Query 002593
Match_columns 903
No_of_seqs 377 out of 1380
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 03:08:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002593hhsearch_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 1.7E-52 3.6E-57 471.6 -1.2 301 414-758 2-338 (443)
2 KOG2031 Tyrosyl-DNA phosphodie 100.0 2.1E-43 4.5E-48 390.3 14.7 307 397-760 63-391 (519)
3 PF00498 FHA: FHA domain; Int 99.5 7.4E-14 1.6E-18 118.6 6.3 67 71-174 1-67 (68)
4 cd00060 FHA Forkhead associate 99.1 5.8E-10 1.3E-14 99.6 10.8 79 60-175 13-92 (102)
5 TIGR03354 VI_FHA type VI secre 99.0 1.2E-09 2.5E-14 123.5 8.6 74 61-174 17-94 (396)
6 KOG1882 Transcriptional regula 98.9 5.9E-10 1.3E-14 116.9 4.2 96 57-176 182-277 (293)
7 COG1716 FOG: FHA domain [Signa 98.9 2.9E-09 6.4E-14 106.5 9.1 68 69-176 89-156 (191)
8 smart00240 FHA Forkhead associ 98.7 2.6E-08 5.6E-13 80.1 5.7 52 71-158 1-52 (52)
9 PLN02927 antheraxanthin epoxid 98.7 3E-08 6.5E-13 118.5 7.7 96 56-197 542-649 (668)
10 COG3456 Predicted component of 98.4 3.3E-07 7.2E-12 103.1 6.1 72 63-174 21-95 (430)
11 KOG1881 Anion exchanger adapto 97.9 4.4E-06 9.5E-11 98.8 1.5 92 56-174 164-255 (793)
12 KOG0615 Serine/threonine prote 97.8 1.6E-05 3.4E-10 90.0 4.2 90 61-176 57-147 (475)
13 KOG1880 Nuclear inhibitor of p 97.1 0.00029 6.3E-09 76.9 2.5 86 56-177 26-111 (337)
14 TIGR02500 type_III_yscD type I 96.0 0.017 3.7E-07 66.3 7.8 47 48-99 2-50 (410)
15 PF06087 Tyr-DNA_phospho: Tyro 95.0 0.019 4.1E-07 66.6 3.7 76 796-871 156-267 (443)
16 KOG0245 Kinesin-like protein [ 91.3 0.53 1.1E-05 59.2 7.8 75 63-175 471-547 (1221)
17 PF08797 HIRAN: HIRAN domain; 91.2 0.049 1.1E-06 51.0 -0.7 78 712-794 29-106 (107)
18 TIGR01663 PNK-3'Pase polynucle 90.5 0.48 1E-05 56.5 6.5 79 61-179 25-103 (526)
19 KOG2293 Daxx-interacting prote 79.5 4.3 9.4E-05 48.3 6.9 74 64-174 443-522 (547)
20 KOG1892 Actin filament-binding 75.3 8.6 0.00019 48.7 8.0 90 46-176 355-447 (1629)
21 PF00614 PLDc: Phospholipase D 71.2 3.2 6.9E-05 31.1 2.0 24 525-551 3-26 (28)
22 smart00155 PLDc Phospholipase 69.2 4.6 0.0001 29.5 2.5 24 525-551 3-26 (28)
23 cd00138 PLDc Phospholipase D. 62.3 9.7 0.00021 37.6 4.1 37 525-564 112-149 (176)
24 PF13091 PLDc_2: PLD-like doma 58.2 7.4 0.00016 36.2 2.4 36 526-564 74-110 (126)
25 TIGR02868 CydC thiol reductant 52.7 5.9 0.00013 46.6 0.9 67 191-281 350-416 (529)
26 PRK13657 cyclic beta-1,2-gluca 45.3 8.5 0.00018 46.0 0.7 67 191-280 350-416 (588)
27 cd01764 Urm1 Urm1-like ubuitin 45.3 19 0.00041 33.8 2.8 27 151-177 62-90 (94)
28 COG1908 FrhD Coenzyme F420-red 42.1 7.2 0.00016 38.7 -0.5 21 882-902 40-60 (132)
29 PRK13912 nuclease NucT; Provis 41.7 24 0.00052 36.2 3.2 94 449-555 49-145 (177)
30 TIGR02988 YaaA_near_RecF S4 do 41.3 30 0.00064 29.3 3.2 25 149-174 34-58 (59)
31 PF01479 S4: S4 domain; Inter 40.0 23 0.00051 28.3 2.3 25 147-172 24-48 (48)
32 PF02662 FlpD: Methyl-viologen 39.5 8.4 0.00018 37.8 -0.5 20 882-901 39-58 (124)
33 smart00363 S4 S4 RNA-binding d 38.5 42 0.0009 26.4 3.5 28 147-175 24-51 (60)
34 TIGR01687 moaD_arch MoaD famil 38.3 34 0.00074 30.8 3.3 28 149-176 56-83 (88)
35 cd00754 MoaD Ubiquitin domain 37.0 36 0.00077 29.7 3.1 27 148-176 49-75 (80)
36 TIGR02857 CydD thiol reductant 31.4 18 0.00039 42.7 0.4 52 190-262 336-387 (529)
37 PRK01777 hypothetical protein; 30.7 48 0.001 31.4 3.1 28 146-175 47-74 (95)
38 cd00165 S4 S4/Hsp/ tRNA synthe 30.5 60 0.0013 26.2 3.3 28 147-175 24-51 (70)
39 COG1188 Ribosome-associated he 28.0 68 0.0015 31.0 3.6 29 149-179 34-62 (100)
40 COG2501 S4-like RNA binding pr 26.4 65 0.0014 29.5 2.9 26 147-174 35-61 (73)
41 PF09565 RE_NgoFVII: NgoFVII r 26.3 55 0.0012 36.9 3.1 26 527-552 81-107 (296)
42 cd03292 ABC_FtsE_transporter F 25.9 35 0.00075 35.0 1.4 48 190-258 15-62 (214)
43 TIGR00958 3a01208 Conjugate Tr 25.8 22 0.00048 43.9 -0.1 53 190-263 495-547 (711)
44 PF02824 TGS: TGS domain; Int 25.1 60 0.0013 27.8 2.4 27 147-175 33-59 (60)
45 TIGR01193 bacteriocin_ABC ABC- 24.6 27 0.00059 42.8 0.4 51 191-262 489-539 (708)
46 COG1124 DppF ABC-type dipeptid 24.0 26 0.00057 38.6 0.1 52 191-263 22-73 (252)
47 PRK11507 ribosome-associated p 23.3 89 0.0019 28.4 3.2 26 147-174 35-61 (70)
48 PF02597 ThiS: ThiS family; I 23.3 54 0.0012 28.3 1.8 28 149-176 44-72 (77)
49 TIGR02673 FtsE cell division A 22.6 49 0.0011 34.0 1.7 48 191-259 17-64 (214)
50 PRK06944 sulfur carrier protei 22.4 94 0.002 26.4 3.1 26 151-176 33-60 (65)
51 PRK11174 cysteine/glutathione 22.4 29 0.00063 41.5 -0.0 50 190-261 364-413 (588)
52 PRK11176 lipid transporter ATP 22.4 29 0.00062 41.4 -0.0 50 191-261 358-407 (582)
53 PRK10790 putative multidrug tr 22.1 38 0.00082 40.6 0.9 51 191-262 356-406 (592)
54 TIGR00960 3a0501s02 Type II (G 21.7 49 0.0011 34.1 1.5 49 191-260 18-66 (216)
55 TIGR02982 heterocyst_DevA ABC 21.7 38 0.00082 35.2 0.7 48 191-259 20-67 (220)
56 PRK06437 hypothetical protein; 21.5 1.2E+02 0.0026 26.7 3.6 26 149-176 37-62 (67)
57 cd00565 ThiS ThiaminS ubiquiti 21.5 1E+02 0.0022 26.5 3.2 27 150-176 32-60 (65)
58 cd01666 TGS_DRG_C TGS_DRG_C: 21.4 76 0.0016 28.9 2.4 21 153-175 54-74 (75)
59 TIGR00216 ispH_lytB (E)-4-hydr 21.1 49 0.0011 37.0 1.4 47 845-891 208-254 (280)
60 PRK12360 4-hydroxy-3-methylbut 21.1 50 0.0011 37.0 1.5 48 844-891 208-255 (281)
61 TIGR01682 moaD molybdopterin c 20.9 1.1E+02 0.0023 27.3 3.3 24 151-176 52-75 (80)
62 TIGR03873 F420-0_ABC_ATP propo 20.9 54 0.0012 34.9 1.6 33 213-259 31-63 (256)
63 PF09014 Sushi_2: Beta-2-glyco 20.4 1.6E+02 0.0036 27.8 4.4 39 151-195 13-54 (85)
64 PF14451 Ub-Mut7C: Mut7-C ubiq 20.3 1.1E+02 0.0023 28.3 3.2 26 149-176 50-75 (81)
65 PRK10908 cell division protein 20.2 47 0.001 34.5 1.0 49 190-259 16-64 (222)
66 PRK11160 cysteine/glutathione 20.1 38 0.00082 40.7 0.3 51 191-262 355-405 (574)
67 PF11673 DUF3269: Protein of u 20.1 69 0.0015 29.4 1.8 36 794-836 31-66 (73)
68 TIGR03797 NHPM_micro_ABC2 NHPM 20.0 34 0.00074 41.9 -0.1 52 190-262 467-518 (686)
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=1.7e-52 Score=471.62 Aligned_cols=301 Identities=26% Similarity=0.435 Sum_probs=196.0
Q ss_pred CcEEEEEeccCCCC-CCCCCccccccccCCchhHHHHHHhhcccchhhhhhhcCCC-C-CCcEEEEEccCccccccCCCC
Q 002593 414 KKFYLNRLEFMDLT-SLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIP-S-HLPVTIACHNTERCWSTSADK 490 (903)
Q Consensus 414 spFyLnrI~~lp~~-~~n~dtISL~DLLgP~~~L~~allfnF~~DidWLLs~f~~~-r-~lpVtIVvh~~~~~wk~e~~~ 490 (903)
.+|++|++.+.+.. ..+.++|||+|||++ ++|+++|+||||+|++|||++|+.. + .+||+++.+....... .
T Consensus 2 ~~~~~~~i~~~~~~~~~~~~~itl~dil~~-~~l~~~~~~nf~~D~~wll~~~~~~~~~~~~i~~v~g~~~~~~~----~ 76 (443)
T PF06087_consen 2 FKLYLTTIYDLPPRSNNNPDTITLEDILGD-PDLEEALLFNFMIDLDWLLSQFPPSTRKNIPITIVHGTKDPPDK----R 76 (443)
T ss_dssp CEEEEBTTTTS-GG--GTTTEE-HHHHCSG-TTEEEEEEE-SSEEHHHHHCCS-CCGTTCEEEEEECTSEEHHHH----H
T ss_pred cceEEeeecCCCccccCCCCcEeHHHHcCC-ccHHHHHhhhheeeHHHHHHhCCHhhcccceEEEEeCCCcchhh----h
Confidence 46899999999987 347999999999997 6899999999999999999999842 2 4688886442222111 1
Q ss_pred CcCCCCCCCCCeEEEcCCCCccccccccccCCCcccccceEEEEEeCCc-EEEEEeCCCCCHHhhccccCeEEeecC-CC
Q 002593 491 RTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDS-IRVIVTSANLGAKQWNAVTNTVWWQDF-PR 568 (903)
Q Consensus 491 rl~~~~~~~pNv~li~PpMPe~I~FG~d~~~~g~GtHHSKMmIL~Y~D~-LRVVI~TANLi~~DW~~~TQ~VWiQDF-P~ 568 (903)
.+......++|+++|.|||| ++|| |||||||||+|+|+ ||||||||||++.||+.+||+||+||| |+
T Consensus 77 ~~~~~~~~~~nv~~~~~~mp--~~~g---------~hHsKm~ll~y~~~~lRVvI~TaNl~~~Dw~~~~q~vw~~d~lP~ 145 (443)
T PF06087_consen 77 EIRQQAAIYPNVKLIFPPMP--IPFG---------THHSKMMLLFYEDGSLRVVIPTANLTPYDWNNKTQGVWIQDFLPR 145 (443)
T ss_dssp HHHHHHCCHTTEEEEEE-----STT-----------B--EEEEEEETTCEEEEEEESS-BSHHHHCSSB-EEEE---E-B
T ss_pred hhhhhcccCCCeEEEccCCC--cccc---------cccceeEEEEeCCccEEEEEECCCCCHHHHCCcceeEEEecccCc
Confidence 11112347899999999999 4687 99999999999987 999999999999999999999999999 99
Q ss_pred CCCCCccccccCCCcccccCCCCCcHHHHHHHHHHHhccCCCchHHHHHhhcccccccccEEEEEecCCcccCCCCCCCC
Q 002593 569 RCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSE 648 (903)
Q Consensus 569 l~~~~~~~~~~~~~~~e~~~~~~sdFk~dL~~YL~sy~~~~Ps~~~~i~~L~kyDFSsakv~LVaSVPG~H~g~~~~~~~ 648 (903)
++..... ....+++|+.+|++||.+|+. +....|++.|++||||+++|+||+||||+|. .+ .
T Consensus 146 ~~~~~~~-----------~~~~~~~F~~dL~~yL~~y~~--~~~~~~~~~l~~yDFS~~~v~lV~SvPG~h~-~~----~ 207 (443)
T PF06087_consen 146 LPSSKSS-----------SEESGSRFKKDLVAYLNSYGK--SPLDKLIERLRKYDFSSARVHLVASVPGKHK-ED----K 207 (443)
T ss_dssp -ECTS-S-------------SSTTHHHHHHHHHHHTT----HHHHHCHHHHHTEE-CCGTSEEEEE-SECCC-GG----G
T ss_pred ccccccc-----------cCCCCCchHHHHHHHHHHhCC--cchhHHHHHHHhcCCccCceEEEeccCcccc-CC----C
Confidence 9752211 135789999999999999984 3366899999999999999999999999999 21 1
Q ss_pred CcccCCCcCCcccccccccccceeccc----cCcceeEEeecccccchhhhhH-HHhhhhh-hcccchhh--hhc-----
Q 002593 649 STYSKPVDHGAIWSSDGKFLGSVETSV----VGLSHLFRTAADSNGTQIKKLA-AFLGKSF-SAHGMLKI--LLR----- 715 (903)
Q Consensus 649 ~~~G~~~l~n~~~~~~~s~LgSv~~s~----~g~s~l~~q~~DSs~asLg~~~-~wL~~~~-~~~~~~E~--v~~----- 715 (903)
..||+++| ++.|....... ....+++.|+ ||+++++... .||...+ ..+..... ...
T Consensus 208 ~~~G~~~L--------~~~L~~~~~~~~~~~~~~~~~~~Q~--SSIGs~~~~~~~Wl~~~f~~sl~~~~~~~~~~~~~~~ 277 (443)
T PF06087_consen 208 DKWGHMRL--------RKVLKRLGLPSNKDKDKESDIVCQF--SSIGSLGSSPKDWLTSEFLTSLYPASFSSPSTPSSKS 277 (443)
T ss_dssp GGSHHHHH--------HHHHHHCCTT---TTCCCCEEEEE---SBB---SSSTTTTTTTHHHHHCCHHCCT------HHH
T ss_pred cchhHHHH--------HHHHHhccccccCCcCCCCeEEEEc--ccccccCcchhhhHHHHHHHHHhhccccccccccccc
Confidence 26997655 44444433332 1246888898 8899997555 3765433 33322100 000
Q ss_pred cCCCCCCCCCCeEEEecCCCccc-------CCcee-----------ecCCcchhhhcccCC
Q 002593 716 RNTNVPADANAVSVLVPNPDELS-------DGDCI-----------QLGFMPRDIAKWVSP 758 (903)
Q Consensus 716 sn~n~p~~~~~~~IIfPT~deVr-------sg~Sk-----------QL~fL~~~l~kW~s~ 758 (903)
.........++++|||||.++|+ +|+++ +..||+++||+|.++
T Consensus 278 ~~~~~~~~~~~~~IvfPT~e~Vr~S~~G~~~ggsi~~~~~~~~~~~~~~~l~~~~~~w~~~ 338 (443)
T PF06087_consen 278 SSSQQENNRPPLKIVFPTVEEVRNSPEGYNGGGSIPFKYKWWEPNFPQEWLRPYFHKWYAS 338 (443)
T ss_dssp HHHHCCHHTEEEEEE--BCHHHCTSTTGGGGGGGSB--HC--GHHCCHHHHHHCCE-EEEC
T ss_pred cccccccCCCCceEECCCHHHHhhCccCCcCceeEEecchhccccchHHHHHHHHhhhccc
Confidence 00011123678999999999999 55552 235889999999887
No 2
>KOG2031 consensus Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair]
Probab=100.00 E-value=2.1e-43 Score=390.25 Aligned_cols=307 Identities=20% Similarity=0.307 Sum_probs=225.2
Q ss_pred CCCCCcccCCCCCCCCCCcEEEEEeccCC-CCCCCCCccccccccCC-chhHHHHHHhhcccchhhhhhhcC-CCCCCcE
Q 002593 397 GSMDKSKSLGSSCSPPGKKFYLNRLEFMD-LTSLNYDVISLPELLYP-VESISRMFIATFTSDILWFMSYCE-IPSHLPV 473 (903)
Q Consensus 397 ~~~~~~~~~~~~~~~~gspFyLnrI~~lp-~~~~n~dtISL~DLLgP-~~~L~~allfnF~~DidWLLs~f~-~~r~lpV 473 (903)
.+.+...+...+|.|-+ ++++.+.+.- ..+.+...+++.+||.+ .+++..+++||||+|++||+.+|+ .++..|+
T Consensus 63 ~e~~~~~~~~~~~~p~~--~~ft~v~~~s~~~~~s~~s~sl~~il~~i~g~~v~silfsfmvdid~Lv~~y~~~~~~~~i 140 (519)
T KOG2031|consen 63 QEKDDSERILTNDNPKG--AVFTTVKGDSVPRYDSMGSVSLMEILADIFGTPVNSILFSFMVDIDWLVGQYPPSVRIKPI 140 (519)
T ss_pred cccccHHHHhccCCccc--ccccccccccccccCcccchHHHHHHHHhhCCchhheEEEEEeEHHHHHhhCcchhccCce
Confidence 34444457777887776 6667766622 22234467777777762 246899999999999999999998 4688888
Q ss_pred EEEEccCccccccCCCCCcCCCCCCCCCeEEEcCCCCccccccccccCCCcccccceEEEEEeCCcEEEEEeCCCCCHHh
Q 002593 474 TIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQ 553 (903)
Q Consensus 474 tIVvh~~~~~wk~e~~~rl~~~~~~~pNv~li~PpMPe~I~FG~d~~~~g~GtHHSKMmIL~Y~D~LRVVI~TANLi~~D 553 (903)
|++ |++.. ..++..+.....+++++.+.|| |||| |||+|||+|+|++++|||||||||++.|
T Consensus 141 ~l~-~G~~d------~~~~~~~~K~~~l~~~~~~~Lp--ipF~---------thHtKm~~l~y~~G~rvvv~taNl~~~D 202 (519)
T KOG2031|consen 141 TLV-HGEPD------EARLLAQTKAPILVTVKLASLP--IPFG---------THHTKMIILFYEEGCRVVVHTANLIHDD 202 (519)
T ss_pred EEE-ecCCc------hHHHHhhhhccceeeeeccccc--cccc---------ccccceEEEeccCccEEEEecCCcceec
Confidence 875 54431 1122222334559999999999 8999 9999999999999999999999999999
Q ss_pred hccccCeEEeecCCCCCCCCccccccCCCcccccCCCCCcHHHHHHHHHHHhccCCCchHHHHHhhcccccccccEEEEE
Q 002593 554 WNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVA 633 (903)
Q Consensus 554 W~~~TQ~VWiQDFP~l~~~~~~~~~~~~~~~e~~~~~~sdFk~dL~~YL~sy~~~~Ps~~~~i~~L~kyDFSsakv~LVa 633 (903)
|+++||++|++++++.... ....++.|+.||++||++|.. |.++.|++.|++||||.++|+||+
T Consensus 203 w~~ktQ~~w~sp~~~~~~~--------------~g~~~~~Fk~DLi~YL~~Y~~--~~l~~~i~~lkk~DfS~i~v~fIg 266 (519)
T KOG2031|consen 203 WNNKTQGFWCSPLLKIGDK--------------KGVSPTGFKQDLIEYLNSYRL--PQLKEWIASLKKVDFSAINVRFIG 266 (519)
T ss_pred ccccccceeecCCcccccC--------------CCCCCCchHHHHHHHHHHhcc--chhHHHHHHHHhcchhhceEEEEe
Confidence 9999999999976666421 136788999999999999964 788999999999999999999999
Q ss_pred ecCCcccCCCCCCCCCcccCCCcCCcccccccccccceecc-ccCcceeEEeecccccchhhhhH-HHhhhhh-hcccch
Q 002593 634 SVPGIHSYRNPNLSESTYSKPVDHGAIWSSDGKFLGSVETS-VVGLSHLFRTAADSNGTQIKKLA-AFLGKSF-SAHGML 710 (903)
Q Consensus 634 SVPG~H~g~~~~~~~~~~G~~~l~n~~~~~~~s~LgSv~~s-~~g~s~l~~q~~DSs~asLg~~~-~wL~~~~-~~~~~~ 710 (903)
||||++.+.... +|||.+| ++.|.-..++ .......+.|. ||+++||+.- +|+...+ ..+.
T Consensus 267 StPG~f~gs~~~----~WGh~kL--------~kiL~~~~~~~~~~r~~~v~q~--sS~gsl~~~~~~~~~~~f~~~l~-- 330 (519)
T KOG2031|consen 267 STPGKFQGSGLL----SWGHNKL--------KKILKEHAASPYLERTPVVGQS--SSIGSLGSLWSAWFIGDFVESLA-- 330 (519)
T ss_pred ecCCcccCcccc----cccHHHH--------HHHHHhhccCcccccCceeeee--eccccccchhhhhhhhhhccchh--
Confidence 999998776543 6998765 3333322221 11112344566 7788888554 5655545 4332
Q ss_pred hhhhccCCCCCCCCCCeEEEecCCCccc-------CCce---------eecCCcchhhhcccCCCC
Q 002593 711 KILLRRNTNVPADANAVSVLVPNPDELS-------DGDC---------IQLGFMPRDIAKWVSPLW 760 (903)
Q Consensus 711 E~v~~sn~n~p~~~~~~~IIfPT~deVr-------sg~S---------kQL~fL~~~l~kW~s~~~ 760 (903)
+.++.....++.+.+||||.++|| +|+| +|. ||..|||||.+...
T Consensus 331 ----kdt~~~gk~~~~~yiIfPTveeVrtS~~G~~~Ggsipy~~~~~~kq~-~lk~y~~kW~A~~s 391 (519)
T KOG2031|consen 331 ----KDTTPPGKLRPPFYIIFPTVEEVRTSLLGYAGGGSLPYGKNTNEKQP-WLKKYLCKWKAMDS 391 (519)
T ss_pred ----hccCCCCCCCCCeeEEcccHHHhhccccccccCceecccchhhhhhH-HHHHHHHhhhhhhh
Confidence 232332223477999999999999 6776 444 99999999998754
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=99.47 E-value=7.4e-14 Score=118.56 Aligned_cols=67 Identities=43% Similarity=0.762 Sum_probs=57.7
Q ss_pred EEEcCCCCCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccccccccccccccc
Q 002593 71 YSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNG 150 (903)
Q Consensus 71 ~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~~~L~~~~~S~NG 150 (903)
|+|||++ .|||+++++.|||+||.|.++.. + .| +|+| + .|+||
T Consensus 1 ~~iGR~~-~~di~l~~~~iSr~Ha~i~~~~~--------~------------~~------~i~d------~----~s~ng 43 (68)
T PF00498_consen 1 VTIGRSP-DCDIVLPDPSISRRHARISFDDD--------G------------QF------YIED------L----GSTNG 43 (68)
T ss_dssp EEEESST-TSSEEETSTTSSTTSEEEEEETT--------E------------EE------EEEE------S----SSSS-
T ss_pred CEEcCCC-CCCEEECCHheeeeeeEEEEece--------e------------eE------EEEe------C----CCCCc
Confidence 6899999 99999999999999999996532 1 14 7888 3 79999
Q ss_pred eEECCEEccCCCeeeCCCCCEEEE
Q 002593 151 VFVNGIRLKSGIVRELNAGDEVLF 174 (903)
Q Consensus 151 TfVNG~RI~k~~~~~L~~GD~I~~ 174 (903)
|||||+++.+++.++|.+||+|.|
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 999999999999999999999998
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=99.10 E-value=5.8e-10 Score=99.58 Aligned_cols=79 Identities=38% Similarity=0.558 Sum_probs=65.8
Q ss_pred ceeEEecCCCCEEEcCCCCCC-CEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccc
Q 002593 60 VDSLTLEPDRPYSIGRASINC-DFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEED 138 (903)
Q Consensus 60 ~~~i~L~~~~~~tIGR~~~~c-DiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~ 138 (903)
...+.|..+..++|||++ .| |++|+++.|||+||+|.++.. ++ + ++.|
T Consensus 13 ~~~~~l~~~~~~~iGr~~-~~~~i~l~~~~iS~~H~~i~~~~~-------~~-------------~------~~~~---- 61 (102)
T cd00060 13 GRRYYLDPGGTYTIGRDS-DNCDIVLDDPSVSRRHAVIRYDGD-------GG-------------V------VLID---- 61 (102)
T ss_pred eeEEEECCCCeEEECcCC-CcCCEEcCCCCeeCcceEEEEcCC-------CC-------------E------EEEE----
Confidence 458888875679999999 88 999999999999999997631 11 2 3344
Q ss_pred cccccccccccceEECCEEccCCCeeeCCCCCEEEEE
Q 002593 139 EGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (903)
Q Consensus 139 ~~L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~~ 175 (903)
. .|.|||||||+++.++....|.+||+|.|+
T Consensus 62 ~------~s~~g~~vn~~~~~~~~~~~l~~gd~i~ig 92 (102)
T cd00060 62 L------GSTNGTFVNGQRVSPGEPVRLRDGDVIRLG 92 (102)
T ss_pred C------CCCCCeEECCEECCCCCcEECCCCCEEEEC
Confidence 2 799999999999998778999999999994
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=98.96 E-value=1.2e-09 Score=123.49 Aligned_cols=74 Identities=35% Similarity=0.612 Sum_probs=64.1
Q ss_pred eeEEecCCCCEEEcCCCCCCCEEecCCc--cccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccc
Q 002593 61 DSLTLEPDRPYSIGRASINCDFTFDNRL--VSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEED 138 (903)
Q Consensus 61 ~~i~L~~~~~~tIGR~~~~cDiVi~d~~--VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~ 138 (903)
.++.+..+ .++|||++ +||++|+|+. ||++||+|.++ +| .| +|+|
T Consensus 17 ~~~~f~~~-~~~IGR~~-~~d~~l~d~~~~VS~~Ha~I~~~---------~g------------~~------~l~D---- 63 (396)
T TIGR03354 17 AQKTFGTN-GGTIGRSE-DCDWVLPDPERHVSGRHARIRYR---------DG------------AY------LLTD---- 63 (396)
T ss_pred eEEEECCC-CEEEecCC-CCCEEeCCCCCCcchhhcEEEEE---------CC------------EE------EEEE----
Confidence 36777764 59999999 9999999998 99999999954 22 25 7889
Q ss_pred cccccccccccceEEC--CEEccCCCeeeCCCCCEEEE
Q 002593 139 EGFSRVMVSLNGVFVN--GIRLKSGIVRELNAGDEVLF 174 (903)
Q Consensus 139 ~~L~~~~~S~NGTfVN--G~RI~k~~~~~L~~GD~I~~ 174 (903)
.|+|||||| |.+|.++..+.|++||+|.|
T Consensus 64 -------lStNGT~VN~sg~~l~~~~~~~L~~GD~I~i 94 (396)
T TIGR03354 64 -------LSTNGVFLNGSGSPLGRGNPVRLEQGDRLRL 94 (396)
T ss_pred -------CCCCCeEECCCCCCCCCCCceEcCCCCEEEE
Confidence 599999999 99999988899999999999
No 6
>KOG1882 consensus Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms]
Probab=98.93 E-value=5.9e-10 Score=116.91 Aligned_cols=96 Identities=25% Similarity=0.259 Sum_probs=77.3
Q ss_pred CCcceeEEecCCCCEEEcCCCCCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcc
Q 002593 57 GSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEE 136 (903)
Q Consensus 57 g~~~~~i~L~~~~~~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~ 136 (903)
++++.++.++....|.+||...-.||-|++|..|+|||+|+|....+. -.||+ ..+++..+|.|
T Consensus 182 ~e~l~~l~iHrqs~yL~gRerkIaDi~idhpScSKQHaviQyR~v~~~--r~dGt------------~grrvkpYiiD-- 245 (293)
T KOG1882|consen 182 YEVLPVLYIHRQSCYLDGRERKIADIPIDHPSCSKQHAVIQYRLVEFT--RADGT------------VGRRVKPYIID-- 245 (293)
T ss_pred CcccchheeeeeeeeecCceeeeeccCCCCccccccceeeeeeecccc--cCCCc------------cceeeeeEEEe--
Confidence 344456677777789999988779999999999999999999765322 24652 33444557889
Q ss_pred cccccccccccccceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 137 EDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 137 ~~~~L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
| +|+||||+|..+|...++.+|..+|+|.|++
T Consensus 246 ----L----gS~NgTfLNnk~IepqRYyEL~ekDvlkfgf 277 (293)
T KOG1882|consen 246 ----L----GSGNGTFLNNKVIEPQRYYELREKDVLKFGF 277 (293)
T ss_pred ----c----CCCCcceecCcccCchheeeeecCceeeecc
Confidence 4 9999999999999999999999999999954
No 7
>COG1716 FOG: FHA domain [Signal transduction mechanisms]
Probab=98.93 E-value=2.9e-09 Score=106.46 Aligned_cols=68 Identities=31% Similarity=0.489 Sum_probs=57.8
Q ss_pred CCEEEcCCCCCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccccccccccccc
Q 002593 69 RPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSL 148 (903)
Q Consensus 69 ~~~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~~~L~~~~~S~ 148 (903)
..++|||++ ++|+++++..|||+||.|..+. +. + +++| | +|+
T Consensus 89 ~~~tigr~~-~~~i~~~~~~vSR~Ha~l~~~~--------~~-------------~------~~~d------~----~S~ 130 (191)
T COG1716 89 PVTTIGRDP-DNDIVLDDDVVSRRHAELRREG--------NE-------------V------FLED------L----GST 130 (191)
T ss_pred ceEEeccCC-CCCEEcCCCccccceEEEEEeC--------Cc-------------e------EEEE------C----CCC
Confidence 479999999 9999999999999999998442 22 3 6678 4 899
Q ss_pred cceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 149 NGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 149 NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
|||||||.++... +.|.+||.|.|+.
T Consensus 131 nGt~vn~~~v~~~--~~l~~gd~i~i~~ 156 (191)
T COG1716 131 NGTYVNGEKVRQR--VLLQDGDVIRLGG 156 (191)
T ss_pred cceEECCeEccCc--EEcCCCCEEEECc
Confidence 9999999999973 6799999999943
No 8
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=98.70 E-value=2.6e-08 Score=80.14 Aligned_cols=52 Identities=44% Similarity=0.800 Sum_probs=42.7
Q ss_pred EEEcCCCCCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccccccccccccccc
Q 002593 71 YSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNG 150 (903)
Q Consensus 71 ~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~~~L~~~~~S~NG 150 (903)
++|||++..||++++++.||+.||.|.++.. + .| +++| + .|+||
T Consensus 1 ~~iGr~~~~~~i~~~~~~vs~~H~~i~~~~~--------~------------~~------~i~d------~----~s~~g 44 (52)
T smart00240 1 VTIGRSSEDCDIQLPGPSISRRHAEIVYDGG--------G------------RF------YLID------L----GSTNG 44 (52)
T ss_pred CEeCCCCCCCCEEeCCCCcchhHcEEEECCC--------C------------eE------EEEE------C----CCCCC
Confidence 4799998679999999999999999997632 1 13 6777 2 67999
Q ss_pred eEECCEEc
Q 002593 151 VFVNGIRL 158 (903)
Q Consensus 151 TfVNG~RI 158 (903)
|||||++|
T Consensus 45 t~vng~~v 52 (52)
T smart00240 45 TFVNGKRI 52 (52)
T ss_pred eeECCEEC
Confidence 99999986
No 9
>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase
Probab=98.67 E-value=3e-08 Score=118.49 Aligned_cols=96 Identities=23% Similarity=0.404 Sum_probs=70.7
Q ss_pred CCCcceeEEec--CCCCEEEcCCCCCCCE-----EecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcc
Q 002593 56 TGSPVDSLTLE--PDRPYSIGRASINCDF-----TFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKR 128 (903)
Q Consensus 56 ~g~~~~~i~L~--~~~~~tIGR~~~~cDi-----Vi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~ 128 (903)
.+...+.+.|. .+.|++|||.+ +||+ ||+++.||++||+|.++ ++ .|
T Consensus 542 ~~~~~~~~~l~~~~~~p~~iG~~~-~~~~~~~~i~i~~~~vS~~Ha~i~~~---------~~------------~~---- 595 (668)
T PLN02927 542 DCCVSETLCLTKDEDQPCIVGSEP-DQDFPGMRIVIPSSQVSKMHARVIYK---------DG------------AF---- 595 (668)
T ss_pred CCcccceeeeecCCCCCeEecCCC-CcCCCCceEEecCCccChhHeEEEEE---------CC------------EE----
Confidence 33334567772 23689999999 9996 99999999999999843 33 25
Q ss_pred cccccCcccccccccccccccceEECCEE---cc--CCCeeeCCCCCEEEEEeCCCccccccceEEEEEEEEEE
Q 002593 129 DKSLEDEEEDEGFSRVMVSLNGVFVNGIR---LK--SGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIF 197 (903)
Q Consensus 129 ~v~i~D~~~~~~L~~~~~S~NGTfVNG~R---I~--k~~~~~L~~GD~I~~~~g~~~~~~~~~~igf~v~~i~~ 197 (903)
+|+| | +|+|||||||.+ |. .+..+.|++||+|.|+-.++ +.|.|+.+..
T Consensus 596 --~~~D------l----~S~nGT~v~~~~~~r~~~~p~~~~~l~~~d~I~~g~~~~--------~~fr~~~~~~ 649 (668)
T PLN02927 596 --FLMD------L----RSEHGTYVTDNEGRRYRATPNFPARFRSSDIIEFGSDKK--------AAFRVKVIRK 649 (668)
T ss_pred --EEEE------C----CCCCccEEeCCCCceEecCCCCceEeCCCCEEEeCCCcc--------eeEEEEeecC
Confidence 8999 4 999999996665 54 45568999999999944322 2466665543
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=98.40 E-value=3.3e-07 Score=103.08 Aligned_cols=72 Identities=42% Similarity=0.738 Sum_probs=59.8
Q ss_pred EEecCCCCEEEcCCCCCCCEEecC--CccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccccc
Q 002593 63 LTLEPDRPYSIGRASINCDFTFDN--RLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEG 140 (903)
Q Consensus 63 i~L~~~~~~tIGR~~~~cDiVi~d--~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~~~ 140 (903)
..+..+ ..+|||++ +||.+|+| +.||++||+|.++ +|. | +++|
T Consensus 21 ~~f~~~-~g~IGrs~-dcdW~i~D~~~~VS~~Hc~I~~~---------dg~------------f------~L~D------ 65 (430)
T COG3456 21 KLFDRG-GGVIGRSP-DCDWQIDDPERFVSKQHCTISYR---------DGG------------F------CLTD------ 65 (430)
T ss_pred hhhhcC-CcccccCC-CCCccccCcccccchhheEEEec---------CCe------------E------EEEe------
Confidence 344433 47999999 99999997 5899999999954 342 6 8889
Q ss_pred cccccccccceEECCEEccCCCe-eeCCCCCEEEE
Q 002593 141 FSRVMVSLNGVFVNGIRLKSGIV-RELNAGDEVLF 174 (903)
Q Consensus 141 L~~~~~S~NGTfVNG~RI~k~~~-~~L~~GD~I~~ 174 (903)
.|.|||||||..+..|.. ..|+.||+|.|
T Consensus 66 -----tS~g~l~VNgs~~~~g~~~~RLqqGd~i~i 95 (430)
T COG3456 66 -----TSNGGLLVNGSDLPLGEGSARLQQGDEILI 95 (430)
T ss_pred -----cCCCceeecccccCCCCCccccccCCEEee
Confidence 689999999999987766 88999999999
No 11
>KOG1881 consensus Anion exchanger adaptor protein Kanadaptin, contains FHA domain [General function prediction only]
Probab=97.87 E-value=4.4e-06 Score=98.82 Aligned_cols=92 Identities=23% Similarity=0.371 Sum_probs=73.5
Q ss_pred CCCcceeEEecCCCCEEEcCCCCCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCc
Q 002593 56 TGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDE 135 (903)
Q Consensus 56 ~g~~~~~i~L~~~~~~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~ 135 (903)
.|..+.+.+|.....|+|||.. .||+.+.||.|||.||.|.+.... .++ |-++--+ -| +|.|
T Consensus 164 eg~iiet~~l~~~~~~~fgr~~-~cD~~~eHpsISr~h~vlQy~~~~-----~~~----p~~s~~~-g~------~i~d- 225 (793)
T KOG1881|consen 164 EGAIIETEDLKGAAACLFGRLG-GCDVALEHPSISRFHAVLQYKASG-----PDD----PCASNGE-GW------YIYD- 225 (793)
T ss_pred cCceeeeeecccceeEEecccC-CCccccccCcccccceeeeccCCC-----CCc----cccCCCC-ce------EEee-
Confidence 5777889999888889999999 999999999999999999975442 111 0000001 14 7778
Q ss_pred ccccccccccccccceEECCEEccCCCeeeCCCCCEEEE
Q 002593 136 EEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLF 174 (903)
Q Consensus 136 ~~~~~L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~ 174 (903)
| +|+-|||+|..||.+.++..++.|+++.|
T Consensus 226 -----l----gsThgt~~NK~rvppk~yir~~Vg~v~~f 255 (793)
T KOG1881|consen 226 -----L----GSTHGTFLNKDRVPPKVYIRDRVGHVARF 255 (793)
T ss_pred -----c----cccccceeccccCCCcchhhhhHHHHHHh
Confidence 3 99999999999999999999999999988
No 12
>KOG0615 consensus Serine/threonine protein kinase Chk2 and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.80 E-value=1.6e-05 Score=89.96 Aligned_cols=90 Identities=32% Similarity=0.513 Sum_probs=68.0
Q ss_pred eeEEecCCCCEEEcCCCCCCCEEecCCccccccEEEEEccCcceE-EecCCcccccccccccchhhhcccccccCccccc
Q 002593 61 DSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKI-YVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDE 139 (903)
Q Consensus 61 ~~i~L~~~~~~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i-~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~~ 139 (903)
..+.+..+ .|++||.+ .||++++...+|..|..+.+-...-++ +..++ . ..-.+++++|
T Consensus 57 ~~~d~~nd-~f~fGR~~-~~d~~ln~~~~s~~~~~i~~~~~~~~~~f~~dr---------~----~~sn~~y~~D----- 116 (475)
T KOG0615|consen 57 KSIDLAND-EFTFGRGD-SCDAPLNLNNVSNKHFKILLYNKISKIHFRIDR---------D----KNSNRVYLHD----- 116 (475)
T ss_pred ccceeccc-eEEecCCC-cccccccCccccccchheeeeeeeeeeeecccC---------C----CccceEEEEe-----
Confidence 45666654 69999999 999999999999999998864221111 11111 0 0112458889
Q ss_pred ccccccccccceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 140 GFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 140 ~L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
.|+||||||-++++++..++|++||+|.|..
T Consensus 117 ------hS~nGT~VN~e~i~k~~~r~lkN~dei~is~ 147 (475)
T KOG0615|consen 117 ------HSRNGTFVNDEMIGKGLSRILKNGDEISISI 147 (475)
T ss_pred ------cccCcccccHhHhhccccccccCCCEEEecc
Confidence 7999999999999999999999999999843
No 13
>KOG1880 consensus Nuclear inhibitor of phosphatase-1 [General function prediction only]
Probab=97.06 E-value=0.00029 Score=76.95 Aligned_cols=86 Identities=24% Similarity=0.348 Sum_probs=67.3
Q ss_pred CCCcceeEEecCCCCEEEcCCCCCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCc
Q 002593 56 TGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDE 135 (903)
Q Consensus 56 ~g~~~~~i~L~~~~~~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~ 135 (903)
++.+.+.+.+. ++.|.+||.+..||++|++..+||+|+-+.+- ... + ++++.|
T Consensus 26 d~li~kl~idd-kr~y~Fgrn~q~~df~idh~scSrvhaa~vyh--------khl-----------~------~~~lid- 78 (337)
T KOG1880|consen 26 DKLIQKLIIDD-KRRYLFGRNHQTCDFVIDHASCSRVHAALVYH--------KHL-----------S------RIFLID- 78 (337)
T ss_pred chhHHHHHhhh-hhhhhhccCCCccceEeecchhhhhHhhhhhh--------hcc-----------c------eEEEEE-
Confidence 34444455554 46799999999999999999999999987732 111 1 126678
Q ss_pred ccccccccccccccceEECCEEccCCCeeeCCCCCEEEEEeC
Q 002593 136 EEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCR 177 (903)
Q Consensus 136 ~~~~~L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~~~g 177 (903)
| +|+-|||+...|++..+.++|..|....|+.+
T Consensus 79 -----l----~s~hgtf~g~~rL~~~~p~~l~i~~~~~fgas 111 (337)
T KOG1880|consen 79 -----L----GSTHGTFLGNERLEPHKPVQLEIGSTFHFGAS 111 (337)
T ss_pred -----c----cCCcceeeeeeeeccCCCccccCCceEEEecc
Confidence 3 89999999999999999999999999999553
No 14
>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=95.99 E-value=0.017 Score=66.26 Aligned_cols=47 Identities=21% Similarity=0.449 Sum_probs=39.6
Q ss_pred eeeEEecC-CCCcceeEEecCCCCEEEc-CCCCCCCEEecCCccccccEEEEEc
Q 002593 48 HLPLVSTA-TGSPVDSLTLEPDRPYSIG-RASINCDFTFDNRLVSRQHCQILFD 99 (903)
Q Consensus 48 ~~plis~~-~g~~~~~i~L~~~~~~tIG-R~~~~cDiVi~d~~VSR~Ha~I~fd 99 (903)
.+-++++. .|. .+.|.++. ++|| |++ +|||++.|+.||++|+.|..+
T Consensus 2 ~lrvl~G~~~G~---~~~L~~g~-~~iG~~~~-~~di~L~d~~~~~~h~~l~v~ 50 (410)
T TIGR02500 2 KLRVLSGPHRGA---ELPLPEGN-LVLGTDAA-DCDIVLSDGGIAAVHVSLHVR 50 (410)
T ss_pred EEEEecCCCCCc---EEECCCCc-eEeccCCC-CcEEEeCCCCccchheEEEEc
Confidence 35667777 565 77888875 9999 999 999999999999999999854
No 15
>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=95.01 E-value=0.019 Score=66.56 Aligned_cols=76 Identities=32% Similarity=0.445 Sum_probs=54.7
Q ss_pred cCCCh-hhhhhhhchhhHHHHHHHHHHhHh-----------------------hhchhhHHHHhhcCCCCc----ccccc
Q 002593 796 QGPKF-SDISKMMQIEHVVALSSLIASIQR-----------------------CRGLWRLQEVLGQYRWPE----LQESD 847 (903)
Q Consensus 796 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~----~~~~~ 847 (903)
.|..| .|+...+..........|+..|++ .+|+.||.++|.++.++. ..+.+
T Consensus 156 ~~~~F~~dL~~yL~~y~~~~~~~~~~~l~~yDFS~~~v~lV~SvPG~h~~~~~~~G~~~L~~~L~~~~~~~~~~~~~~~~ 235 (443)
T PF06087_consen 156 SGSRFKKDLVAYLNSYGKSPLDKLIERLRKYDFSSARVHLVASVPGKHKEDKDKWGHMRLRKVLKRLGLPSNKDKDKESD 235 (443)
T ss_dssp STTHHHHHHHHHHHTT--HHHHHCHHHHHTEE-CCGTSEEEEE-SECCCGGGGGSHHHHHHHHHHHCCTT---TTCCCCE
T ss_pred CCCchHHHHHHHHHHhCCcchhHHHHHHHhcCCccCceEEEeccCccccCCCcchhHHHHHHHHHhccccccCCcCCCCe
Confidence 57777 456666655554445556666655 599999999999999987 88999
Q ss_pred eeeeccCcccc--------cHHHHHHHHHhhc
Q 002593 848 FSYGSSSIGSI--------NAQFLAAFAAASG 871 (903)
Q Consensus 848 ~~~~~~~~~~~--------~~~~~~~~~~~~~ 871 (903)
|+|-+|||||. +..|+.+++.++.
T Consensus 236 ~~~Q~SSIGs~~~~~~~Wl~~~f~~sl~~~~~ 267 (443)
T PF06087_consen 236 IVCQFSSIGSLGSSPKDWLTSEFLTSLYPASF 267 (443)
T ss_dssp EEEE-SBB---SSSTTTTTTTHHHHHCCHHCC
T ss_pred EEEEcccccccCcchhhhHHHHHHHHHhhccc
Confidence 99999999977 6779998888776
No 16
>KOG0245 consensus Kinesin-like protein [Cytoskeleton]
Probab=91.25 E-value=0.53 Score=59.20 Aligned_cols=75 Identities=24% Similarity=0.420 Sum_probs=52.5
Q ss_pred EEecCCCCEEEcCCC--CCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccccc
Q 002593 63 LTLEPDRPYSIGRAS--INCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEG 140 (903)
Q Consensus 63 i~L~~~~~~tIGR~~--~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~~~ 140 (903)
++.-++...+|||.+ ...||+++-..|--+||.|.-++... + |--- -.+|
T Consensus 471 lY~ikeG~TrVG~~~a~~~~DI~LsG~~I~~qHC~i~~~~g~~-~---------------vtl~------p~e~------ 522 (1221)
T KOG0245|consen 471 LYYIKEGETRVGREDASSRQDIVLSGQLIREQHCSIRNEGGND-V---------------VTLE------PCED------ 522 (1221)
T ss_pred EEEeccCceecCCCCcccCCceEecchhhhhhceEEEecCCCc-e---------------EEec------cCCc------
Confidence 344445578999976 36899999999999999998332210 1 0000 1223
Q ss_pred cccccccccceEECCEEccCCCeeeCCCCCEEEEE
Q 002593 141 FSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (903)
Q Consensus 141 L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~~ 175 (903)
--|||||..|..- ..|+.||+|.|+
T Consensus 523 --------aetyVNGk~v~ep--~qL~~GdRiilG 547 (1221)
T KOG0245|consen 523 --------AETYVNGKLVTEP--TQLRSGDRIILG 547 (1221)
T ss_pred --------cceeEccEEcCCc--ceeccCCEEEEc
Confidence 3499999999875 579999999993
No 17
>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=91.17 E-value=0.049 Score=51.01 Aligned_cols=78 Identities=33% Similarity=0.549 Sum_probs=49.0
Q ss_pred hhhccCCCCCCCCCCeEEEecCCCcccCCceeecCCcchhhhcccCCCCCCccceEeeccchHHHHHHHhccccceEEEE
Q 002593 712 ILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLI 791 (903)
Q Consensus 712 ~v~~sn~n~p~~~~~~~IIfPT~deVrsg~SkQL~fL~~~l~kW~s~~~D~g~~~f~~~~~p~~~l~~a~~~~~~~vq~~ 791 (903)
+.+++..+.|.|.+|+++.....-....| .++|||++..++|.+++-|.+...|.|.+.+.+. +......+|.|.
T Consensus 29 v~L~re~~N~~D~nAi~v~~~~~~~~~~~--~~iGylp~~~a~~l~~Lld~~~~~~~~~v~~~~~---~~~~~~~~i~l~ 103 (107)
T PF08797_consen 29 VVLVREPDNPYDPNAIKVYTIDRFSNSRG--REIGYLPREIAKWLSPLLDSGGVKFEGTVVFVPD---KRLRIGIEIYLF 103 (107)
T ss_dssp EEEEEETT-TTHCCCCCEEETT------B--GCCCCCHHHHHHHHHHHCCT-TEEEEEEEECCCT---TT-----EEEEE
T ss_pred EEEEEcCCCCCCcccEEEEEeecccccCC--CEEEEecHHHHHHHHHHHhCCCcEEEEEEEECCc---cccccCeEEEEE
Confidence 34455555566788888888765322222 3899999999999999999999999999976665 334445555555
Q ss_pred Eee
Q 002593 792 LHV 794 (903)
Q Consensus 792 ~~~ 794 (903)
+++
T Consensus 104 ~~~ 106 (107)
T PF08797_consen 104 LKC 106 (107)
T ss_dssp E--
T ss_pred EEC
Confidence 543
No 18
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=90.51 E-value=0.48 Score=56.55 Aligned_cols=79 Identities=22% Similarity=0.274 Sum_probs=62.4
Q ss_pred eeEEecCCCCEEEcCCCCCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCcccccc
Q 002593 61 DSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEG 140 (903)
Q Consensus 61 ~~i~L~~~~~~tIGR~~~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~~~~ 140 (903)
..|+|.. ....|||.| .-.|.|...||+..+|.-|-.. | + |.+.- +
T Consensus 25 ~~~~~~~-~~~~~gr~p---et~i~d~~cs~~qv~l~a~~~~-------~-------------~-----v~~k~----l- 70 (526)
T TIGR01663 25 HFIHLDA-GALFLGRGP---ETGIRDRKCSKRQIELQADLEK-------A-------------T-----VALKQ----L- 70 (526)
T ss_pred CeeccCC-CceEEccCc---ccccchhhhchhhheeeecccC-------c-------------e-----EEEEE----c-
Confidence 4778775 568899999 6777899999999998855332 1 1 23434 2
Q ss_pred cccccccccceEECCEEccCCCeeeCCCCCEEEEEeCCC
Q 002593 141 FSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDE 179 (903)
Q Consensus 141 L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~~~g~~ 179 (903)
..|-+-|||+-+.++...+|++||.+.|+.|..
T Consensus 71 ------g~np~~~~~~~~~~~~~~~l~~g~~l~~v~~~~ 103 (526)
T TIGR01663 71 ------GVNPCGTGGLELKPGGEGELGHGDLLEIVNGLH 103 (526)
T ss_pred ------cCCCcccCceEecCCCeeeecCCCEEEEecccc
Confidence 559999999999999999999999999988764
No 19
>KOG2293 consensus Daxx-interacting protein MSP58/p78, contains FHA domain [Transcription; Signal transduction mechanisms]
Probab=79.54 E-value=4.3 Score=48.30 Aligned_cols=74 Identities=23% Similarity=0.302 Sum_probs=53.2
Q ss_pred EecCCCCEEEcCCCCCCCEEec------CCccccccEEEEEccCcceEEecCCcccccccccccchhhhcccccccCccc
Q 002593 64 TLEPDRPYSIGRASINCDFTFD------NRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEE 137 (903)
Q Consensus 64 ~L~~~~~~tIGR~~~~cDiVi~------d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~~r~~~~v~i~D~~~ 137 (903)
|+...+.+|+||+..+|-+=|| .-.|||+.++|... .+| .| +|..
T Consensus 443 h~mrk~EVtlGRat~d~~VDIDLgkegpatKISRRQa~IkL~--------n~G------------sF------~IkN--- 493 (547)
T KOG2293|consen 443 HYMRKKEVTLGRATGDLKVDIDLGKEGPATKISRRQALIKLK--------NDG------------SF------FIKN--- 493 (547)
T ss_pred hhhcCcceEeeccCCCcceeeeccccCccceeeccceeEEec--------cCC------------cE------Eecc---
Confidence 3445678999999865555554 25789999998732 445 25 6666
Q ss_pred ccccccccccccceEECCEEccCCCeeeCCCCCEEEE
Q 002593 138 DEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLF 174 (903)
Q Consensus 138 ~~~L~~~~~S~NGTfVNG~RI~k~~~~~L~~GD~I~~ 174 (903)
+ ..--.||||.+|..|+.+.|.+.-.|.|
T Consensus 494 -l-------GK~~I~vng~~l~~gq~~~L~~nclveI 522 (547)
T KOG2293|consen 494 -L-------GKRSILVNGGELDRGQKVILKNNCLVEI 522 (547)
T ss_pred -C-------cceeEEeCCccccCCceEEeccCcEEEE
Confidence 2 3455899999999998888887777666
No 20
>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]
Probab=75.33 E-value=8.6 Score=48.72 Aligned_cols=90 Identities=20% Similarity=0.321 Sum_probs=61.5
Q ss_pred eeeeeEEecCCCCcc-eeEEecCCCCEEEcCCC-CCCCEEecCCccccccEEEEEccCcceEEecCCcccccccccccch
Q 002593 46 ILHLPLVSTATGSPV-DSLTLEPDRPYSIGRAS-INCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNE 123 (903)
Q Consensus 46 ~~~~plis~~~g~~~-~~i~L~~~~~~tIGR~~-~~cDiVi~d~~VSR~Ha~I~fd~~~~~i~i~~g~~~~~~~~~~v~~ 123 (903)
.+-+.+.-+.+|.-- ..|.|..+ +.-+|-+. .++.|.+.-|.|-.+||-|.+ -+||.
T Consensus 355 ~lPvLve~s~dG~~s~~ri~L~~~-vtEVGs~~~~~~~iqLfGP~IqprHc~it~---------meGVv----------- 413 (1629)
T KOG1892|consen 355 KLPVLVELSPDGSDSRKRIRLQLS-VTEVGSEKLDDNSIQLFGPGIQPRHCDITN---------MEGVV----------- 413 (1629)
T ss_pred cCcEEEEEcCCCCCcceeEEeccC-ceeccccccCCcceeeeCCCCCccccchhh---------ccceE-----------
Confidence 333444445555432 57777764 57789887 346899999999999998873 35532
Q ss_pred hhhcccccccCcccccccccccccc-cceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 124 FRKKRDKSLEDEEEDEGFSRVMVSL-NGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 124 ~r~~~~v~i~D~~~~~~L~~~~~S~-NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
.++- .++ -=|||||.+|.+- ..|+.|+.|.|+.
T Consensus 414 -------TvTP-----------~~~DA~t~VnGh~isqt--tiL~~G~~v~fGa 447 (1629)
T KOG1892|consen 414 -------TVTP-----------RSMDAETYVNGHRISQT--TILQSGMKVQFGA 447 (1629)
T ss_pred -------Eecc-----------cccchhhhccceecchh--hhhccCCEEEecc
Confidence 2222 122 3499999999874 6799999999954
No 21
>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=71.24 E-value=3.2 Score=31.09 Aligned_cols=24 Identities=33% Similarity=0.429 Sum_probs=13.7
Q ss_pred ccccceEEEEEeCCcEEEEEeCCCCCH
Q 002593 525 ACHHPKLFVLQREDSIRVIVTSANLGA 551 (903)
Q Consensus 525 GtHHSKMmIL~Y~D~LRVVI~TANLi~ 551 (903)
++||+|++|+-- -+..|.++||..
T Consensus 3 ~~~H~K~~vvD~---~~a~vGg~nl~~ 26 (28)
T PF00614_consen 3 GSHHQKFVVVDD---RVAFVGGANLCD 26 (28)
T ss_dssp BEE---EEEETT---TEEEEE---SSH
T ss_pred cceeeEEEEEcC---CEEEECceecCC
Confidence 489999999843 388999999864
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=69.16 E-value=4.6 Score=29.49 Aligned_cols=24 Identities=29% Similarity=0.394 Sum_probs=19.5
Q ss_pred ccccceEEEEEeCCcEEEEEeCCCCCH
Q 002593 525 ACHHPKLFVLQREDSIRVIVTSANLGA 551 (903)
Q Consensus 525 GtHHSKMmIL~Y~D~LRVVI~TANLi~ 551 (903)
+.+|+|+|+.-. -.++|.|+||..
T Consensus 3 ~~~H~K~~v~D~---~~~~iGs~N~~~ 26 (28)
T smart00155 3 GVLHTKLMIVDD---EIAYIGSANLDG 26 (28)
T ss_pred CcEEeEEEEEcC---CEEEEeCccCCC
Confidence 479999999844 379999999864
No 23
>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=62.30 E-value=9.7 Score=37.59 Aligned_cols=37 Identities=22% Similarity=0.228 Sum_probs=28.2
Q ss_pred ccccceEEEEEeCCcEEEEEeCCCCCHHhhc-cccCeEEee
Q 002593 525 ACHHPKLFVLQREDSIRVIVTSANLGAKQWN-AVTNTVWWQ 564 (903)
Q Consensus 525 GtHHSKMmIL~Y~D~LRVVI~TANLi~~DW~-~~TQ~VWiQ 564 (903)
+.+|+|+||+= .=.++|.|+|+....|. +.+.++.+.
T Consensus 112 ~~~H~K~~iiD---~~~~~vGS~N~~~~~~~~~~e~~~~~~ 149 (176)
T cd00138 112 GVLHTKLVIVD---DETAYIGSANLDGRSLTLNSEVGVVIY 149 (176)
T ss_pred cceeeeEEEEc---CCEEEEECCcCChhhhhhhcceEEEEe
Confidence 48999999994 34899999999999885 344445444
No 24
>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=58.24 E-value=7.4 Score=36.16 Aligned_cols=36 Identities=25% Similarity=0.358 Sum_probs=22.3
Q ss_pred cccceEEEEEeCCcEEEEEeCCCCCHHhhccc-cCeEEee
Q 002593 526 CHHPKLFVLQREDSIRVIVTSANLGAKQWNAV-TNTVWWQ 564 (903)
Q Consensus 526 tHHSKMmIL~Y~D~LRVVI~TANLi~~DW~~~-TQ~VWiQ 564 (903)
.+|.|+++.- +. .++|.|+|++...|..- +.++.+.
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 6899999993 22 99999999999988654 3344433
No 25
>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.
Probab=52.69 E-value=5.9 Score=46.57 Aligned_cols=67 Identities=16% Similarity=0.106 Sum_probs=48.0
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHHHHhhhhhc
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLSQCRNILN 270 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~~~~r~il~ 270 (903)
++++++|+ +..++.+ .+.|.|+ |||+ ++..-..||+++..|.|.-.+..+-+. ++-|.
T Consensus 350 vL~~isl~---i~~G~~v----aIvG~SG----sGKS----------TLl~lL~g~~~p~~G~I~i~g~~i~~~-~~~lr 407 (529)
T TIGR02868 350 VLDGVSLD---LPPGERV----AILGPSG----SGKS----------TLLMLLTGLLDPLQGEVTLDGVSVSSL-QDELR 407 (529)
T ss_pred eeecceEE---EcCCCEE----EEECCCC----CCHH----------HHHHHHhcCCCCCCcEEEECCEEhhhH-HHHHH
Confidence 56667776 4443432 4679999 9999 999999999999999998887666554 44443
Q ss_pred CCCchhhhhhh
Q 002593 271 SNDPVSCIQQI 281 (903)
Q Consensus 271 s~dp~s~~~~~ 281 (903)
+. |+|+.|-
T Consensus 408 ~~--i~~V~Q~ 416 (529)
T TIGR02868 408 RR--ISVFAQD 416 (529)
T ss_pred hh--eEEEccC
Confidence 22 6777553
No 26
>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional
Probab=45.28 E-value=8.5 Score=46.02 Aligned_cols=67 Identities=15% Similarity=0.119 Sum_probs=47.3
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHHHHhhhhhc
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLSQCRNILN 270 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~~~~r~il~ 270 (903)
++++++++ +..++.+ .+.|+|+ +||+ +++.-..|+++|..|.|.-.+..+-+.=+.-+.
T Consensus 350 iL~~inl~---i~~G~~v----~IvG~sG----sGKS----------TLl~lL~gl~~p~~G~I~i~g~~i~~~~~~~~r 408 (588)
T PRK13657 350 GVEDVSFE---AKPGQTV----AIVGPTG----AGKS----------TLINLLQRVFDPQSGRILIDGTDIRTVTRASLR 408 (588)
T ss_pred eecceeEE---ECCCCEE----EEECCCC----CCHH----------HHHHHHhcCcCCCCCEEEECCEEhhhCCHHHHH
Confidence 56777776 4444442 4679999 9999 999999999999999998888766543333333
Q ss_pred CCCchhhhhh
Q 002593 271 SNDPVSCIQQ 280 (903)
Q Consensus 271 s~dp~s~~~~ 280 (903)
+. |+|+.|
T Consensus 409 ~~--i~~v~Q 416 (588)
T PRK13657 409 RN--IAVVFQ 416 (588)
T ss_pred hh--eEEEec
Confidence 33 566644
No 27
>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=45.28 E-value=19 Score=33.78 Aligned_cols=27 Identities=26% Similarity=0.409 Sum_probs=22.0
Q ss_pred eEECCEEcc--CCCeeeCCCCCEEEEEeC
Q 002593 151 VFVNGIRLK--SGIVRELNAGDEVLFVCR 177 (903)
Q Consensus 151 TfVNG~RI~--k~~~~~L~~GD~I~~~~g 177 (903)
++|||+.|. .+...+|++||+|.|...
T Consensus 62 VlvN~~di~~l~g~~t~L~dgD~v~i~P~ 90 (94)
T cd01764 62 VLINDTDWELLGEEDYILEDGDHVVFIST 90 (94)
T ss_pred EEECCccccccCCcccCCCCcCEEEEECC
Confidence 678999885 466688999999999653
No 28
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=42.12 E-value=7.2 Score=38.72 Aligned_cols=21 Identities=38% Similarity=0.740 Sum_probs=16.8
Q ss_pred CCCcccceecccCCeeeeeec
Q 002593 882 ESDPEYFFTVSKSGAAGVLVK 902 (903)
Q Consensus 882 ~~~~~~~~~~~~~~~~~~~~~ 902 (903)
--||||+-+|+..||+||||-
T Consensus 40 rvn~~fvl~Al~~GaDGV~v~ 60 (132)
T COG1908 40 RVNPEFVLKALRKGADGVLVA 60 (132)
T ss_pred ccCHHHHHHHHHcCCCeEEEe
Confidence 346777778888999999983
No 29
>PRK13912 nuclease NucT; Provisional
Probab=41.71 E-value=24 Score=36.16 Aligned_cols=94 Identities=14% Similarity=0.185 Sum_probs=52.9
Q ss_pred HHHhhcccchhhhhhhcC--CCCCCcEEEEEccCccccccCCCCCcCCCCCCCCCeEEEcC-CCCccccccccccCCCcc
Q 002593 449 MFIATFTSDILWFMSYCE--IPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFP-PFPESVAFGENCKKQGIA 525 (903)
Q Consensus 449 allfnF~~DidWLLs~f~--~~r~lpVtIVvh~~~~~wk~e~~~rl~~~~~~~pNv~li~P-pMPe~I~FG~d~~~~g~G 525 (903)
..+..|.+.-+.+.+.+- ..|++.|-|+.+..... ......+. ....++|+.+..- +.+ ...+ ...+
T Consensus 49 I~i~~Y~~~~~~i~~aL~~Aa~RGV~VrIlld~~~~~--~~~~~~~~-~l~~~~~~~~~~~~~~~--~~~~-----~~~~ 118 (177)
T PRK13912 49 IKIAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNH--NNDQSTIG-YLDKYPNIKVCLLKGLK--AKNG-----KYYG 118 (177)
T ss_pred EEEEEEEEchHHHHHHHHHHHHCCCEEEEEEeCcccc--CcchhHHH-HHHhCCCceEEEecCcc--ccCc-----cccc
Confidence 344567777777777663 24888888887743210 00000000 0124556655431 111 0001 1235
Q ss_pred cccceEEEEEeCCcEEEEEeCCCCCHHhhc
Q 002593 526 CHHPKLFVLQREDSIRVIVTSANLGAKQWN 555 (903)
Q Consensus 526 tHHSKMmIL~Y~D~LRVVI~TANLi~~DW~ 555 (903)
.+|.|+||+ |.-.+++.|+|+...-+.
T Consensus 119 ~~H~K~~vi---D~~~~~iGS~N~t~~s~~ 145 (177)
T PRK13912 119 IMHQKVAII---DDKIVVLGSANWSKNAFE 145 (177)
T ss_pred ccceeEEEE---cCCEEEEeCCCCChhHhc
Confidence 899999998 555699999999976544
No 30
>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=41.31 E-value=30 Score=29.28 Aligned_cols=25 Identities=32% Similarity=0.379 Sum_probs=20.0
Q ss_pred cceEECCEEccCCCeeeCCCCCEEEE
Q 002593 149 NGVFVNGIRLKSGIVRELNAGDEVLF 174 (903)
Q Consensus 149 NGTfVNG~RI~k~~~~~L~~GD~I~~ 174 (903)
+.++|||.++.+. ...|..||+|.|
T Consensus 34 G~V~VNg~~~~~~-~~~l~~Gd~v~i 58 (59)
T TIGR02988 34 NEVLVNGELENRR-GKKLYPGDVIEI 58 (59)
T ss_pred CCEEECCEEccCC-CCCCCCCCEEEe
Confidence 7799999998432 257999999986
No 31
>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=40.00 E-value=23 Score=28.34 Aligned_cols=25 Identities=28% Similarity=0.278 Sum_probs=19.9
Q ss_pred cccceEECCEEccCCCeeeCCCCCEE
Q 002593 147 SLNGVFVNGIRLKSGIVRELNAGDEV 172 (903)
Q Consensus 147 S~NGTfVNG~RI~k~~~~~L~~GD~I 172 (903)
-.++++|||+.+.... ..+..||+|
T Consensus 24 ~~g~V~VNg~~v~~~~-~~v~~~d~I 48 (48)
T PF01479_consen 24 KQGRVKVNGKVVKDPS-YIVKPGDVI 48 (48)
T ss_dssp HTTTEEETTEEESSTT-SBESTTEEE
T ss_pred CCCEEEECCEEEcCCC-CCCCCcCCC
Confidence 3488999999999442 578999987
No 32
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=39.50 E-value=8.4 Score=37.75 Aligned_cols=20 Identities=45% Similarity=0.798 Sum_probs=18.1
Q ss_pred CCCcccceecccCCeeeeee
Q 002593 882 ESDPEYFFTVSKSGAAGVLV 901 (903)
Q Consensus 882 ~~~~~~~~~~~~~~~~~~~~ 901 (903)
-=||+|+.+++..||+||+|
T Consensus 39 rv~~~~il~Af~~GADGV~V 58 (124)
T PF02662_consen 39 RVDPEFILRAFEKGADGVLV 58 (124)
T ss_pred ccCHHHHHHHHHcCCCEEEE
Confidence 35899999999999999998
No 33
>smart00363 S4 S4 RNA-binding domain.
Probab=38.50 E-value=42 Score=26.38 Aligned_cols=28 Identities=21% Similarity=0.226 Sum_probs=21.2
Q ss_pred cccceEECCEEccCCCeeeCCCCCEEEEE
Q 002593 147 SLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (903)
Q Consensus 147 S~NGTfVNG~RI~k~~~~~L~~GD~I~~~ 175 (903)
..++.+|||+++... ...|..||.|.+.
T Consensus 24 ~~g~i~vng~~~~~~-~~~l~~gd~i~~~ 51 (60)
T smart00363 24 EQGRVKVNGKKVTKP-SYIVKPGDVISVR 51 (60)
T ss_pred HcCCEEECCEEecCC-CeEeCCCCEEEEc
Confidence 356899999999332 3578999999883
No 34
>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=38.29 E-value=34 Score=30.81 Aligned_cols=28 Identities=32% Similarity=0.390 Sum_probs=21.2
Q ss_pred cceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 149 NGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 149 NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
--++|||+.+......+|++||+|.|..
T Consensus 56 ~~v~vN~~~v~~~~~~~l~dgdev~i~P 83 (88)
T TIGR01687 56 VIILVNGRNVDWGLGTELKDGDVVAIFP 83 (88)
T ss_pred EEEEECCEecCccCCCCCCCCCEEEEeC
Confidence 4467888888765334799999999954
No 35
>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=36.96 E-value=36 Score=29.75 Aligned_cols=27 Identities=30% Similarity=0.361 Sum_probs=21.5
Q ss_pred ccceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 148 LNGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 148 ~NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
.--++|||+.+... ..|++||+|.|..
T Consensus 49 ~~~v~vNg~~v~~~--~~l~~gD~v~i~p 75 (80)
T cd00754 49 RVRIAVNGEYVRLD--TPLKDGDEVAIIP 75 (80)
T ss_pred cEEEEECCeEcCCC--cccCCCCEEEEeC
Confidence 34578899998854 5799999999964
No 36
>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD
Probab=31.35 E-value=18 Score=42.66 Aligned_cols=52 Identities=21% Similarity=0.091 Sum_probs=39.4
Q ss_pred EEEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHH
Q 002593 190 FLILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLL 262 (903)
Q Consensus 190 f~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~ 262 (903)
.++++++|+ +..++.+ .+.|.|+ |||+ +++.-..||+++..|.|.-.+..+-
T Consensus 336 ~il~~i~l~---i~~G~~~----~ivG~sG----sGKS----------TL~~ll~g~~~~~~G~I~~~g~~i~ 387 (529)
T TIGR02857 336 PALRPVSFT---VPPGERV----ALVGPSG----AGKS----------TLLNLLLGFVDPTEGSIAVNGVPLA 387 (529)
T ss_pred ccccceeEE---ECCCCEE----EEECCCC----CCHH----------HHHHHHhcCCCCCCcEEEECCEehh
Confidence 356677776 4433332 4669999 9999 9999999999999999987776543
No 37
>PRK01777 hypothetical protein; Validated
Probab=30.66 E-value=48 Score=31.42 Aligned_cols=28 Identities=25% Similarity=0.160 Sum_probs=24.0
Q ss_pred ccccceEECCEEccCCCeeeCCCCCEEEEE
Q 002593 146 VSLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (903)
Q Consensus 146 ~S~NGTfVNG~RI~k~~~~~L~~GD~I~~~ 175 (903)
.+.+-+.|||+.+.-. ..|++||+|.|.
T Consensus 47 ~~~~~vgI~Gk~v~~d--~~L~dGDRVeIy 74 (95)
T PRK01777 47 LAKNKVGIYSRPAKLT--DVLRDGDRVEIY 74 (95)
T ss_pred cccceEEEeCeECCCC--CcCCCCCEEEEe
Confidence 3668899999999876 469999999994
No 38
>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=30.54 E-value=60 Score=26.23 Aligned_cols=28 Identities=21% Similarity=0.251 Sum_probs=21.6
Q ss_pred cccceEECCEEccCCCeeeCCCCCEEEEE
Q 002593 147 SLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (903)
Q Consensus 147 S~NGTfVNG~RI~k~~~~~L~~GD~I~~~ 175 (903)
..++.+|||+++... ...+..||.|.+.
T Consensus 24 ~~g~V~vn~~~~~~~-~~~v~~~d~i~i~ 51 (70)
T cd00165 24 KHGHVLVNGKVVTKP-SYKVKPGDVIEVD 51 (70)
T ss_pred HcCCEEECCEEccCC-ccCcCCCCEEEEc
Confidence 457899999999432 2468999999884
No 39
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=28.01 E-value=68 Score=31.00 Aligned_cols=29 Identities=31% Similarity=0.433 Sum_probs=23.7
Q ss_pred cceEECCEEccCCCeeeCCCCCEEEEEeCCC
Q 002593 149 NGVFVNGIRLKSGIVRELNAGDEVLFVCRDE 179 (903)
Q Consensus 149 NGTfVNG~RI~k~~~~~L~~GD~I~~~~g~~ 179 (903)
.-+.|||.+++.+ .++..||+|.|..++.
T Consensus 34 GrV~vNG~~aKpS--~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 34 GRVKVNGQRAKPS--KEVKVGDILTIRFGNK 62 (100)
T ss_pred CeEEECCEEcccc--cccCCCCEEEEEeCCc
Confidence 3477999999876 4699999999988763
No 40
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=26.40 E-value=65 Score=29.54 Aligned_cols=26 Identities=35% Similarity=0.415 Sum_probs=21.0
Q ss_pred cccceEECCEEc-cCCCeeeCCCCCEEEE
Q 002593 147 SLNGVFVNGIRL-KSGIVRELNAGDEVLF 174 (903)
Q Consensus 147 S~NGTfVNG~RI-~k~~~~~L~~GD~I~~ 174 (903)
+-+.++|||+.- +++ ..|++||+|.|
T Consensus 35 ~eg~V~vNGe~EtRRg--kKlr~gd~V~i 61 (73)
T COG2501 35 AEGEVKVNGEVETRRG--KKLRDGDVVEI 61 (73)
T ss_pred HCCeEEECCeeeeccC--CEeecCCEEEE
Confidence 557899999965 455 45999999999
No 41
>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=26.27 E-value=55 Score=36.93 Aligned_cols=26 Identities=27% Similarity=0.507 Sum_probs=22.9
Q ss_pred ccceEEEEEeCC-cEEEEEeCCCCCHH
Q 002593 527 HHPKLFVLQRED-SIRVIVTSANLGAK 552 (903)
Q Consensus 527 HHSKMmIL~Y~D-~LRVVI~TANLi~~ 552 (903)
-|+||.+...++ -.+++|.||||...
T Consensus 81 ~HgKlY~f~k~g~~~~a~IGSANfS~~ 107 (296)
T PF09565_consen 81 YHGKLYIFSKNGKPFRAYIGSANFSQI 107 (296)
T ss_pred cccEEEEEecCCCceEEEEeecccccc
Confidence 699999997764 69999999999985
No 42
>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane. The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.
Probab=25.89 E-value=35 Score=35.03 Aligned_cols=48 Identities=13% Similarity=-0.067 Sum_probs=35.1
Q ss_pred EEEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechh
Q 002593 190 FLILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRA 258 (903)
Q Consensus 190 f~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~ 258 (903)
.+++.++|+ +..+..+ .+.|.|+ |||+ +++....|+.++..|.|.-.+
T Consensus 15 ~~l~~~sl~---i~~G~~~----~i~G~nG----sGKS----------TLl~~l~G~~~~~~G~i~~~g 62 (214)
T cd03292 15 AALDGINIS---ISAGEFV----FLVGPSG----AGKS----------TLLKLIYKEELPTSGTIRVNG 62 (214)
T ss_pred eeeeeeEEE---EcCCCEE----EEECCCC----CCHH----------HHHHHHhcCCCCCceEEEECC
Confidence 356777776 3332322 4669999 9999 999999999998888776554
No 43
>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein.
Probab=25.80 E-value=22 Score=43.88 Aligned_cols=53 Identities=17% Similarity=0.140 Sum_probs=39.5
Q ss_pred EEEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHHH
Q 002593 190 FLILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLS 263 (903)
Q Consensus 190 f~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~~ 263 (903)
.++++++|+ +..++.+ .+.|.|+ |||+ +++.-..|++++..|.|.-.+..+-+
T Consensus 495 ~vL~~isl~---i~~Ge~v----aIvG~SG----sGKS----------TLl~lL~gl~~p~~G~I~idg~~i~~ 547 (711)
T TIGR00958 495 PVLKGLTFT---LHPGEVV----ALVGPSG----SGKS----------TVAALLQNLYQPTGGQVLLDGVPLVQ 547 (711)
T ss_pred ccccCceEE---EcCCCEE----EEECCCC----CCHH----------HHHHHHHhccCCCCCEEEECCEEHHh
Confidence 345666665 4433332 4669999 9999 99999999999999999888776543
No 44
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=25.10 E-value=60 Score=27.83 Aligned_cols=27 Identities=26% Similarity=0.279 Sum_probs=21.6
Q ss_pred cccceEECCEEccCCCeeeCCCCCEEEEE
Q 002593 147 SLNGVFVNGIRLKSGIVRELNAGDEVLFV 175 (903)
Q Consensus 147 S~NGTfVNG~RI~k~~~~~L~~GD~I~~~ 175 (903)
..-+..|||+++.-. .+|++||+|.|.
T Consensus 33 ~~~~A~Vng~~vdl~--~~L~~~d~v~ii 59 (60)
T PF02824_consen 33 RAVAAKVNGQLVDLD--HPLEDGDVVEII 59 (60)
T ss_dssp CEEEEEETTEEEETT--SBB-SSEEEEEE
T ss_pred heeEEEEcCEECCCC--CCcCCCCEEEEE
Confidence 446777999999886 579999999985
No 45
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=24.55 E-value=27 Score=42.84 Aligned_cols=51 Identities=16% Similarity=0.146 Sum_probs=38.6
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLL 262 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~ 262 (903)
++++++|+ +..+..+ .+.|.|+ |||+ +++.-..|+++|..|.|.-.+..+-
T Consensus 489 iL~~isl~---i~~G~~v----aIvG~SG----sGKS----------TLlklL~gl~~p~~G~I~idg~~i~ 539 (708)
T TIGR01193 489 ILSDISLT---IKMNSKT----TIVGMSG----SGKS----------TLAKLLVGFFQARSGEILLNGFSLK 539 (708)
T ss_pred ceeceeEE---ECCCCEE----EEECCCC----CCHH----------HHHHHHhccCCCCCcEEEECCEEHH
Confidence 45566665 4433332 4669999 9999 9999999999999999988886653
No 46
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=23.98 E-value=26 Score=38.61 Aligned_cols=52 Identities=15% Similarity=0.138 Sum_probs=38.7
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHHH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLS 263 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~~ 263 (903)
.+++|.|+ |.-+..+ .+.|.|+ |||+ +|-...-|+.++..|.|.-.++-+..
T Consensus 22 ~l~~VS~~---i~~Ge~l----givGeSG----sGKS----------TL~r~l~Gl~~p~~G~I~~~G~~~~~ 73 (252)
T COG1124 22 ALNNVSLE---IERGETL----GIVGESG----SGKS----------TLARLLAGLEKPSSGSILLDGKPLAP 73 (252)
T ss_pred hhcceeEE---ecCCCEE----EEEcCCC----CCHH----------HHHHHHhcccCCCCceEEECCcccCc
Confidence 56666665 3332332 3449999 9999 88888999999999999998876655
No 47
>PRK11507 ribosome-associated protein; Provisional
Probab=23.30 E-value=89 Score=28.43 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=20.3
Q ss_pred cccceEECCEEc-cCCCeeeCCCCCEEEE
Q 002593 147 SLNGVFVNGIRL-KSGIVRELNAGDEVLF 174 (903)
Q Consensus 147 S~NGTfVNG~RI-~k~~~~~L~~GD~I~~ 174 (903)
..+.+.|||+.- +++ +.|++||+|.|
T Consensus 35 ~eg~V~VNGeve~rRg--kKl~~GD~V~~ 61 (70)
T PRK11507 35 AEGQVKVDGAVETRKR--CKIVAGQTVSF 61 (70)
T ss_pred HcCceEECCEEecccC--CCCCCCCEEEE
Confidence 447799999944 455 45999999999
No 48
>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=23.25 E-value=54 Score=28.33 Aligned_cols=28 Identities=36% Similarity=0.440 Sum_probs=20.6
Q ss_pred cceEECCEEccC-CCeeeCCCCCEEEEEe
Q 002593 149 NGVFVNGIRLKS-GIVRELNAGDEVLFVC 176 (903)
Q Consensus 149 NGTfVNG~RI~k-~~~~~L~~GD~I~~~~ 176 (903)
--++|||+.+.+ +....|++||+|.|..
T Consensus 44 ~~v~vN~~~v~~~~~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 44 VAVAVNGEIVPDDGLDTPLKDGDEVAILP 72 (77)
T ss_dssp EEEEETTEEEGGGTTTSBEETTEEEEEEE
T ss_pred EEEEECCEEcCCccCCcCcCCCCEEEEEC
Confidence 446678887777 2235799999999965
No 49
>TIGR02673 FtsE cell division ATP-binding protein FtsE. This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.
Probab=22.64 E-value=49 Score=34.03 Aligned_cols=48 Identities=10% Similarity=0.000 Sum_probs=34.0
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRAS 259 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~ 259 (903)
+++.++|+ +..+.. +.+.|.++ |||+ +++....|..++..|-|.-.+.
T Consensus 17 il~~is~~---i~~G~~----~~l~G~nG----sGKS----------TLl~~i~Gl~~~~~G~i~~~g~ 64 (214)
T TIGR02673 17 ALHDVSLH---IRKGEF----LFLTGPSG----AGKT----------TLLKLLYGALTPSRGQVRIAGE 64 (214)
T ss_pred eecceeEE---EcCCCE----EEEECCCC----CCHH----------HHHHHHhCCCCCCCceEEECCE
Confidence 56666666 333222 24569999 9999 8999999999888887765543
No 50
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=22.43 E-value=94 Score=26.42 Aligned_cols=26 Identities=38% Similarity=0.394 Sum_probs=18.8
Q ss_pred eEECCEEccCC--CeeeCCCCCEEEEEe
Q 002593 151 VFVNGIRLKSG--IVRELNAGDEVLFVC 176 (903)
Q Consensus 151 TfVNG~RI~k~--~~~~L~~GD~I~~~~ 176 (903)
+.|||+.+.+. ....|++||+|.|+.
T Consensus 33 v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 33 VAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred EEECCEEcCchhcccccCCCCCEEEEEe
Confidence 45688777653 235799999999964
No 51
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=22.39 E-value=29 Score=41.48 Aligned_cols=50 Identities=20% Similarity=0.078 Sum_probs=37.4
Q ss_pred EEEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHH
Q 002593 190 FLILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFL 261 (903)
Q Consensus 190 f~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l 261 (903)
.++++++|+ +..++.+ .+.|.|+ |||+ ++..-..||+ |..|.|.-.+..+
T Consensus 364 ~vL~~i~l~---i~~G~~v----aIvG~SG----sGKS----------TL~~lL~g~~-p~~G~I~i~g~~i 413 (588)
T PRK11174 364 TLAGPLNFT---LPAGQRI----ALVGPSG----AGKT----------SLLNALLGFL-PYQGSLKINGIEL 413 (588)
T ss_pred eeeeeeEEE---EcCCCEE----EEECCCC----CCHH----------HHHHHHhcCC-CCCcEEEECCEec
Confidence 456777777 4433332 5679999 9999 9999999999 7778777766554
No 52
>PRK11176 lipid transporter ATP-binding/permease protein; Provisional
Probab=22.37 E-value=29 Score=41.40 Aligned_cols=50 Identities=24% Similarity=0.269 Sum_probs=38.1
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFL 261 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l 261 (903)
++++++++ +..++.+ .+.|.|+ |||+ ++..-..|+++|..|-|.-.+..+
T Consensus 358 il~~i~l~---i~~G~~~----aIvG~sG----sGKS----------TLl~ll~gl~~p~~G~I~i~g~~i 407 (582)
T PRK11176 358 ALRNINFK---IPAGKTV----ALVGRSG----SGKS----------TIANLLTRFYDIDEGEILLDGHDL 407 (582)
T ss_pred cccCceEE---eCCCCEE----EEECCCC----CCHH----------HHHHHHHhccCCCCceEEECCEEh
Confidence 45666666 4433332 4679999 9999 999999999999999998877654
No 53
>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=22.06 E-value=38 Score=40.63 Aligned_cols=51 Identities=22% Similarity=0.169 Sum_probs=39.3
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLL 262 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~ 262 (903)
++++++|+ +..+..+ .+.|.|+ +||. +++.-..|+++|..|.|.-.+..+-
T Consensus 356 il~~i~l~---i~~Ge~i----aIvG~SG----sGKS----------TLl~lL~gl~~p~~G~I~idg~~i~ 406 (592)
T PRK10790 356 VLQNINLS---VPSRGFV----ALVGHTG----SGKS----------TLASLLMGYYPLTEGEIRLDGRPLS 406 (592)
T ss_pred eeeceeEE---EcCCCEE----EEECCCC----CCHH----------HHHHHHhcccCCCCceEEECCEEhh
Confidence 56667666 4433332 4669999 9999 9999999999999999988876553
No 54
>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein.
Probab=21.73 E-value=49 Score=34.12 Aligned_cols=49 Identities=18% Similarity=0.071 Sum_probs=35.8
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASF 260 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~ 260 (903)
+++.++|+ +..+.. +.+.|.|+ |||+ +++.-..|..++..|.|.-++..
T Consensus 18 il~~isl~---i~~Ge~----~~i~G~nG----sGKS----------TLl~~l~Gl~~~~~G~i~~~g~~ 66 (216)
T TIGR00960 18 ALDNLNFH---ITKGEM----VFLVGHSG----AGKS----------TFLKLILGIEKPTRGKIRFNGQD 66 (216)
T ss_pred EEEeeEEE---EcCCCE----EEEECCCC----CCHH----------HHHHHHhCCCCCCceEEEECCEe
Confidence 56667666 332222 24669999 9999 99999999999988888766643
No 55
>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts.
Probab=21.68 E-value=38 Score=35.21 Aligned_cols=48 Identities=10% Similarity=0.090 Sum_probs=35.1
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRAS 259 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~ 259 (903)
+++.++|+ +..+.. +.+.|.++ +||+ +++.-..|+.++..|-|.-.+.
T Consensus 20 il~~vs~~---i~~G~~----~~I~G~nG----sGKS----------tLl~~l~G~~~~~~G~i~~~g~ 67 (220)
T TIGR02982 20 VLFDINLE---INPGEI----VILTGPSG----SGKT----------TLLTLIGGLRSVQEGSLKVLGQ 67 (220)
T ss_pred EEeeeEEE---EcCCCE----EEEECCCC----CCHH----------HHHHHHhCCCCCCCeEEEECCE
Confidence 56667766 333222 24669999 9999 8999999999998887876554
No 56
>PRK06437 hypothetical protein; Provisional
Probab=21.54 E-value=1.2e+02 Score=26.72 Aligned_cols=26 Identities=27% Similarity=0.364 Sum_probs=20.8
Q ss_pred cceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 149 NGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 149 NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
=.+.+||+.|... ..|++||+|.|+.
T Consensus 37 vaV~vNg~iv~~~--~~L~dgD~Veiv~ 62 (67)
T PRK06437 37 YVVIVNGSPVLED--HNVKKEDDVLILE 62 (67)
T ss_pred EEEEECCEECCCc--eEcCCCCEEEEEe
Confidence 3566899999854 6799999999953
No 57
>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=21.52 E-value=1e+02 Score=26.51 Aligned_cols=27 Identities=26% Similarity=0.346 Sum_probs=20.5
Q ss_pred ceEECCEEccCC--CeeeCCCCCEEEEEe
Q 002593 150 GVFVNGIRLKSG--IVRELNAGDEVLFVC 176 (903)
Q Consensus 150 GTfVNG~RI~k~--~~~~L~~GD~I~~~~ 176 (903)
.+.|||+-|.+. ....|++||+|.|..
T Consensus 32 ~V~vNg~~v~~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 32 AVALNGEIVPRSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred EEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 456799988775 225799999999954
No 58
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=21.41 E-value=76 Score=28.86 Aligned_cols=21 Identities=24% Similarity=0.166 Sum_probs=18.2
Q ss_pred ECCEEccCCCeeeCCCCCEEEEE
Q 002593 153 VNGIRLKSGIVRELNAGDEVLFV 175 (903)
Q Consensus 153 VNG~RI~k~~~~~L~~GD~I~~~ 175 (903)
++|+||+.. .+|++||+|.|.
T Consensus 54 ~~gq~Vgl~--~~L~d~DvVeI~ 74 (75)
T cd01666 54 HSPQRVGLD--HVLEDEDVVQIV 74 (75)
T ss_pred CCCeECCCC--CEecCCCEEEEe
Confidence 489999987 679999999984
No 59
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=21.14 E-value=49 Score=37.03 Aligned_cols=47 Identities=26% Similarity=0.181 Sum_probs=38.1
Q ss_pred ccceeeeccCcccccHHHHHHHHHhhcCccccccCCcCCCcccceec
Q 002593 845 ESDFSYGSSSIGSINAQFLAAFAAASGKKSLRFYDSEESDPEYFFTV 891 (903)
Q Consensus 845 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 891 (903)
+.|.+.=--+-=|-|++=|+.-+...|+++..--+-+|=||+||-..
T Consensus 208 ~vD~miVVGg~nSsNT~rL~ei~~~~~~~t~~Ie~~~el~~~~l~~~ 254 (280)
T TIGR00216 208 EVDLMIVIGGKNSSNTTRLYEIAEEHGPPSYLIETAEELPEEWLKGV 254 (280)
T ss_pred hCCEEEEECCCCCchHHHHHHHHHHhCCCEEEECChHHCCHHHhCCC
Confidence 47877643222299999999999999999999888899999998544
No 60
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=21.13 E-value=50 Score=36.99 Aligned_cols=48 Identities=19% Similarity=0.129 Sum_probs=40.2
Q ss_pred cccceeeeccCcccccHHHHHHHHHhhcCccccccCCcCCCcccceec
Q 002593 844 QESDFSYGSSSIGSINAQFLAAFAAASGKKSLRFYDSEESDPEYFFTV 891 (903)
Q Consensus 844 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 891 (903)
.+.|.+.=-.+--|-|++=|+.-+...|+++..--+-+|=||+||-..
T Consensus 208 ~~vD~miVVGg~~SsNT~rL~eia~~~~~~t~~Ie~~~el~~~~~~~~ 255 (281)
T PRK12360 208 KEVDVMIVIGGKHSSNTQKLVKICEKNCPNTFHIETADELDLEMLKDY 255 (281)
T ss_pred HhCCEEEEecCCCCccHHHHHHHHHHHCCCEEEECChHHCCHHHhCCC
Confidence 378887754444499999999999999999999899999999998554
No 61
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=20.89 E-value=1.1e+02 Score=27.33 Aligned_cols=24 Identities=42% Similarity=0.473 Sum_probs=19.0
Q ss_pred eEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 151 VFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 151 TfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
++|||+.+... ..|++||+|.|..
T Consensus 52 v~vn~~~v~~~--~~l~dgDevai~P 75 (80)
T TIGR01682 52 VAVNEEYVTDD--ALLNEGDEVAFIP 75 (80)
T ss_pred EEECCEEcCCC--cCcCCCCEEEEeC
Confidence 56788877754 5799999999964
No 62
>TIGR03873 F420-0_ABC_ATP proposed F420-0 ABC transporter, ATP-binding protein. This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.
Probab=20.86 E-value=54 Score=34.95 Aligned_cols=33 Identities=9% Similarity=-0.101 Sum_probs=27.3
Q ss_pred eccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhH
Q 002593 213 ASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRAS 259 (903)
Q Consensus 213 ~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~ 259 (903)
.+.|.++ +||+ +++.-..|..++..|.|.-.+.
T Consensus 31 ~i~G~nG----sGKS----------TLl~~i~G~~~~~~G~i~~~g~ 63 (256)
T TIGR03873 31 GLLGPNG----SGKS----------TLLRLLAGALRPDAGTVDLAGV 63 (256)
T ss_pred EEECCCC----CCHH----------HHHHHHcCCCCCCCCEEEECCE
Confidence 3559999 9999 9999999999998887775554
No 63
>PF09014 Sushi_2: Beta-2-glycoprotein-1 fifth domain; InterPro: IPR015104 The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies []. ; PDB: 1C1Z_A 3OP8_B 2KRI_A 1QUB_A 1G4G_A 1G4F_A.
Probab=20.39 E-value=1.6e+02 Score=27.75 Aligned_cols=39 Identities=23% Similarity=0.428 Sum_probs=25.9
Q ss_pred eEECCEEccC--CCeeeCCCCCEEEEEeCC-CccccccceEEEEEEEE
Q 002593 151 VFVNGIRLKS--GIVRELNAGDEVLFVCRD-ESLCRLQTRIGFLILGI 195 (903)
Q Consensus 151 TfVNG~RI~k--~~~~~L~~GD~I~~~~g~-~~~~~~~~~igf~v~~i 195 (903)
++.||+|+.- -..-.+.+||.|+|.|.+ +..| ||.+...
T Consensus 13 Vly~g~k~~i~d~~~~~v~Hge~VsffCknkekkC------sy~~~~q 54 (85)
T PF09014_consen 13 VLYNGEKVWIQDLFKNGVLHGEIVSFFCKNKEKKC------SYTVDAQ 54 (85)
T ss_dssp EEETTEEEEHHHHTTT-BETT-EEEEEEEETTTTE------EEEEEEE
T ss_pred EEECCEEechhhcccCceeeCCEEEEEEcCCcccC------CCccccE
Confidence 3457776621 111237899999999988 6677 8888877
No 64
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=20.25 E-value=1.1e+02 Score=28.32 Aligned_cols=26 Identities=27% Similarity=0.310 Sum_probs=21.6
Q ss_pred cceEECCEEccCCCeeeCCCCCEEEEEe
Q 002593 149 NGVFVNGIRLKSGIVRELNAGDEVLFVC 176 (903)
Q Consensus 149 NGTfVNG~RI~k~~~~~L~~GD~I~~~~ 176 (903)
.-.+|||+.+.-. ..+++||+|.+..
T Consensus 50 ~~i~vNG~~v~~~--~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 50 GLILVNGRPVDFD--YRLKDGDRVAVYP 75 (81)
T ss_pred EEEEECCEECCCc--ccCCCCCEEEEEe
Confidence 4578999999886 5799999999853
No 65
>PRK10908 cell division protein FtsE; Provisional
Probab=20.18 E-value=47 Score=34.47 Aligned_cols=49 Identities=14% Similarity=0.142 Sum_probs=35.1
Q ss_pred EEEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhH
Q 002593 190 FLILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRAS 259 (903)
Q Consensus 190 f~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~ 259 (903)
.+++.++|+ +..+..+ .+.|.++ +||+ +++.-..|..++..|-|.-.+.
T Consensus 16 ~~l~~vsl~---i~~Ge~~----~i~G~nG----sGKS----------TLl~~l~G~~~~~~G~i~~~g~ 64 (222)
T PRK10908 16 QALQGVTFH---MRPGEMA----FLTGHSG----AGKS----------TLLKLICGIERPSAGKIWFSGH 64 (222)
T ss_pred eEEeeeeEE---EcCCCEE----EEECCCC----CCHH----------HHHHHHhCCCCCCceEEEECCE
Confidence 356667666 3332322 4569999 9999 9999999999988887765554
No 66
>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=20.11 E-value=38 Score=40.71 Aligned_cols=51 Identities=10% Similarity=0.128 Sum_probs=38.5
Q ss_pred EEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHH
Q 002593 191 LILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLL 262 (903)
Q Consensus 191 ~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~ 262 (903)
++++++|+ +..+..+ .+.|.|+ |||+ ++..-..||+++..|.|.-.+..+-
T Consensus 355 il~~i~~~---i~~G~~~----aivG~sG----sGKS----------TL~~ll~g~~~p~~G~I~i~g~~i~ 405 (574)
T PRK11160 355 VLKGLSLQ---IKAGEKV----ALLGRTG----CGKS----------TLLQLLTRAWDPQQGEILLNGQPIA 405 (574)
T ss_pred ceecceEE---ECCCCEE----EEECCCC----CCHH----------HHHHHHhcCCCCCCceEEECCEEhh
Confidence 46666666 4433332 4669999 9999 9999999999999999988876543
No 67
>PF11673 DUF3269: Protein of unknown function (DUF3269); InterPro: IPR021687 This entry is represented by Bacteriophage 92, Orf70. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.08 E-value=69 Score=29.36 Aligned_cols=36 Identities=22% Similarity=0.227 Sum_probs=30.3
Q ss_pred eccCCChhhhhhhhchhhHHHHHHHHHHhHhhhchhhHHHHhh
Q 002593 794 VSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLG 836 (903)
Q Consensus 794 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 836 (903)
=..|..|+.+.+-|+.+.+ ..++|.|+|.|=||+=.
T Consensus 31 ~l~g~hfs~~~~~~T~~El-------~~fK~~~~L~~~eELg~ 66 (73)
T PF11673_consen 31 NLTGAHFSHINKNMTDDEL-------KKFKAKHNLLYEEELGQ 66 (73)
T ss_pred ccccchhhcccCcccHHHH-------HHHHHHHhhhhHHHhcc
Confidence 3469999999999999875 67899999999998633
No 68
>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif
Probab=20.02 E-value=34 Score=41.86 Aligned_cols=52 Identities=15% Similarity=0.119 Sum_probs=40.1
Q ss_pred EEEEEEEEEEeeeeCCceeeceeeccccCCCcccCCCccceeeeeecCCccCCCCCCCcccccceechhHHHH
Q 002593 190 FLILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLL 262 (903)
Q Consensus 190 f~v~~i~~~~~~v~g~k~l~~~~~f~g~s~g~~~~g~~~krvfa~~~~~~~~~~~~f~~~~~~~~~~~~~~l~ 262 (903)
.++++|+|+ +..++.+ .+.|.|+ |||+ ++..--.||+.|..|.|.-.+..+-
T Consensus 467 ~vL~~isl~---i~~Ge~v----aIvG~sG----sGKS----------TLlklL~gl~~p~~G~I~idg~~i~ 518 (686)
T TIGR03797 467 LILDDVSLQ---IEPGEFV----AIVGPSG----SGKS----------TLLRLLLGFETPESGSVFYDGQDLA 518 (686)
T ss_pred cceeeeEEE---ECCCCEE----EEECCCC----CCHH----------HHHHHHhCCCCCCCCEEEECCEEcC
Confidence 456777776 4443432 5679999 9999 9999999999999999988876553
Done!