sum_probs=14.0
Q ss_pred cccccceEEeeeCCceEEEEeCCCCCh
Q 001181 525 ACHHPKLFVLQREDSIRVIVTSANLGA 551 (1131)
Q Consensus 525 GcHHSKMMLL~Y~D~LRVVI~TANLi~ 551 (1131)
++||+|++++ |.-+..|.++||..
T Consensus 3 ~~~H~K~~vv---D~~~a~vGg~nl~~ 26 (28)
T PF00614_consen 3 GSHHQKFVVV---DDRVAFVGGANLCD 26 (28)
T ss_dssp BEE---EEEE---TTTEEEEE---SSH
T ss_pred cceeeEEEEE---cCCEEEECceecCC
Confidence 4899999998 44489999999864
No 24
>PRK11263 cardiolipin synthase 2; Provisional
Probab=63.03 E-value=5.6 Score=47.29 Aligned_cols=24 Identities=29% Similarity=0.324 Sum_probs=20.9
Q ss_pred cccccceEEeeeCCceEEEEeCCCCCh
Q 001181 525 ACHHPKLFVLQREDSIRVIVTSANLGA 551 (1131)
Q Consensus 525 GcHHSKMMLL~Y~D~LRVVI~TANLi~ 551 (1131)
+.+|.|++|+ |+-..+|.+.|+..
T Consensus 109 ~R~HrKiiVI---Dg~~a~vGg~N~~~ 132 (411)
T PRK11263 109 RRMHRKIVVI---DGRIAFVGGINYSA 132 (411)
T ss_pred cCCcceEEEE---cCCEEEEcCeEchH
Confidence 5799999999 67789999999965
No 25
>PF13091 PLDc_2: PLD-like domain; PDB: 2ZE4_A 2ZE9_A 1BYS_A 1BYR_A 1V0T_A 1V0U_A 1V0V_A 1V0S_A 1V0R_A 1V0W_A ....
Probab=59.07 E-value=9.2 Score=36.41 Aligned_cols=36 Identities=25% Similarity=0.358 Sum_probs=23.2
Q ss_pred ccccceEEeeeCCceEEEEeCCCCChhhhccc-ccEEEEe
Q 001181 526 CHHPKLFVLQREDSIRVIVTSANLGAKQWNAV-TNTVWWQ 564 (1131)
Q Consensus 526 cHHSKMMLL~Y~D~LRVVI~TANLi~~DW~~~-TQ~VWiq 564 (1131)
.+|.|+++.. +. .++|.|+||+...|..- +.++.+.
T Consensus 74 ~~H~K~~i~d--~~-~~iiGS~N~t~~~~~~n~E~~~~~~ 110 (126)
T PF13091_consen 74 RLHAKFYIID--DK-VAIIGSANLTSSSFRRNYELGVIID 110 (126)
T ss_dssp -B--EEEEET--TT-EEEEES--CSCCCSCTSEEEEEEEE
T ss_pred CCCcceEEec--Cc-cEEEcCCCCCcchhcCCcceEEEEE
Confidence 6899999994 22 99999999999998664 4444444
No 26
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=57.04 E-value=8.5 Score=34.56 Aligned_cols=26 Identities=31% Similarity=0.443 Sum_probs=18.9
Q ss_pred ceEeeceEecccceEeecCCCeEEEEec
Q 001181 150 GVFVNGIRLKSGIVRELNAGDEVLFVCR 177 (1131)
Q Consensus 150 g~fvng~r~~kg~~~el~~gd~v~~~~~ 177 (1131)
-++|||..+. ....|+.||||.|+-+
T Consensus 51 ~v~vNg~~v~--~~~~l~~gD~v~i~pp 76 (80)
T cd00754 51 RIAVNGEYVR--LDTPLKDGDEVAIIPP 76 (80)
T ss_pred EEEECCeEcC--CCcccCCCCEEEEeCC
Confidence 3555555555 5678999999999864
No 27
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=56.52 E-value=7.8 Score=34.44 Aligned_cols=31 Identities=39% Similarity=0.565 Sum_probs=22.0
Q ss_pred eeeeeccceEeeceEecccceEeecCCCeEEEEec
Q 001181 143 RVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCR 177 (1131)
Q Consensus 143 ~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~~~ 177 (1131)
.++++.||.++.- .+....|+.||+|.|+-+
T Consensus 43 ~~~v~vN~~~v~~----~~~~~~l~~gD~V~i~pp 73 (77)
T PF02597_consen 43 RVAVAVNGEIVPD----DGLDTPLKDGDEVAILPP 73 (77)
T ss_dssp TEEEEETTEEEGG----GTTTSBEETTEEEEEEES
T ss_pred cEEEEECCEEcCC----ccCCcCcCCCCEEEEECC
Confidence 3455555555443 288889999999999864
No 28
>cd00138 PLDc Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
Probab=56.41 E-value=14 Score=37.37 Aligned_cols=37 Identities=22% Similarity=0.228 Sum_probs=28.8
Q ss_pred cccccceEEeeeCCceEEEEeCCCCChhhhc-ccccEEEEe
Q 001181 525 ACHHPKLFVLQREDSIRVIVTSANLGAKQWN-AVTNTVWWQ 564 (1131)
Q Consensus 525 GcHHSKMMLL~Y~D~LRVVI~TANLi~~DW~-~~TQ~VWiq 564 (1131)
+.+|+|+||.- .=.++|.|+|+....|. +.+.++.+.
T Consensus 112 ~~~H~K~~iiD---~~~~~vGS~N~~~~~~~~~~e~~~~~~ 149 (176)
T cd00138 112 GVLHTKLVIVD---DETAYIGSANLDGRSLTLNSEVGVVIY 149 (176)
T ss_pred cceeeeEEEEc---CCEEEEECCcCChhhhhhhcceEEEEe
Confidence 58999999993 44899999999999884 455555554
No 29
>PF09565 RE_NgoFVII: NgoFVII restriction endonuclease; InterPro: IPR019065 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This domain is found in NgoFVII restriction endonuclease, which recognises GCSGC but cleavage site is unknown. It is also found as the C-terminal domain of the res subunit of some type III restriction endonucleases.
Probab=55.49 E-value=9.8 Score=43.73 Aligned_cols=33 Identities=33% Similarity=0.459 Sum_probs=22.6
Q ss_pred CCCcceEEEEeeecCCCCCceeEEEEcccccchhhcCC
Q 001181 953 GHPMHVKVAWRRFQSRTDTSLGWVYCGSHNFSAAAWGR 990 (1131)
Q Consensus 953 galPHiKty~Rrf~s~~~~~igWvYVGSANLSkAAWG~ 990 (1131)
...-|.|+|. |..+ +..+ =+|+||||||.= ||.
T Consensus 78 ~~~~HgKlY~--f~k~-g~~~-~a~IGSANfS~~-~~~ 110 (296)
T PF09565_consen 78 DPPYHGKLYI--FSKN-GKPF-RAYIGSANFSQI-NGF 110 (296)
T ss_pred CCCcccEEEE--EecC-CCce-EEEEeecccccc-ccc
Confidence 5678999998 4332 2233 489999999874 444
No 30
>cd00138 PLDc Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
Probab=55.15 E-value=8.2 Score=39.01 Aligned_cols=29 Identities=24% Similarity=0.343 Sum_probs=22.9
Q ss_pred CCCcceEEEEeeecCCCCCceeEEEEcccccchhhcC
Q 001181 953 GHPMHVKVAWRRFQSRTDTSLGWVYCGSHNFSAAAWG 989 (1131)
Q Consensus 953 galPHiKty~Rrf~s~~~~~igWvYVGSANLSkAAWG 989 (1131)
...+|.|+++. |. .=+++||+|++..+|.
T Consensus 111 ~~~~H~K~~ii---D~-----~~~~vGS~N~~~~~~~ 139 (176)
T cd00138 111 GGVLHTKLVIV---DD-----ETAYIGSANLDGRSLT 139 (176)
T ss_pred ccceeeeEEEE---cC-----CEEEEECCcCChhhhh
Confidence 46899999986 21 1499999999888765
No 31
>PRK09428 pssA phosphatidylserine synthase; Provisional
Probab=53.29 E-value=14 Score=44.56 Aligned_cols=43 Identities=23% Similarity=0.505 Sum_probs=33.0
Q ss_pred CCCCCcceEEEEeeecCCCCCceeEEEEcccccchhhcCCCccCCCCCCCCCCCccCCCCCCceeEeeeeeeEEEeCC
Q 001181 951 RVGHPMHVKVAWRRFQSRTDTSLGWVYCGSHNFSAAAWGRPIQTPSTIKPNGSEKTKSSSSQRLHICNYELGIVFVFP 1028 (1131)
Q Consensus 951 R~galPHiKty~Rrf~s~~~~~igWvYVGSANLSkAAWG~l~knr~~~Ks~~~~~~~ss~~~qL~IrNYELGVLfp~P 1028 (1131)
+.+.+.|.|++.. | + .|.+|||+||-.-+| -.|+|+|+++-.|
T Consensus 351 ~~~~~~HaK~i~v---D--~---~~~~iGS~Nld~RS~---------------------------~ln~E~~l~i~d~ 393 (451)
T PRK09428 351 DGDNSYHLKGIWV---D--D---RWMLLTGNNLNPRAW---------------------------RLDLENALLIHDP 393 (451)
T ss_pred cCCCcceEEEEEE---e--C---CEEEEcCCCCChhHh---------------------------hhcccceEEEECC
Confidence 5678999999985 2 1 499999999965554 3488999999554
No 32
>KOG0245 consensus Kinesin-like protein [Cytoskeleton]
Probab=50.19 E-value=35 Score=45.00 Aligned_cols=75 Identities=23% Similarity=0.432 Sum_probs=58.4
Q ss_pred eeeeecCCceeecCCC--cccceEEccccccccceeEeeeccceeEEEEcCcccccccchhhHHHhhhcccccccccccc
Q 001181 62 SLTLEPDRPYSIGRAS--INCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDE 139 (1131)
Q Consensus 62 ~~~l~~d~~~~igr~~--~~~d~~~~~~~vs~~hcqi~~d~~~~k~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 (1131)
++..-+|-.-+|||.. ..-|.+++...+=.|||.|.-++..- |+.+- .++
T Consensus 470 LlY~ikeG~TrVG~~~a~~~~DI~LsG~~I~~qHC~i~~~~g~~-~vtl~---------------------p~e------ 521 (1221)
T KOG0245|consen 470 LLYYIKEGETRVGREDASSRQDIVLSGQLIREQHCSIRNEGGND-VVTLE---------------------PCE------ 521 (1221)
T ss_pred EEEEeccCceecCCCCcccCCceEecchhhhhhceEEEecCCCc-eEEec---------------------cCC------
Confidence 5666788888999988 67799999999999999999888765 44433 222
Q ss_pred cceeeeeeccceEeeceEecccceEeecCCCeEEE
Q 001181 140 GFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLF 174 (1131)
Q Consensus 140 ~~~~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~ 174 (1131)
+. -+||||..|.- ..-|+.||||.|
T Consensus 522 ~a--------etyVNGk~v~e--p~qL~~GdRiil 546 (1221)
T KOG0245|consen 522 DA--------ETYVNGKLVTE--PTQLRSGDRIIL 546 (1221)
T ss_pred cc--------ceeEccEEcCC--cceeccCCEEEE
Confidence 22 47999999864 556999999976
No 33
>COG1502 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism]
Probab=50.15 E-value=11 Score=43.71 Aligned_cols=34 Identities=21% Similarity=0.241 Sum_probs=26.4
Q ss_pred CCccccccceEEeeeCCceEEEEeCCCCChhhhcccc
Q 001181 522 QGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVT 558 (1131)
Q Consensus 522 ~g~GcHHSKMMLL~Y~D~LRVVI~TANLi~~DW~~~T 558 (1131)
..-..+|-|+++.- +--+++..+|+.....+..+
T Consensus 160 ~~~~r~H~K~~viD---~~i~~vGg~N~~d~y~~~~~ 193 (438)
T COG1502 160 RLNRRLHRKIVVID---GKVAFVGGANIGDEYFHKDK 193 (438)
T ss_pred hhhccccceEEEEc---CCEEEecCcccchhhhccCc
Confidence 34567999999985 66667777999998887765
No 34
>PRK12452 cardiolipin synthetase; Reviewed
Probab=48.23 E-value=15 Score=44.98 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=19.5
Q ss_pred ccccceEEeeeCCceEEEEeCCCCCh
Q 001181 526 CHHPKLFVLQREDSIRVIVTSANLGA 551 (1131)
Q Consensus 526 cHHSKMMLL~Y~D~LRVVI~TANLi~ 551 (1131)
.+|-|++|. |+-...+.+.|+..
T Consensus 241 RnHRKi~VI---Dg~ia~~GG~Ni~d 263 (509)
T PRK12452 241 RNHRKIVIV---DGEIGFTGGLNVGD 263 (509)
T ss_pred CCCCeEEEE---cCCEEEeCCcccch
Confidence 489999998 67678999999875
No 35
>PRK01777 hypothetical protein; Validated
Probab=47.91 E-value=17 Score=35.39 Aligned_cols=32 Identities=22% Similarity=0.121 Sum_probs=26.4
Q ss_pred eeeeccceEeeceEecccceEeecCCCeEEEEec
Q 001181 144 VMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCR 177 (1131)
Q Consensus 144 ~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~~~ 177 (1131)
+.++.+-+.|||..+.- ...|+.||||.+..+
T Consensus 45 i~~~~~~vgI~Gk~v~~--d~~L~dGDRVeIyrP 76 (95)
T PRK01777 45 IDLAKNKVGIYSRPAKL--TDVLRDGDRVEIYRP 76 (95)
T ss_pred cccccceEEEeCeECCC--CCcCCCCCEEEEecC
Confidence 45677889999999965 567999999999873
No 36
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=46.01 E-value=16 Score=33.87 Aligned_cols=26 Identities=35% Similarity=0.506 Sum_probs=16.9
Q ss_pred eEeeceEecccceEeecCCCeEEEEe
Q 001181 151 VFVNGIRLKSGIVRELNAGDEVLFVC 176 (1131)
Q Consensus 151 ~fvng~r~~kg~~~el~~gd~v~~~~ 176 (1131)
++|||..+.......|+.||||.|+=
T Consensus 58 v~vN~~~v~~~~~~~l~dgdev~i~P 83 (88)
T TIGR01687 58 ILVNGRNVDWGLGTELKDGDVVAIFP 83 (88)
T ss_pred EEECCEecCccCCCCCCCCCEEEEeC
Confidence 34444444443326799999999874
No 37
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=42.00 E-value=25 Score=32.54 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=19.1
Q ss_pred eeeeccceEeeceEecccceEeecCCCeEEEEec
Q 001181 144 VMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCR 177 (1131)
Q Consensus 144 ~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~~~ 177 (1131)
++++.||.++ +....|..||||.|+=+
T Consensus 51 ~~~aVN~~~~-------~~~~~l~dgDeVai~PP 77 (81)
T PRK11130 51 LLAAVNQTLV-------SFDHPLTDGDEVAFFPP 77 (81)
T ss_pred EEEEECCEEc-------CCCCCCCCCCEEEEeCC
Confidence 4566666554 35567999999999743
No 38
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=39.92 E-value=30 Score=31.69 Aligned_cols=28 Identities=43% Similarity=0.554 Sum_probs=20.6
Q ss_pred eeeeeccceEeeceEecccceEeecCCCeEEEEec
Q 001181 143 RVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCR 177 (1131)
Q Consensus 143 ~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~~~~ 177 (1131)
.++++.||.+++ ....|..||||.|+-+
T Consensus 49 ~~~v~vn~~~v~-------~~~~l~dgDevai~Pp 76 (80)
T TIGR01682 49 QVMVAVNEEYVT-------DDALLNEGDEVAFIPP 76 (80)
T ss_pred ceEEEECCEEcC-------CCcCcCCCCEEEEeCC
Confidence 456666666655 2578999999999864
No 39
>smart00363 S4 S4 RNA-binding domain.
Probab=38.38 E-value=35 Score=27.55 Aligned_cols=29 Identities=21% Similarity=0.242 Sum_probs=21.2
Q ss_pred eeccceEeeceEecccceEeecCCCeEEEE
Q 001181 146 VSLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (1131)
Q Consensus 146 ~s~ng~fvng~r~~kg~~~el~~gd~v~~~ 175 (1131)
+..++++|||.++.. ....|..||.|.+-
T Consensus 23 i~~g~i~vng~~~~~-~~~~l~~gd~i~~~ 51 (60)
T smart00363 23 IEQGRVKVNGKKVTK-PSYIVKPGDVISVR 51 (60)
T ss_pred HHcCCEEECCEEecC-CCeEeCCCCEEEEc
Confidence 345678999999833 24457899998774
No 40
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=38.18 E-value=27 Score=30.55 Aligned_cols=26 Identities=35% Similarity=0.339 Sum_probs=18.3
Q ss_pred EeeceEeccc--ceEeecCCCeEEEEec
Q 001181 152 FVNGIRLKSG--IVRELNAGDEVLFVCR 177 (1131)
Q Consensus 152 fvng~r~~kg--~~~el~~gd~v~~~~~ 177 (1131)
.|||.-+.|. ....|+.||+|.++.+
T Consensus 34 ~vN~~~v~~~~~~~~~L~~gD~vei~~~ 61 (65)
T PRK06944 34 AVNGDFVARTQHAARALAAGDRLDLVQP 61 (65)
T ss_pred EECCEEcCchhcccccCCCCCEEEEEee
Confidence 4455546543 4677999999999864
No 41
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=37.82 E-value=28 Score=30.28 Aligned_cols=27 Identities=33% Similarity=0.416 Sum_probs=19.8
Q ss_pred eeccceEeeceEec-ccceEeecCCCeEEE
Q 001181 146 VSLNGVFVNGIRLK-SGIVRELNAGDEVLF 174 (1131)
Q Consensus 146 ~s~ng~fvng~r~~-kg~~~el~~gd~v~~ 174 (1131)
+.-+.|+|||..+. ++. .|.+||+|.+
T Consensus 31 i~~G~V~VNg~~~~~~~~--~l~~Gd~v~i 58 (59)
T TIGR02988 31 LQENEVLVNGELENRRGK--KLYPGDVIEI 58 (59)
T ss_pred HHcCCEEECCEEccCCCC--CCCCCCEEEe
Confidence 34567899999884 343 6889999875
No 42
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=37.79 E-value=29 Score=30.68 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=19.5
Q ss_pred eEeeceEeccc--ceEeecCCCeEEEEec
Q 001181 151 VFVNGIRLKSG--IVRELNAGDEVLFVCR 177 (1131)
Q Consensus 151 ~fvng~r~~kg--~~~el~~gd~v~~~~~ 177 (1131)
|.|||.-|.+. ....|+.||+|.++..
T Consensus 33 V~vNg~~v~~~~~~~~~L~~gD~V~ii~~ 61 (65)
T cd00565 33 VALNGEIVPRSEWASTPLQDGDRIEIVTA 61 (65)
T ss_pred EEECCEEcCHHHcCceecCCCCEEEEEEe
Confidence 45666666665 4567999999999863
No 43
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=37.04 E-value=47 Score=31.70 Aligned_cols=34 Identities=24% Similarity=0.294 Sum_probs=29.7
Q ss_pred eeeeeccceEeeceEec-----ccceEeecCCCeEEEEe
Q 001181 143 RVMVSLNGVFVNGIRLK-----SGIVRELNAGDEVLFVC 176 (1131)
Q Consensus 143 ~~~~s~ng~fvng~r~~-----kg~~~el~~gd~v~~~~ 176 (1131)
.|.++.+|||+||.-|. -|..++++.||.+....
T Consensus 18 ~~~l~~~GV~~ngrlV~T~F~fDG~~l~~~~G~~~~~y~ 56 (79)
T PF11012_consen 18 EFTLNESGVFRNGRLVATSFEFDGKTLEYRTGSGTYRYQ 56 (79)
T ss_pred EEEECCCcEEECCCEEeeEEEECCCEEEEEECCeEEEEE
Confidence 57799999999999997 48999999999887665
No 44
>PRK13912 nuclease NucT; Provisional
Probab=36.63 E-value=41 Score=35.35 Aligned_cols=98 Identities=14% Similarity=0.151 Sum_probs=53.2
Q ss_pred HhhcccCHHHHhhhcC--CCCCccEEEEecCCccccccCcCCcCCCCCCCCCCeEEEcC-CCCccccccccccCCCcccc
Q 001181 451 IATFTSDILWFMSYCE--IPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFP-PFPESVAFGENCKKQGIACH 527 (1131)
Q Consensus 451 lfnFm~DidWLLs~f~--~~r~vpVtIv~h~~e~~ws~~~~~rl~~~~~~~pNV~li~P-pMPe~IpFG~dr~~~g~GcH 527 (1131)
+..|.+.-+.+.+.+. ..|.+.|-|+....... ............++|+.+..- +... .. ...++.+
T Consensus 51 i~~Y~~~~~~i~~aL~~Aa~RGV~VrIlld~~~~~---~~~~~~~~~l~~~~~~~~~~~~~~~~--~~-----~~~~~~~ 120 (177)
T PRK13912 51 IAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNH---NNDQSTIGYLDKYPNIKVCLLKGLKA--KN-----GKYYGIM 120 (177)
T ss_pred EEEEEEchHHHHHHHHHHHHCCCEEEEEEeCcccc---CcchhHHHHHHhCCCceEEEecCccc--cC-----ccccccc
Confidence 3467777777776543 34788888887642110 000000000123456655431 1110 00 1123579
Q ss_pred ccceEEeeeCCceEEEEeCCCCChhhhc-ccccEE
Q 001181 528 HPKLFVLQREDSIRVIVTSANLGAKQWN-AVTNTV 561 (1131)
Q Consensus 528 HSKMMLL~Y~D~LRVVI~TANLi~~DW~-~~TQ~V 561 (1131)
|.|+||+ |+-.+++.|+|+...-+. +.+.++
T Consensus 121 H~K~~vi---D~~~~~iGS~N~t~~s~~~N~E~~l 152 (177)
T PRK13912 121 HQKVAII---DDKIVVLGSANWSKNAFENNYEVLL 152 (177)
T ss_pred ceeEEEE---cCCEEEEeCCCCChhHhccCCceEE
Confidence 9999998 555699999999976554 344434
No 45
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=35.52 E-value=26 Score=28.96 Aligned_cols=25 Identities=28% Similarity=0.460 Sum_probs=19.6
Q ss_pred eeccceEeeceEec-ccceEeecCCCeE
Q 001181 146 VSLNGVFVNGIRLK-SGIVRELNAGDEV 172 (1131)
Q Consensus 146 ~s~ng~fvng~r~~-kg~~~el~~gd~v 172 (1131)
+..++|+|||..++ .+.. +.+||+|
T Consensus 23 I~~g~V~VNg~~v~~~~~~--v~~~d~I 48 (48)
T PF01479_consen 23 IKQGRVKVNGKVVKDPSYI--VKPGDVI 48 (48)
T ss_dssp HHTTTEEETTEEESSTTSB--ESTTEEE
T ss_pred cCCCEEEECCEEEcCCCCC--CCCcCCC
Confidence 55688999999999 6665 4588876
No 46
>PRK06437 hypothetical protein; Provisional
Probab=34.11 E-value=39 Score=30.57 Aligned_cols=25 Identities=28% Similarity=0.319 Sum_probs=18.7
Q ss_pred ceEeeceEecccceEeecCCCeEEEEe
Q 001181 150 GVFVNGIRLKSGIVRELNAGDEVLFVC 176 (1131)
Q Consensus 150 g~fvng~r~~kg~~~el~~gd~v~~~~ 176 (1131)
.+.+||.-|+ ....|+.||+|.++-
T Consensus 38 aV~vNg~iv~--~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 38 VVIVNGSPVL--EDHNVKKEDDVLILE 62 (67)
T ss_pred EEEECCEECC--CceEcCCCCEEEEEe
Confidence 3445555555 777899999999985
No 47
>PF09138 Urm1: Urm1 (Ubiquitin related modifier); InterPro: IPR015221 Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway []. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily []. ; GO: 0034227 tRNA thio-modification, 0005737 cytoplasm; PDB: 2AX5_A 2QJL_A 2PKO_A 1WGK_A 1XO3_A 2K9X_A.
Probab=27.05 E-value=23 Score=34.70 Aligned_cols=27 Identities=26% Similarity=0.396 Sum_probs=17.5
Q ss_pred eEeeceE--ecccceEeecCCCeEEEEec
Q 001181 151 VFVNGIR--LKSGIVRELNAGDEVLFVCR 177 (1131)
Q Consensus 151 ~fvng~r--~~kg~~~el~~gd~v~~~~~ 177 (1131)
|+||+.- +.-++.-+|+.||.|+|+--
T Consensus 64 vLINd~DwEl~g~~~y~l~~~D~I~FiST 92 (96)
T PF09138_consen 64 VLINDADWELLGEEDYVLKDGDNITFIST 92 (96)
T ss_dssp EEETTCEHHHHTCCCSB--TTEEEEEEET
T ss_pred EEEcCccceeecCcceEcCCCCEEEEEcc
Confidence 4556553 44466779999999999853
No 48
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=26.84 E-value=56 Score=27.15 Aligned_cols=30 Identities=20% Similarity=0.235 Sum_probs=21.7
Q ss_pred eeccceEeeceEecccceEeecCCCeEEEEe
Q 001181 146 VSLNGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (1131)
Q Consensus 146 ~s~ng~fvng~r~~kg~~~el~~gd~v~~~~ 176 (1131)
+..++++|||.++.+ ....+..||+|.+.-
T Consensus 23 i~~g~V~vn~~~~~~-~~~~v~~~d~i~i~~ 52 (70)
T cd00165 23 IKHGHVLVNGKVVTK-PSYKVKPGDVIEVDG 52 (70)
T ss_pred HHcCCEEECCEEccC-CccCcCCCCEEEEcC
Confidence 456789999999833 233567899987763
No 49
>PRK11507 ribosome-associated protein; Provisional
Probab=25.68 E-value=25 Score=32.75 Aligned_cols=35 Identities=20% Similarity=0.313 Sum_probs=24.0
Q ss_pred ccceeeeeeccceEeeceEecccceEeecCCCeEEE
Q 001181 139 EGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLF 174 (1131)
Q Consensus 139 ~~~~~~~~s~ng~fvng~r~~kg~~~el~~gd~v~~ 174 (1131)
.|-++..+..+.|.|||. +..-.-+.|.+||.|+|
T Consensus 27 GG~AK~~I~eg~V~VNGe-ve~rRgkKl~~GD~V~~ 61 (70)
T PRK11507 27 GAQAKIAIAEGQVKVDGA-VETRKRCKIVAGQTVSF 61 (70)
T ss_pred hHHHHHHHHcCceEECCE-EecccCCCCCCCCEEEE
Confidence 444555677788889985 33333456899999987
No 50
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=25.49 E-value=60 Score=28.71 Aligned_cols=29 Identities=28% Similarity=0.334 Sum_probs=19.6
Q ss_pred eeeeccceEeeceEecccc--eEeecCCCeEEEEec
Q 001181 144 VMVSLNGVFVNGIRLKSGI--VRELNAGDEVLFVCR 177 (1131)
Q Consensus 144 ~~~s~ng~fvng~r~~kg~--~~el~~gd~v~~~~~ 177 (1131)
+.+..||.+ |.|.. ...|+.||+|.++..
T Consensus 30 v~v~vN~~i-----v~~~~~~~~~L~~gD~veii~~ 60 (64)
T TIGR01683 30 VAVAVNGEI-----VPRSEWDDTILKEGDRIEIVTF 60 (64)
T ss_pred EEEEECCEE-----cCHHHcCceecCCCCEEEEEEe
Confidence 445555555 55443 467999999999863
No 51
>PHA02820 phospholipase-D-like protein; Provisional
Probab=24.29 E-value=46 Score=39.99 Aligned_cols=26 Identities=27% Similarity=0.653 Sum_probs=21.7
Q ss_pred cccccceEEeeeCCceEEEEeCCCCChhhhcc
Q 001181 525 ACHHPKLFVLQREDSIRVIVTSANLGAKQWNA 556 (1131)
Q Consensus 525 GcHHSKMMLL~Y~D~LRVVI~TANLi~~DW~~ 556 (1131)
+..|+|+|+. |+-.+.|.|+|+ ||..
T Consensus 112 ~~~HrK~~VI---Dg~~~~iGS~Ni---d~rs 137 (424)
T PHA02820 112 GVLHTKFWIS---DNTHIYLGSANM---DWRS 137 (424)
T ss_pred ccceeeEEEE---CCCEEEEeCCcC---Chhh
Confidence 4699999995 788899999999 6655
No 52
>PF09565 RE_NgoFVII: NgoFVII restriction endonuclease; InterPro: IPR019065 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This domain is found in NgoFVII restriction endonuclease, which recognises GCSGC but cleavage site is unknown. It is also found as the C-terminal domain of the res subunit of some type III restriction endonucleases.
Probab=20.19 E-value=83 Score=36.47 Aligned_cols=26 Identities=27% Similarity=0.507 Sum_probs=22.7
Q ss_pred cccceEEeeeCC-ceEEEEeCCCCChh
Q 001181 527 HHPKLFVLQRED-SIRVIVTSANLGAK 552 (1131)
Q Consensus 527 HHSKMMLL~Y~D-~LRVVI~TANLi~~ 552 (1131)
-|+||.+...++ -.+++|.||||+..
T Consensus 81 ~HgKlY~f~k~g~~~~a~IGSANfS~~ 107 (296)
T PF09565_consen 81 YHGKLYIFSKNGKPFRAYIGSANFSQI 107 (296)
T ss_pred cccEEEEEecCCCceEEEEeecccccc
Confidence 699999996664 69999999999984
Done!