Query 039731
Match_columns 315
No_of_seqs 380 out of 2397
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 12:41:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039731.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039731hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03210 Resistant to P. syrin 100.0 8.1E-57 1.8E-61 487.4 19.3 277 1-291 1-316 (1153)
2 PLN03194 putative disease resi 100.0 2.8E-41 6.1E-46 291.8 13.6 129 11-156 24-154 (187)
3 PF01582 TIR: TIR domain; Int 99.9 6.5E-26 1.4E-30 190.4 3.1 133 16-148 1-141 (141)
4 smart00255 TIR Toll - interleu 99.9 7.4E-23 1.6E-27 170.4 12.9 137 13-151 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.7 4.4E-17 9.6E-22 128.8 4.1 91 16-114 1-91 (102)
6 KOG4658 Apoptotic ATPase [Sign 99.0 4.4E-10 9.5E-15 119.4 4.8 108 171-289 161-279 (889)
7 PF00931 NB-ARC: NB-ARC domain 98.8 3.2E-09 6.9E-14 98.3 5.5 93 189-290 17-120 (287)
8 KOG3678 SARM protein (with ste 98.7 2.2E-08 4.7E-13 97.4 7.6 91 10-106 609-708 (832)
9 PF08937 DUF1863: MTH538 TIR-l 98.3 8.4E-07 1.8E-11 73.5 5.9 89 14-107 1-107 (130)
10 PF08357 SEFIR: SEFIR domain; 97.6 0.00038 8.3E-09 58.6 8.4 64 15-78 2-70 (150)
11 PF10137 TIR-like: Predicted n 95.6 0.04 8.6E-07 45.5 6.4 60 15-77 1-61 (125)
12 cd01128 rho_factor Transcripti 95.0 0.016 3.5E-07 53.3 2.7 83 202-284 20-116 (249)
13 PF13401 AAA_22: AAA domain; P 94.9 0.026 5.7E-07 45.5 3.3 79 203-283 9-99 (131)
14 PRK09376 rho transcription ter 94.8 0.032 6.9E-07 54.7 4.1 85 201-285 172-270 (416)
15 TIGR00767 rho transcription te 94.6 0.061 1.3E-06 52.9 5.6 85 199-283 169-267 (415)
16 TIGR02928 orc1/cdc6 family rep 93.3 0.088 1.9E-06 50.4 4.0 49 235-283 87-141 (365)
17 PRK00411 cdc6 cell division co 93.3 0.087 1.9E-06 51.1 3.9 79 205-284 62-151 (394)
18 TIGR03015 pepcterm_ATPase puta 93.1 0.3 6.5E-06 44.5 6.9 80 203-284 48-136 (269)
19 COG2256 MGS1 ATPase related to 91.6 0.27 6E-06 48.1 4.8 87 203-314 53-144 (436)
20 PF13271 DUF4062: Domain of un 91.1 0.77 1.7E-05 34.7 6.0 66 15-81 1-67 (83)
21 COG1474 CDC6 Cdc6-related prot 91.0 0.35 7.7E-06 47.0 5.1 79 205-284 49-136 (366)
22 COG4916 Uncharacterized protei 89.1 0.47 1E-05 43.7 3.8 100 10-114 174-281 (329)
23 PF05729 NACHT: NACHT domain 85.9 0.85 1.8E-05 37.7 3.4 17 269-285 79-95 (166)
24 PTZ00112 origin recognition co 81.6 1.4 3E-05 47.7 3.5 50 235-284 829-882 (1164)
25 PF05014 Nuc_deoxyrib_tr: Nucl 81.2 7.4 0.00016 30.8 7.0 67 27-94 13-88 (113)
26 PF13191 AAA_16: AAA ATPase do 81.0 1.1 2.3E-05 38.0 2.1 19 266-284 144-163 (185)
27 COG4271 Predicted nucleotide-b 75.9 7.6 0.00017 34.6 5.8 65 10-79 80-146 (233)
28 cd00860 ThrRS_anticodon ThrRS 69.8 19 0.0004 26.6 6.2 61 13-77 1-61 (91)
29 KOG2543 Origin recognition com 69.6 3.8 8.1E-05 40.2 2.7 79 205-288 37-132 (438)
30 cd00009 AAA The AAA+ (ATPases 67.9 7.3 0.00016 30.6 3.8 16 268-283 81-96 (151)
31 cd01133 F1-ATPase_beta F1 ATP 65.7 6.5 0.00014 36.8 3.4 81 202-283 73-175 (274)
32 smart00382 AAA ATPases associa 61.6 13 0.00028 28.7 4.1 28 261-288 67-95 (148)
33 PF14258 DUF4350: Domain of un 59.5 57 0.0012 23.2 6.9 61 31-103 8-68 (70)
34 cd00738 HGTP_anticodon HGTP an 58.8 35 0.00077 25.2 5.9 59 14-76 2-63 (94)
35 PF03129 HGTP_anticodon: Antic 58.2 29 0.00062 26.1 5.3 47 27-76 15-61 (94)
36 cd02042 ParA ParA and ParB of 55.3 90 0.0019 23.6 8.2 74 16-93 3-84 (104)
37 PF12780 AAA_8: P-loop contain 52.5 19 0.00041 33.5 4.1 61 203-281 36-99 (268)
38 cd00858 GlyRS_anticodon GlyRS 50.8 46 0.001 26.6 5.7 60 13-77 26-87 (121)
39 KOG2227 Pre-initiation complex 48.7 23 0.00051 35.7 4.2 76 205-284 182-269 (529)
40 PF04665 Pox_A32: Poxvirus A32 48.7 13 0.00029 34.1 2.3 11 272-282 99-109 (241)
41 PF00004 AAA: ATPase family as 47.4 12 0.00027 29.3 1.8 17 271-287 58-74 (132)
42 PTZ00202 tuzin; Provisional 47.0 1.5E+02 0.0032 30.3 9.4 96 169-277 263-367 (550)
43 PRK13342 recombination factor 44.3 26 0.00057 34.4 3.9 15 269-283 90-104 (413)
44 PRK04841 transcriptional regul 43.9 63 0.0014 34.6 7.0 80 204-284 38-134 (903)
45 PRK08116 hypothetical protein; 42.2 37 0.0008 31.4 4.3 17 264-281 172-188 (268)
46 PRK04195 replication factor C 40.0 36 0.00077 34.3 4.1 14 271-284 98-111 (482)
47 cd02426 Pol_gamma_b_Cterm C-te 39.1 22 0.00047 29.2 2.0 31 27-57 43-77 (128)
48 PF07728 AAA_5: AAA domain (dy 38.0 9 0.0002 31.0 -0.4 14 271-284 65-78 (139)
49 PRK12289 GTPase RsgA; Reviewed 37.9 89 0.0019 30.3 6.3 46 63-114 86-132 (352)
50 cd01136 ATPase_flagellum-secre 37.9 64 0.0014 31.0 5.3 22 264-285 150-173 (326)
51 PRK05922 type III secretion sy 35.5 37 0.00081 33.9 3.4 21 264-284 238-260 (434)
52 PRK13341 recombination factor 34.8 25 0.00055 37.5 2.2 14 270-283 108-121 (725)
53 PRK08149 ATP synthase SpaL; Va 34.8 39 0.00085 33.7 3.4 85 200-285 153-255 (428)
54 PRK02551 flavoprotein NrdI; Pr 34.3 2.2E+02 0.0048 24.2 7.5 119 15-149 6-149 (154)
55 PRK07261 topology modulation p 33.9 51 0.0011 28.1 3.6 20 202-221 4-24 (171)
56 PF01637 Arch_ATPase: Archaeal 33.7 40 0.00086 29.1 3.0 14 271-284 118-131 (234)
57 PF09441 Abp2: ARS binding pro 33.6 14 0.00031 31.7 0.0 62 81-151 54-115 (175)
58 PRK08972 fliI flagellum-specif 33.2 37 0.0008 34.0 2.9 20 264-283 243-264 (444)
59 KOG1969 DNA replication checkp 31.6 1.2E+02 0.0027 32.5 6.4 72 191-284 326-400 (877)
60 PLN00020 ribulose bisphosphate 30.6 96 0.0021 30.7 5.2 14 269-282 210-223 (413)
61 TIGR00635 ruvB Holliday juncti 30.1 58 0.0013 30.1 3.6 28 262-289 99-126 (305)
62 PRK06002 fliI flagellum-specif 29.7 53 0.0012 33.0 3.4 21 264-284 245-267 (450)
63 TIGR00362 DnaA chromosomal rep 29.7 49 0.0011 32.3 3.1 24 70-93 32-55 (405)
64 PF03720 UDPG_MGDP_dh_C: UDP-g 29.1 69 0.0015 25.0 3.3 56 22-77 11-77 (106)
65 PF00308 Bac_DnaA: Bacterial d 28.9 41 0.00089 30.0 2.2 15 205-219 41-60 (219)
66 PRK00149 dnaA chromosomal repl 28.7 53 0.0011 32.7 3.2 24 69-92 37-60 (450)
67 PF10087 DUF2325: Uncharacteri 28.2 2.6E+02 0.0057 21.2 6.5 57 28-85 10-67 (97)
68 PF02310 B12-binding: B12 bind 28.2 2.4E+02 0.0052 21.8 6.4 69 30-106 17-86 (121)
69 cd07363 45_DOPA_Dioxygenase Th 28.1 2.7E+02 0.0058 25.4 7.5 69 27-97 80-150 (253)
70 PF14359 DUF4406: Domain of un 27.6 2.8E+02 0.006 21.3 6.4 60 32-93 20-84 (92)
71 COG0125 Tmk Thymidylate kinase 27.0 3.3E+02 0.0072 24.2 7.7 98 16-114 4-141 (208)
72 KOG0735 AAA+-type ATPase [Post 27.0 95 0.0021 33.3 4.6 22 264-285 487-508 (952)
73 TIGR00418 thrS threonyl-tRNA s 26.8 1.4E+02 0.003 30.5 6.0 61 12-76 469-529 (563)
74 KOG0991 Replication factor C, 26.4 56 0.0012 30.4 2.6 9 205-213 55-63 (333)
75 PF05621 TniB: Bacterial TniB 26.4 1.1E+02 0.0024 29.1 4.7 79 203-283 66-157 (302)
76 PF12775 AAA_7: P-loop contain 26.0 17 0.00036 33.8 -0.8 16 269-284 98-113 (272)
77 COG1658 Small primase-like pro 24.8 1.1E+02 0.0023 25.4 3.8 54 14-68 30-83 (127)
78 cd00861 ProRS_anticodon_short 24.6 2E+02 0.0043 21.1 5.1 48 27-77 17-64 (94)
79 PRK14088 dnaA chromosomal repl 24.2 75 0.0016 31.7 3.3 24 70-93 34-57 (440)
80 TIGR01287 nifH nitrogenase iro 23.8 36 0.00079 31.1 1.0 10 204-213 6-15 (275)
81 PRK12608 transcription termina 23.7 1.8E+02 0.0039 28.6 5.7 81 202-283 137-232 (380)
82 PF05673 DUF815: Protein of un 23.4 59 0.0013 30.0 2.2 39 257-297 94-138 (249)
83 KOG1954 Endocytosis/signaling 23.4 2E+02 0.0043 28.6 5.8 79 49-130 164-242 (532)
84 PRK14087 dnaA chromosomal repl 23.3 85 0.0018 31.4 3.5 20 263-283 199-218 (450)
85 PRK13236 nitrogenase reductase 23.3 46 0.001 31.1 1.6 9 205-213 13-21 (296)
86 PRK07196 fliI flagellum-specif 23.2 89 0.0019 31.3 3.6 18 269-286 243-260 (434)
87 PRK05688 fliI flagellum-specif 23.1 77 0.0017 31.9 3.1 20 264-283 249-270 (451)
88 PF11074 DUF2779: Domain of un 23.0 59 0.0013 26.9 1.9 35 55-91 59-93 (130)
89 cd00859 HisRS_anticodon HisRS 22.6 2.7E+02 0.0059 19.7 5.5 59 14-76 2-60 (91)
90 PRK13230 nitrogenase reductase 22.3 31 0.00068 31.7 0.2 11 203-213 6-16 (279)
91 COG0710 AroD 3-dehydroquinate 22.1 3.3E+02 0.0071 24.9 6.8 69 27-99 78-146 (231)
92 TIGR02546 III_secr_ATP type II 22.1 1.3E+02 0.0028 30.0 4.4 20 264-283 226-247 (422)
93 cd01424 MGS_CPS_II Methylglyox 22.0 2E+02 0.0043 22.3 4.8 61 15-77 2-76 (110)
94 PF13207 AAA_17: AAA domain; P 21.9 44 0.00095 26.0 1.0 22 203-224 4-26 (121)
95 PRK09361 radB DNA repair and r 21.6 1.1E+02 0.0024 26.8 3.7 21 263-283 99-119 (225)
96 PLN03025 replication factor C 21.6 87 0.0019 29.5 3.1 14 271-284 99-112 (319)
97 CHL00201 syh histidine-tRNA sy 21.2 2.1E+02 0.0046 28.3 5.8 62 11-76 323-384 (430)
98 TIGR03496 FliI_clade1 flagella 21.0 1.3E+02 0.0029 29.8 4.3 20 264-283 218-239 (411)
99 PF01990 ATP-synt_F: ATP synth 21.0 3.6E+02 0.0078 20.4 6.0 47 33-81 9-55 (95)
100 TIGR01242 26Sp45 26S proteasom 20.5 55 0.0012 31.5 1.5 13 271-283 215-227 (364)
101 PRK00080 ruvB Holliday junctio 20.4 1.3E+02 0.0028 28.4 4.0 27 262-288 120-146 (328)
102 cd07373 2A5CPDO_A The alpha su 20.2 6.5E+02 0.014 23.1 8.6 76 27-105 90-172 (271)
103 PRK06793 fliI flagellum-specif 20.1 1.4E+02 0.0031 29.8 4.4 23 264-286 237-261 (432)
No 1
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=8.1e-57 Score=487.38 Aligned_cols=277 Identities=29% Similarity=0.390 Sum_probs=235.0
Q ss_pred CCCCCCCCCCCCceeEEEccccccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeeccccC
Q 039731 1 MASSSFGLTSQSKYDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNYAS 80 (315)
Q Consensus 1 m~~~s~s~~~~~~ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 80 (315)
||||||| ++.++|||||||||+|+|++|++||+++|.++||++|.|+++++|+.|.+++.+||++|+++|||||++|++
T Consensus 1 ~~~~~~~-~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~ 79 (1153)
T PLN03210 1 MASSSSS-SRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYAS 79 (1153)
T ss_pred CCCCCCC-CCCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCccc
Confidence 6776654 468999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHhHHHHHHHHHHhhhCCCeeeeEEEecCCcccccccCchhHHHHHHHHhhcCChHHHHHHHHHHHHHhcccCCCCccC
Q 039731 81 SKWCLDELVKILECHKMNSQMVVPVFYRIDPSDVRKQSGRFKDAFVKHEEQFKDMPEKIQIWRAFSVQYRCFEKGPKVHS 160 (315)
Q Consensus 81 S~wcl~El~~i~~~~~~~~~~ViPIfy~v~ps~V~~q~g~f~~~f~~~~~~~~~~~e~v~~W~~aL~~v~~i~g~~~~~~ 160 (315)
|.||++||++|++|+++.+++|+||||+|+|+|||+|+|.||++|.+++++. +.+++++||+||++||+++|+.....
T Consensus 80 s~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~~~ 157 (1153)
T PLN03210 80 SSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQNW 157 (1153)
T ss_pred chHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecCCC
Confidence 9999999999999999999999999999999999999999999999998764 47899999999999999999753322
Q ss_pred C-------------------CccccccccCCCCCCceeeeeCCCCCcccceeeeeeeccccccccCCCcc-----chhcc
Q 039731 161 C-------------------GVCPVYAHPNGTKPNTFTVNVLPPNEEECTQIRKLHYDFHDNVGTSGNSE-----SIDRS 216 (315)
Q Consensus 161 ~-------------------~~~~V~~~~Vg~~~r~~~v~~Ll~~~~~~~~l~~i~~d~~~~~GmGGiGK-----~vy~~ 216 (315)
. .+....+.+||++.++.++..++....+.++++||+ ||||+|| ++|++
T Consensus 158 ~~E~~~i~~Iv~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~-------G~gGiGKTTLA~~l~~~ 230 (1153)
T PLN03210 158 PNEAKMIEEIANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIW-------GSSGIGKTTIARALFSR 230 (1153)
T ss_pred CCHHHHHHHHHHHHHHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEE-------cCCCCchHHHHHHHHHH
Confidence 2 233445678999888888887777777778888887 9999999 46788
Q ss_pred cccccccee-ec---cccC----------CccCHHHHHHHHHHHhcC-CCCCcCChhHHHHHHHHhhCCcEEEEEeeCCC
Q 039731 217 GELEVESIC-RE---QINA----------PQQQRSSLFSHIIAKGGG-LYAFLAPSDHASIQIQRRHIRLKVSLLASKVD 281 (315)
Q Consensus 217 i~~~Fe~~~-~~---~s~~----------~~~gl~~Lq~~LL~~il~-~~~~~~~~~~~~~~i~~rL~~kKvLIVLDDVd 281 (315)
+..+|++.| .. +... .......+|+++++++++ ....+... ..++++|++||+||||||||
T Consensus 231 l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~----~~~~~~L~~krvLLVLDdv~ 306 (1153)
T PLN03210 231 LSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHL----GAMEERLKHRKVLIFIDDLD 306 (1153)
T ss_pred HhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCH----HHHHHHHhCCeEEEEEeCCC
Confidence 889999887 21 1110 001245789999999886 34443332 46899999999999999999
Q ss_pred CCCCcccccC
Q 039731 282 SASSPELSTS 291 (315)
Q Consensus 282 ~~~qle~~~~ 291 (315)
+.+|++++..
T Consensus 307 ~~~~l~~L~~ 316 (1153)
T PLN03210 307 DQDVLDALAG 316 (1153)
T ss_pred CHHHHHHHHh
Confidence 9999998864
No 2
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=2.8e-41 Score=291.82 Aligned_cols=129 Identities=29% Similarity=0.493 Sum_probs=120.6
Q ss_pred CCceeEEEccccccCccchHHHHHHHHhhCCCeEEeeC-ccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHH
Q 039731 11 QSKYDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDE-ELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELV 89 (315)
Q Consensus 11 ~~~ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~ 89 (315)
..+|||||||+|+|+|++|++||+.+|+++||+||+|+ ++.+|+.|.++|.+||++|+++|+||||+|++|.||++||+
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~ 103 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELA 103 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHH
Confidence 56899999999999999999999999999999999999 99999999999999999999999999999999999999999
Q ss_pred HHHHHhhhCCCeeeeEEEecCCcccccc-cCchhHHHHHHHHhhcCChHHHHHHHHHHHHHhcccCCC
Q 039731 90 KILECHKMNSQMVVPVFYRIDPSDVRKQ-SGRFKDAFVKHEEQFKDMPEKIQIWRAFSVQYRCFEKGP 156 (315)
Q Consensus 90 ~i~~~~~~~~~~ViPIfy~v~ps~V~~q-~g~f~~~f~~~~~~~~~~~e~v~~W~~aL~~v~~i~g~~ 156 (315)
+|+++. ..||||||+|+|++||+| .|. .+.+++++||.||++|++++|+.
T Consensus 104 ~I~e~~----~~ViPIFY~VdPsdVr~q~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~ 154 (187)
T PLN03194 104 LIMESK----KRVIPIFCDVKPSQLRVVDNGT-------------CPDEEIRRFNWALEEAKYTVGLT 154 (187)
T ss_pred HHHHcC----CEEEEEEecCCHHHhhccccCC-------------CCHHHHHHHHHHHHHHhcccccc
Confidence 999874 489999999999999997 332 23689999999999999999974
No 3
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=99.91 E-value=6.5e-26 Score=190.41 Aligned_cols=133 Identities=38% Similarity=0.624 Sum_probs=117.1
Q ss_pred EEEccccccCccchHHHHHHHHhhC--CCeEEeeC-ccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHH
Q 039731 16 VFLSFRGEDTRDNFTSHLHAALCRK--KIKTFIDE-ELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKIL 92 (315)
Q Consensus 16 VFIS~~~~D~r~~fv~~L~~~L~~~--gi~~f~D~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~ 92 (315)
|||||++.+.+.+|+++|.++|+++ |+++|+++ |+.+|..+.++|.++|++|+++|+|||++|++|+||+.||..|+
T Consensus 1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~ 80 (141)
T PF01582_consen 1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL 80 (141)
T ss_dssp EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence 8999999434588999999999999 99999999 99999999999999999999999999999999999999999999
Q ss_pred HHhhhCC--CeeeeEEEecCCcccc-cccCchhHHHHHHHHhhcCC--hHHHHHHHHHHHH
Q 039731 93 ECHKMNS--QMVVPVFYRIDPSDVR-KQSGRFKDAFVKHEEQFKDM--PEKIQIWRAFSVQ 148 (315)
Q Consensus 93 ~~~~~~~--~~ViPIfy~v~ps~V~-~q~g~f~~~f~~~~~~~~~~--~e~v~~W~~aL~~ 148 (315)
++....+ .+|+||||++.+++++ .+++.|+..|..+......+ ..+...|++++.+
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~~ 141 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRYH 141 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhcC
Confidence 9986644 8999999999999999 79999999998887766543 5788999998753
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.89 E-value=7.4e-23 Score=170.38 Aligned_cols=137 Identities=39% Similarity=0.686 Sum_probs=115.4
Q ss_pred ceeEEEcccc-ccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHH
Q 039731 13 KYDVFLSFRG-EDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKI 91 (315)
Q Consensus 13 ~ydVFIS~~~-~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i 91 (315)
+|||||||++ ++....|+.+|...|...|+.+|.|+....|.... +|.++|++|+++|+|+||+|+.|.||..|+..+
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~~-~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a 79 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDLE-EIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA 79 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccchHH-HHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence 5999999999 45557899999999999999999998433333333 999999999999999999999999999999999
Q ss_pred HHHhhh-CCCeeeeEEEecCCcccccccCchhHHHHHHHHhhcCChHHHHHHHHHHHHHhc
Q 039731 92 LECHKM-NSQMVVPVFYRIDPSDVRKQSGRFKDAFVKHEEQFKDMPEKIQIWRAFSVQYRC 151 (315)
Q Consensus 92 ~~~~~~-~~~~ViPIfy~v~ps~V~~q~g~f~~~f~~~~~~~~~~~e~v~~W~~aL~~v~~ 151 (315)
+++... ...+||||+|+..|.++..+.+.++.++.........+..+ +.|+.++..+.+
T Consensus 80 ~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 80 LENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 987754 66899999999889999999999999998875555443333 789999988753
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.66 E-value=4.4e-17 Score=128.84 Aligned_cols=91 Identities=32% Similarity=0.614 Sum_probs=77.5
Q ss_pred EEEccccccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHHHHh
Q 039731 16 VFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKILECH 95 (315)
Q Consensus 16 VFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~~~ 95 (315)
|||||+++| ..++..|...|++.|+++|+|.++.+|+.+.+.|.++|++|+..|+++|++|..|+||..|+..+.
T Consensus 1 VFIS~~~~D--~~~a~~l~~~L~~~g~~v~~d~~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~--- 75 (102)
T PF13676_consen 1 VFISYSSED--REFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAW--- 75 (102)
T ss_dssp EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHH---
T ss_pred eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHH---
Confidence 899999999 469999999999999999999999999999999999999999999999999999999999999983
Q ss_pred hhCCCeeeeEEEecCCccc
Q 039731 96 KMNSQMVVPVFYRIDPSDV 114 (315)
Q Consensus 96 ~~~~~~ViPIfy~v~ps~V 114 (315)
..+..||||. +++.++
T Consensus 76 -~~~~~iipv~--~~~~~~ 91 (102)
T PF13676_consen 76 -KRGKPIIPVR--LDPCEL 91 (102)
T ss_dssp -CTSESEEEEE--CSGGGS
T ss_pred -HCCCEEEEEE--ECCcCC
Confidence 3455899999 555544
No 6
>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]
Probab=98.96 E-value=4.4e-10 Score=119.40 Aligned_cols=108 Identities=8% Similarity=-0.064 Sum_probs=79.0
Q ss_pred CCCCCCceeeeeCCCCCcccceeeeeeeccccccccCCCccc-----hhcc---cccccccee-eccccCCccCHHHHHH
Q 039731 171 NGTKPNTFTVNVLPPNEEECTQIRKLHYDFHDNVGTSGNSES-----IDRS---GELEVESIC-REQINAPQQQRSSLFS 241 (315)
Q Consensus 171 Vg~~~r~~~v~~Ll~~~~~~~~l~~i~~d~~~~~GmGGiGK~-----vy~~---i~~~Fe~~~-~~~s~~~~~gl~~Lq~ 241 (315)
||++..+..+-..|..++ ..++||+ ||||+||+ +||+ +..+|+..+ +.+|+.. ...++|+
T Consensus 161 VG~e~~~~kl~~~L~~d~--~~iv~i~-------GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f--~~~~iq~ 229 (889)
T KOG4658|consen 161 VGLETMLEKLWNRLMEDD--VGIVGIY-------GMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEF--TTRKIQQ 229 (889)
T ss_pred ccHHHHHHHHHHHhccCC--CCEEEEE-------CCCcccHHHHHHHHhcccchhcccCceEEEEEEcccc--cHHhHHH
Confidence 666655544433333222 2667776 99999994 4553 557888888 7778766 8999999
Q ss_pred HHHHHhcC--CCCCcCChhHHHHHHHHhhCCcEEEEEeeCCCCCCCcccc
Q 039731 242 HIIAKGGG--LYAFLAPSDHASIQIQRRHIRLKVSLLASKVDSASSPELS 289 (315)
Q Consensus 242 ~LL~~il~--~~~~~~~~~~~~~~i~~rL~~kKvLIVLDDVd~~~qle~~ 289 (315)
+++.++.. ......+.++.+..|.+.|.+||+||||||||+...++..
T Consensus 230 ~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I 279 (889)
T KOG4658|consen 230 TILERLGLLDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKI 279 (889)
T ss_pred HHHHHhccCCcccchhhHHHHHHHHHHHhccCceEEEEecccccccHHhc
Confidence 99998865 2223334478899999999999999999999999886543
No 7
>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []. This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.
Probab=98.85 E-value=3.2e-09 Score=98.28 Aligned_cols=93 Identities=12% Similarity=0.087 Sum_probs=68.4
Q ss_pred ccceeeeeeeccccccccCCCccc-----hhcc--cccccccee-eccccCCccCHHHHHHHHHHHhcCC--CC-CcCCh
Q 039731 189 ECTQIRKLHYDFHDNVGTSGNSES-----IDRS--GELEVESIC-REQINAPQQQRSSLFSHIIAKGGGL--YA-FLAPS 257 (315)
Q Consensus 189 ~~~~l~~i~~d~~~~~GmGGiGK~-----vy~~--i~~~Fe~~~-~~~s~~~~~gl~~Lq~~LL~~il~~--~~-~~~~~ 257 (315)
....+++|+ ||||+||+ +++. +..+|++.+ +...... ...+++++|+..+... .. ...+.
T Consensus 17 ~~~~~v~I~-------G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~--~~~~~~~~i~~~l~~~~~~~~~~~~~ 87 (287)
T PF00931_consen 17 NEVRVVAIV-------GMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNP--SLEQLLEQILRQLGEPDSSISDPKDI 87 (287)
T ss_dssp TSSEEEEEE-------ESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-S--CCHHHHHHHHHHHTCC-STSSCCSSH
T ss_pred CCeEEEEEE-------cCCcCCcceeeeeccccccccccccccccccccccc--cccccccccccccccccccccccccc
Confidence 566778887 99999993 4555 778898877 5544444 5578889999888653 22 45667
Q ss_pred hHHHHHHHHhhCCcEEEEEeeCCCCCCCccccc
Q 039731 258 DHASIQIQRRHIRLKVSLLASKVDSASSPELST 290 (315)
Q Consensus 258 ~~~~~~i~~rL~~kKvLIVLDDVd~~~qle~~~ 290 (315)
.+....|++.|+++++||||||||+..+++.+.
T Consensus 88 ~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~ 120 (287)
T PF00931_consen 88 EELQDQLRELLKDKRCLLVLDDVWDEEDLEELR 120 (287)
T ss_dssp HHHHHHHHHHHCCTSEEEEEEEE-SHHHH----
T ss_pred ccccccchhhhccccceeeeeeecccccccccc
Confidence 789999999999999999999999999876554
No 8
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=98.74 E-value=2.2e-08 Score=97.40 Aligned_cols=91 Identities=26% Similarity=0.495 Sum_probs=77.7
Q ss_pred CCCceeEEEccccccCccchHHHHHHHHhhCCCeEEeeC-ccCCCCcchHHHHHHHhhcCeEEEEeecccc--------C
Q 039731 10 SQSKYDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDE-ELNRGDEISPAILKAIEGSKITVIIFSKNYA--------S 80 (315)
Q Consensus 10 ~~~~ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~--------~ 80 (315)
-..+.|||||||...- +..++-|.--|+-+|++||+|- .+..|.. .+.+.+.|..++.+|+|++||.. +
T Consensus 609 ~skq~DVFISYRRstG-nQLASLiKV~LQL~GyrVFIDVdKL~AGKF-dssLlkni~aAkhFiLVLtP~sLDr~lnD~nC 686 (832)
T KOG3678|consen 609 LSKQIDVFISYRRSTG-NQLASLIKVLLQLRGYRVFIDVDKLYAGKF-DSSLLKNIQAAKHFILVLTPNSLDRLLNDDNC 686 (832)
T ss_pred ccCCcceEEEeecccc-HHHHHHHHHHHHhcCceEEEehhhhhcccc-cHHHHHHHHhhheeEEEeCcchHHHHhccccH
Confidence 3568999999987753 6788888888899999999998 7888864 55899999999999999999965 4
Q ss_pred ChHhHHHHHHHHHHhhhCCCeeeeEE
Q 039731 81 SKWCLDELVKILECHKMNSQMVVPVF 106 (315)
Q Consensus 81 S~wcl~El~~i~~~~~~~~~~ViPIf 106 (315)
-.|...||..+++|.+ -|||||
T Consensus 687 eDWVHKEl~~Afe~~K----NIiPI~ 708 (832)
T KOG3678|consen 687 EDWVHKELKCAFEHQK----NIIPIF 708 (832)
T ss_pred HHHHHHHHHHHHHhcC----Ceeeee
Confidence 5788899999998876 799999
No 9
>PF08937 DUF1863: MTH538 TIR-like domain (DUF1863); InterPro: IPR015032 This protein adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein []. This domain is similar to the TIR domain [].; PDB: 3HYN_A.
Probab=98.34 E-value=8.4e-07 Score=73.47 Aligned_cols=89 Identities=25% Similarity=0.430 Sum_probs=48.1
Q ss_pred eeEEEccccccCccchHHHHHHHHhhC-------CCeE-Ee---------eC-ccCCCCcchHHHHHHHhhcCeEEEEee
Q 039731 14 YDVFLSFRGEDTRDNFTSHLHAALCRK-------KIKT-FI---------DE-ELNRGDEISPAILKAIEGSKITVIIFS 75 (315)
Q Consensus 14 ydVFIS~~~~D~r~~fv~~L~~~L~~~-------gi~~-f~---------D~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S 75 (315)
|.|||||++.|. ...+..|..-+... .+.. |. +. +......|...|.++|..|.++||+++
T Consensus 1 ~~vFIS~~~~d~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig 79 (130)
T PF08937_consen 1 YKVFISYSHDDD-DWYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG 79 (130)
T ss_dssp ----------TH-H-HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred CCccccccccCc-HHHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence 579999999985 24777777777662 2221 11 11 222344788899999999999999999
Q ss_pred ccccCChHhHHHHHHHHHHhhhCCCeeeeEEE
Q 039731 76 KNYASSKWCLDELVKILECHKMNSQMVVPVFY 107 (315)
Q Consensus 76 ~~y~~S~wcl~El~~i~~~~~~~~~~ViPIfy 107 (315)
++...|.|+..|+..+++ .+..||.|.+
T Consensus 80 ~~T~~s~wV~~EI~~A~~----~~~~Ii~V~~ 107 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALK----KGKPIIGVYL 107 (130)
T ss_dssp TT----HHHHHHHHHHTT----T---EEEEET
T ss_pred CCcccCcHHHHHHHHHHH----CCCCEEEEEC
Confidence 999999999999998876 4457777763
No 10
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=97.56 E-value=0.00038 Score=58.55 Aligned_cols=64 Identities=22% Similarity=0.371 Sum_probs=51.8
Q ss_pred eEEEccccccCc-cchHHHHHHHHhhC-CCeEEeeC-ccCC--CCcchHHHHHHHhhcCeEEEEeeccc
Q 039731 15 DVFLSFRGEDTR-DNFTSHLHAALCRK-KIKTFIDE-ELNR--GDEISPAILKAIEGSKITVIIFSKNY 78 (315)
Q Consensus 15 dVFIS~~~~D~r-~~fv~~L~~~L~~~-gi~~f~D~-~~~~--G~~i~~~i~~aI~~S~~~Ivv~S~~y 78 (315)
-|||||+..... ...|..|...|++. |+.|.+|. +... +..+..=+.+.+++++.+|+|.||.|
T Consensus 2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~ 70 (150)
T PF08357_consen 2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY 70 (150)
T ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence 499999875432 35689999999999 99999998 6643 66666677888999999999999543
No 11
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=95.58 E-value=0.04 Score=45.49 Aligned_cols=60 Identities=17% Similarity=0.296 Sum_probs=50.0
Q ss_pred eEEEccccccCccchHHHHHHHHhhCCCeEE-eeCccCCCCcchHHHHHHHhhcCeEEEEeecc
Q 039731 15 DVFLSFRGEDTRDNFTSHLHAALCRKKIKTF-IDEELNRGDEISPAILKAIEGSKITVIIFSKN 77 (315)
Q Consensus 15 dVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f-~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (315)
.|||.|+ +| ...+..+...|+..|+.+. +++....|..+.+.+.+.+.+++.+|++++|+
T Consensus 1 kVFIvhg-~~--~~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpD 61 (125)
T PF10137_consen 1 KVFIVHG-RD--LAAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPD 61 (125)
T ss_pred CEEEEeC-CC--HHHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEccc
Confidence 3899997 66 3688889889988888754 34455889999999999999999999999996
No 12
>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
Probab=95.01 E-value=0.016 Score=53.34 Aligned_cols=83 Identities=8% Similarity=-0.027 Sum_probs=50.7
Q ss_pred cccccCCCccc-----hhccccc-ccccee-eccccCCccCHHHHHHHHHHHhcCCCCC------cCChhHHHHHHHHh-
Q 039731 202 DNVGTSGNSES-----IDRSGEL-EVESIC-REQINAPQQQRSSLFSHIIAKGGGLYAF------LAPSDHASIQIQRR- 267 (315)
Q Consensus 202 ~~~GmGGiGK~-----vy~~i~~-~Fe~~~-~~~s~~~~~gl~~Lq~~LL~~il~~~~~------~~~~~~~~~~i~~r- 267 (315)
+|+|.+|+||+ +|+.+.. +|+..| ..++++...++.++|+.+.+.+.-.... ..-........+..
T Consensus 20 ~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a~~~~ 99 (249)
T cd01128 20 LIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKRLV 99 (249)
T ss_pred EEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHHHHHH
Confidence 45699999993 4555433 588877 5545553248899999995544321111 11122334444433
Q ss_pred hCCcEEEEEeeCCCCCC
Q 039731 268 HIRLKVSLLASKVDSAS 284 (315)
Q Consensus 268 L~~kKvLIVLDDVd~~~ 284 (315)
-.+++|+|++|++...-
T Consensus 100 ~~G~~vll~iDei~r~a 116 (249)
T cd01128 100 EHGKDVVILLDSITRLA 116 (249)
T ss_pred HCCCCEEEEEECHHHhh
Confidence 34799999999998653
No 13
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=94.87 E-value=0.026 Score=45.46 Aligned_cols=79 Identities=13% Similarity=0.028 Sum_probs=46.4
Q ss_pred ccccCCCccch-hccccccc--------ccee--eccccCCccCHHHHHHHHHHHhcCCCCCcCChhHHHHHHHHhhCCc
Q 039731 203 NVGTSGNSESI-DRSGELEV--------ESIC--REQINAPQQQRSSLFSHIIAKGGGLYAFLAPSDHASIQIQRRHIRL 271 (315)
Q Consensus 203 ~~GmGGiGK~v-y~~i~~~F--------e~~~--~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~~~~~~~i~~rL~~k 271 (315)
++|-.|.||+. .+++..++ ...+ ....... ....+.+.|+..+......-.+..+....+.+.+.+.
T Consensus 9 i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~ 86 (131)
T PF13401_consen 9 ISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSR--TPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDRR 86 (131)
T ss_dssp EEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHS--SHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHC
T ss_pred EEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCC--CHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHhc
Confidence 34999999943 33444333 2222 2222222 5677888888877542222345666667777777664
Q ss_pred -EEEEEeeCCCCC
Q 039731 272 -KVSLLASKVDSA 283 (315)
Q Consensus 272 -KvLIVLDDVd~~ 283 (315)
.++||+||++..
T Consensus 87 ~~~~lviDe~~~l 99 (131)
T PF13401_consen 87 RVVLLVIDEADHL 99 (131)
T ss_dssp TEEEEEEETTHHH
T ss_pred CCeEEEEeChHhc
Confidence 459999999875
No 14
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=94.76 E-value=0.032 Score=54.67 Aligned_cols=85 Identities=9% Similarity=-0.042 Sum_probs=52.2
Q ss_pred ccccccCCCccc-----hhccccc-ccccee-eccccCCccCHHHHHHHHHHHhcCCCCCcC------ChhHHHHHHHHh
Q 039731 201 HDNVGTSGNSES-----IDRSGEL-EVESIC-REQINAPQQQRSSLFSHIIAKGGGLYAFLA------PSDHASIQIQRR 267 (315)
Q Consensus 201 ~~~~GmGGiGK~-----vy~~i~~-~Fe~~~-~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~------~~~~~~~~i~~r 267 (315)
.+|+|.+|+||+ +|+.+.. +|+.+| +..+++....+.++|++++..+.-....-. ..+.....-+..
T Consensus 172 ~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~ 251 (416)
T PRK09376 172 GLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRL 251 (416)
T ss_pred EEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence 346799999994 5666554 699888 555555433678899999754432111111 112233333332
Q ss_pred -hCCcEEEEEeeCCCCCCC
Q 039731 268 -HIRLKVSLLASKVDSASS 285 (315)
Q Consensus 268 -L~~kKvLIVLDDVd~~~q 285 (315)
-.++.|||++|++...-.
T Consensus 252 ~e~G~dVlL~iDsItR~ar 270 (416)
T PRK09376 252 VEHGKDVVILLDSITRLAR 270 (416)
T ss_pred HHcCCCEEEEEEChHHHHH
Confidence 367999999999986543
No 15
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=94.59 E-value=0.061 Score=52.86 Aligned_cols=85 Identities=8% Similarity=-0.033 Sum_probs=52.3
Q ss_pred ccccccccCCCccch-----hcccccc-cccee-eccccCCccCHHHHHHHHHHHhcCCCCCcCCh------hHHHHHHH
Q 039731 199 DFHDNVGTSGNSESI-----DRSGELE-VESIC-REQINAPQQQRSSLFSHIIAKGGGLYAFLAPS------DHASIQIQ 265 (315)
Q Consensus 199 d~~~~~GmGGiGK~v-----y~~i~~~-Fe~~~-~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~------~~~~~~i~ 265 (315)
+...|+|.+|.||++ ++.+..+ |+..| ...+.+....+.++|++++..+.-........ .......+
T Consensus 169 q~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~Ae 248 (415)
T TIGR00767 169 QRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAK 248 (415)
T ss_pred CEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHHH
Confidence 356688999999943 4444444 88888 44554422488999999977664321111111 12222333
Q ss_pred H-hhCCcEEEEEeeCCCCC
Q 039731 266 R-RHIRLKVSLLASKVDSA 283 (315)
Q Consensus 266 ~-rL~~kKvLIVLDDVd~~ 283 (315)
. +-.+++|+|++|.+...
T Consensus 249 ~~~~~GkdVVLlIDEitR~ 267 (415)
T TIGR00767 249 RLVEHKKDVVILLDSITRL 267 (415)
T ss_pred HHHHcCCCeEEEEEChhHH
Confidence 2 23579999999999855
No 16
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=93.31 E-value=0.088 Score=50.42 Aligned_cols=49 Identities=4% Similarity=-0.034 Sum_probs=31.0
Q ss_pred CHHHHHHHHHHHhc--CCC--CCcCChhHHHHHHHHhhC--CcEEEEEeeCCCCC
Q 039731 235 QRSSLFSHIIAKGG--GLY--AFLAPSDHASIQIQRRHI--RLKVSLLASKVDSA 283 (315)
Q Consensus 235 gl~~Lq~~LL~~il--~~~--~~~~~~~~~~~~i~~rL~--~kKvLIVLDDVd~~ 283 (315)
+...+...|+.++. +.. ..-.+..+....+.+.|. +++++||||++|..
T Consensus 87 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L 141 (365)
T TIGR02928 87 TLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYL 141 (365)
T ss_pred CHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhh
Confidence 45667788888775 211 111133444455666663 56899999999988
No 17
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=93.29 E-value=0.087 Score=51.06 Aligned_cols=79 Identities=13% Similarity=0.031 Sum_probs=45.3
Q ss_pred ccCCCccchh-ccccccc-----cceeec-cccCCccCHHHHHHHHHHHhcC-CC-CCcCChhHHHHHHHHhhC--CcEE
Q 039731 205 GTSGNSESID-RSGELEV-----ESICRE-QINAPQQQRSSLFSHIIAKGGG-LY-AFLAPSDHASIQIQRRHI--RLKV 273 (315)
Q Consensus 205 GmGGiGK~vy-~~i~~~F-----e~~~~~-~s~~~~~gl~~Lq~~LL~~il~-~~-~~~~~~~~~~~~i~~rL~--~kKv 273 (315)
|..|+||++. +.+..+. ...+.. ++... .+...+..+|+.++.+ .. ....+..+....+.+.+. ++.+
T Consensus 62 G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 140 (394)
T PRK00411 62 GPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQID-RTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVL 140 (394)
T ss_pred CCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcC-CCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEE
Confidence 9999999432 2222221 111111 11111 2556777888888765 21 122245556667777775 3569
Q ss_pred EEEeeCCCCCC
Q 039731 274 SLLASKVDSAS 284 (315)
Q Consensus 274 LIVLDDVd~~~ 284 (315)
+||||++|...
T Consensus 141 viviDE~d~l~ 151 (394)
T PRK00411 141 IVALDDINYLF 151 (394)
T ss_pred EEEECCHhHhh
Confidence 99999999864
No 18
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=93.05 E-value=0.3 Score=44.53 Aligned_cols=80 Identities=11% Similarity=0.119 Sum_probs=39.7
Q ss_pred ccccCCCccchh-cccccccc--cee-eccccCCccCHHHHHHHHHHHhcCCCCCcCChhHHHHHHH----Hhh-CCcEE
Q 039731 203 NVGTSGNSESID-RSGELEVE--SIC-REQINAPQQQRSSLFSHIIAKGGGLYAFLAPSDHASIQIQ----RRH-IRLKV 273 (315)
Q Consensus 203 ~~GmGGiGK~vy-~~i~~~Fe--~~~-~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~~~~~~~i~----~rL-~~kKv 273 (315)
++|..|.||++. +.+...+. ..+ ....... ....++...|+..+ +.+..-.+.......+. ..+ .++++
T Consensus 48 l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~-~~~~~~l~~i~~~l-G~~~~~~~~~~~~~~l~~~l~~~~~~~~~~ 125 (269)
T TIGR03015 48 ITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTR-VDAEDLLRMVAADF-GLETEGRDKAALLRELEDFLIEQFAAGKRA 125 (269)
T ss_pred EEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCC-CCHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHHHHHHHhCCCCe
Confidence 349999999543 33333322 111 1111111 14456676776554 32111122222222332 322 56789
Q ss_pred EEEeeCCCCCC
Q 039731 274 SLLASKVDSAS 284 (315)
Q Consensus 274 LIVLDDVd~~~ 284 (315)
+||+||++...
T Consensus 126 vliiDe~~~l~ 136 (269)
T TIGR03015 126 LLVVDEAQNLT 136 (269)
T ss_pred EEEEECcccCC
Confidence 99999999875
No 19
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=91.58 E-value=0.27 Score=48.09 Aligned_cols=87 Identities=14% Similarity=0.132 Sum_probs=52.3
Q ss_pred ccccCCCccchhccc-cccccceeeccccCCccCHHHHHHHHHHHhcCCCCCcCChhHHHHHHHHhhCCcEEEEEeeCCC
Q 039731 203 NVGTSGNSESIDRSG-ELEVESICREQINAPQQQRSSLFSHIIAKGGGLYAFLAPSDHASIQIQRRHIRLKVSLLASKVD 281 (315)
Q Consensus 203 ~~GmGGiGK~vy~~i-~~~Fe~~~~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~~~~~~~i~~rL~~kKvLIVLDDVd 281 (315)
.||..|+||++..++ ...++......+-. ..|+.+|++-+=. .-+.++.++|.+|.+|.|.
T Consensus 53 l~GPPG~GKTTlA~liA~~~~~~f~~~sAv-~~gvkdlr~i~e~-----------------a~~~~~~gr~tiLflDEIH 114 (436)
T COG2256 53 LWGPPGTGKTTLARLIAGTTNAAFEALSAV-TSGVKDLREIIEE-----------------ARKNRLLGRRTILFLDEIH 114 (436)
T ss_pred EECCCCCCHHHHHHHHHHhhCCceEEeccc-cccHHHHHHHHHH-----------------HHHHHhcCCceEEEEehhh
Confidence 479999999777653 33333322221111 1266666554411 1244566899999999997
Q ss_pred CC--CCcccccCCCCCccccCCCCcee--ccCCCCCC
Q 039731 282 SA--SSPELSTSDKIEPKHNVDNGHVT--SSSTNNES 314 (315)
Q Consensus 282 ~~--~qle~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 314 (315)
.. .|-+++.+ -|.||.+| ..+|.|.|
T Consensus 115 RfnK~QQD~lLp-------~vE~G~iilIGATTENPs 144 (436)
T COG2256 115 RFNKAQQDALLP-------HVENGTIILIGATTENPS 144 (436)
T ss_pred hcChhhhhhhhh-------hhcCCeEEEEeccCCCCC
Confidence 44 45566654 36788876 45666655
No 20
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=91.12 E-value=0.77 Score=34.75 Aligned_cols=66 Identities=20% Similarity=0.171 Sum_probs=48.8
Q ss_pred eEEEccccccCccchHHHHHHHHhhCCCeEEe-eCccCCCCcchHHHHHHHhhcCeEEEEeeccccCC
Q 039731 15 DVFLSFRGEDTRDNFTSHLHAALCRKKIKTFI-DEELNRGDEISPAILKAIEGSKITVIIFSKNYASS 81 (315)
Q Consensus 15 dVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~-D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S 81 (315)
.||||-.-.|. ..-...|.+.+.+.|..... +.--..+....+.+.+.|++|+++|.++-..|-..
T Consensus 1 rVFiSSt~~Dl-~~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 1 RVFISSTFRDL-KEERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred CEEEecChhhH-HHHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 38999888886 45667888888888876432 32112355666688999999999999999998754
No 21
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=91.01 E-value=0.35 Score=47.05 Aligned_cols=79 Identities=15% Similarity=0.078 Sum_probs=50.9
Q ss_pred ccCCCccch-hccccccccce------eeccccCCccCHHHHHHHHHHHhcCCCCCcCChhHHHHHHHHhhCC--cEEEE
Q 039731 205 GTSGNSESI-DRSGELEVESI------CREQINAPQQQRSSLFSHIIAKGGGLYAFLAPSDHASIQIQRRHIR--LKVSL 275 (315)
Q Consensus 205 GmGGiGK~v-y~~i~~~Fe~~------~~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~~~~~~~i~~rL~~--kKvLI 275 (315)
|-.|.||++ -..+..+++.. +--++..+ .+..++..+|++++.+.+..-.+..+....+.+.+.. +.++|
T Consensus 49 G~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~-~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~Iv 127 (366)
T COG1474 49 GPTGTGKTATVKFVMEELEESSANVEVVYINCLEL-RTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIV 127 (366)
T ss_pred CCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeC-CCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEE
Confidence 999999943 23333333332 21123332 3677888889988865343344556667777777765 78999
Q ss_pred EeeCCCCCC
Q 039731 276 LASKVDSAS 284 (315)
Q Consensus 276 VLDDVd~~~ 284 (315)
|||+||...
T Consensus 128 vLDEid~L~ 136 (366)
T COG1474 128 ILDEVDALV 136 (366)
T ss_pred EEcchhhhc
Confidence 999999764
No 22
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=89.06 E-value=0.47 Score=43.66 Aligned_cols=100 Identities=17% Similarity=0.169 Sum_probs=67.9
Q ss_pred CCCceeEEEccccccCccchHHHHHHHHh--hCCCeEEeeC----ccCCCCcchHHHHHHH-hhcCeEEEEeeccccCCh
Q 039731 10 SQSKYDVFLSFRGEDTRDNFTSHLHAALC--RKKIKTFIDE----ELNRGDEISPAILKAI-EGSKITVIIFSKNYASSK 82 (315)
Q Consensus 10 ~~~~ydVFIS~~~~D~r~~fv~~L~~~L~--~~gi~~f~D~----~~~~G~~i~~~i~~aI-~~S~~~Ivv~S~~y~~S~ 82 (315)
.++.||+=+||.|+- .+.|.....+++ ...+..|+|. -+-+|+ +..-+...- +.|+..+|....+|..-.
T Consensus 174 ~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~~~L~~~Y~~rC~~~~VF~~~~Y~~K~ 250 (329)
T COG4916 174 SEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LVSTLDPGYDIRCVVTTVFNTGSYICKS 250 (329)
T ss_pred cccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCcc-HHHhcccccCceEEEEEEEeCCceEEee
Confidence 367899999999996 479999999998 4456688886 233442 222333332 256777888899999999
Q ss_pred HhHHHHHHHHHHhhhCCCeeeeEEE-ecCCccc
Q 039731 83 WCLDELVKILECHKMNSQMVVPVFY-RIDPSDV 114 (315)
Q Consensus 83 wcl~El~~i~~~~~~~~~~ViPIfy-~v~ps~V 114 (315)
||.-|...+-+-. .-...+||.| .++-+.+
T Consensus 251 ~c~~E~~~~r~~~--~~d~~~rI~~~~~d~~a~ 281 (329)
T COG4916 251 TCHIEGLEGRLNP--ILDTGFRIKYLYADNIAI 281 (329)
T ss_pred eeccchhhccccc--cccccceEEEEecCCccc
Confidence 9999987663321 2246677776 4555544
No 23
>PF05729 NACHT: NACHT domain
Probab=85.85 E-value=0.85 Score=37.68 Aligned_cols=17 Identities=18% Similarity=0.218 Sum_probs=14.9
Q ss_pred CCcEEEEEeeCCCCCCC
Q 039731 269 IRLKVSLLASKVDSASS 285 (315)
Q Consensus 269 ~~kKvLIVLDDVd~~~q 285 (315)
..+++|||||.+|+...
T Consensus 79 ~~~~~llilDglDE~~~ 95 (166)
T PF05729_consen 79 KNKRVLLILDGLDELEE 95 (166)
T ss_pred cCCceEEEEechHhccc
Confidence 46899999999998876
No 24
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=81.60 E-value=1.4 Score=47.74 Aligned_cols=50 Identities=8% Similarity=-0.070 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHHhcC-CCCCcCChhHHHHHHHHhhC---CcEEEEEeeCCCCCC
Q 039731 235 QRSSLFSHIIAKGGG-LYAFLAPSDHASIQIQRRHI---RLKVSLLASKVDSAS 284 (315)
Q Consensus 235 gl~~Lq~~LL~~il~-~~~~~~~~~~~~~~i~~rL~---~kKvLIVLDDVd~~~ 284 (315)
+...+...|..++.+ ......+..+....+.+.+. +...+||||+||...
T Consensus 829 tp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~ 882 (1164)
T PTZ00112 829 HPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLI 882 (1164)
T ss_pred CHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhC
Confidence 344556666666655 32222233344444555442 234699999999764
No 25
>PF05014 Nuc_deoxyrib_tr: Nucleoside 2-deoxyribosyltransferase; InterPro: IPR007710 Nucleoside 2-deoxyribosyltransferase (2.4.2.6 from EC) catalyses the cleavage of the glycosidic bonds of 2-deoxyribonucleosides. Nucleoside 2-deoxyribosyltransferases can be divided into two groups based on their substrate specificity: class I enzymes are specific for the transfer of deoxyribose between two purines, while class II enzymes will transfer the deoxyribose between either purines or pyrimidines. The structure of the class I [] and class II [] enzymes are very similar. In class I enzymes, the purine base shields the active site from solvent, which the smaller pyrimidine base cannot do, while in class II enzymes the active site is shielded by a loop (residues 48-62). Both classes of enzymes are found in various Lactobacillus species and participate in nucleoside recycling in these microorganisms. This entry represents both classes of enzymes.; GO: 0050144 nucleoside deoxyribosyltransferase activity, 0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity, 0009159 deoxyribonucleoside monophosphate catabolic process; PDB: 1S2L_A 1S2D_C 1S2I_A 1S3F_B 1S2G_C 2A0K_A 2F67_A 2F64_B 2F62_A 2F2T_A ....
Probab=81.23 E-value=7.4 Score=30.84 Aligned_cols=67 Identities=16% Similarity=0.101 Sum_probs=48.3
Q ss_pred cchHHHHHHHHhhCCCeEEeeC--ccC---CCC----cchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHHHH
Q 039731 27 DNFTSHLHAALCRKKIKTFIDE--ELN---RGD----EISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKILEC 94 (315)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~D~--~~~---~G~----~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~~ 94 (315)
..+...+.+.|++.|+.+|... +.. ... .|.+.-.++|++|+++|+++...- .+.=+..|+-.+...
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~al 88 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYAL 88 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHC
Confidence 5688899999999999988755 221 223 333344578999999999997755 566688899888654
No 26
>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A.
Probab=80.97 E-value=1.1 Score=38.03 Aligned_cols=19 Identities=26% Similarity=0.268 Sum_probs=11.9
Q ss_pred HhhCCcE-EEEEeeCCCCCC
Q 039731 266 RRHIRLK-VSLLASKVDSAS 284 (315)
Q Consensus 266 ~rL~~kK-vLIVLDDVd~~~ 284 (315)
.....++ ++||+||++..+
T Consensus 144 ~~~~~~~~~vlviDd~d~~~ 163 (185)
T PF13191_consen 144 ELAARRKPLVLVIDDLDWAD 163 (185)
T ss_dssp TS-SE---EEEEEETTTHHH
T ss_pred HHHhCCCeEEEEEeCCCCCC
Confidence 3334445 999999999554
No 27
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=75.93 E-value=7.6 Score=34.56 Aligned_cols=65 Identities=18% Similarity=0.229 Sum_probs=50.9
Q ss_pred CCCceeEEEccccccCccchHHHHHHHHhhC--CCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeecccc
Q 039731 10 SQSKYDVFLSFRGEDTRDNFTSHLHAALCRK--KIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNYA 79 (315)
Q Consensus 10 ~~~~ydVFIS~~~~D~r~~fv~~L~~~L~~~--gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 79 (315)
|..+ -|||-|+++- .+.....+|.+. -..+|.|.-+..|..+.+.+.+-|++++.+|++.+|+=.
T Consensus 80 p~~k-kvFvv~ghd~----iArael~allrd~~l~~vi~d~~~~~g~~ile~lek~i~~v~FAi~latPDDk 146 (233)
T COG4271 80 PNLK-KVFVVSGHDA----IARAELEALLRDWKLEPVILDGLFSEGQTILESLEKYIAEVKFAIVLATPDDK 146 (233)
T ss_pred CCce-eEEEEeccHH----HHHHHHHHHhhccccceEEecCcccccHHHHHHHHHHhhhceEEEEEecCccc
Confidence 4445 8999995542 666666676643 335788888889999999999999999999999999844
No 28
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=69.79 E-value=19 Score=26.64 Aligned_cols=61 Identities=11% Similarity=0.170 Sum_probs=38.2
Q ss_pred ceeEEEccccccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeecc
Q 039731 13 KYDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKN 77 (315)
Q Consensus 13 ~ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (315)
+++|+|...+.+. ...+-.+.+.|++.|+++-+|. .+..+...+..|-..---.++++.++
T Consensus 1 p~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~---~~~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 1 PVQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDL---RNEKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred CeEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEEC---CCCCHHHHHHHHHHcCCCEEEEECcc
Confidence 3787777655543 4578889999999999998875 13455555555533333334444433
No 29
>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]
Probab=69.60 E-value=3.8 Score=40.19 Aligned_cols=79 Identities=18% Similarity=0.089 Sum_probs=44.5
Q ss_pred ccCCCcc-----chhcccccccccee-eccccCCccCHHHHHHHHHHHhc-C-CC---CCc--CChhHHHHHHHH--hhC
Q 039731 205 GTSGNSE-----SIDRSGELEVESIC-REQINAPQQQRSSLFSHIIAKGG-G-LY---AFL--APSDHASIQIQR--RHI 269 (315)
Q Consensus 205 GmGGiGK-----~vy~~i~~~Fe~~~-~~~s~~~~~gl~~Lq~~LL~~il-~-~~---~~~--~~~~~~~~~i~~--rL~ 269 (315)
|..|-|| ++++....++.-.| ++ .+....|.++||.+.. - .+ .+. .+...-...++. -..
T Consensus 37 G~sgTGKT~~~r~~l~~~n~~~vw~n~~e-----cft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t 111 (438)
T KOG2543|consen 37 GHSGTGKTYLVRQLLRKLNLENVWLNCVE-----CFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAAT 111 (438)
T ss_pred ccCCCchhHHHHHHHhhcCCcceeeehHH-----hccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhh
Confidence 9999999 33444433333222 33 1366788888888873 1 21 111 222222223322 222
Q ss_pred --CcEEEEEeeCCCCCCCccc
Q 039731 270 --RLKVSLLASKVDSASSPEL 288 (315)
Q Consensus 270 --~kKvLIVLDDVd~~~qle~ 288 (315)
+++++||||.+|.....++
T Consensus 112 ~~d~~~~liLDnad~lrD~~a 132 (438)
T KOG2543|consen 112 NRDQKVFLILDNADALRDMDA 132 (438)
T ss_pred ccCceEEEEEcCHHhhhccch
Confidence 4699999999998776554
No 30
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=67.89 E-value=7.3 Score=30.58 Aligned_cols=16 Identities=19% Similarity=0.135 Sum_probs=12.2
Q ss_pred hCCcEEEEEeeCCCCC
Q 039731 268 HIRLKVSLLASKVDSA 283 (315)
Q Consensus 268 L~~kKvLIVLDDVd~~ 283 (315)
...+..+||+||++..
T Consensus 81 ~~~~~~~lilDe~~~~ 96 (151)
T cd00009 81 EKAKPGVLFIDEIDSL 96 (151)
T ss_pred ccCCCeEEEEeChhhh
Confidence 3446789999999864
No 31
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=65.66 E-value=6.5 Score=36.78 Aligned_cols=81 Identities=9% Similarity=0.044 Sum_probs=42.7
Q ss_pred cccccCCCccc-----hhcccccccccee--eccccCCccCHHHHHHHHHHHh-cCCC------CCcCChh-----HHHH
Q 039731 202 DNVGTSGNSES-----IDRSGELEVESIC--REQINAPQQQRSSLFSHIIAKG-GGLY------AFLAPSD-----HASI 262 (315)
Q Consensus 202 ~~~GmGGiGK~-----vy~~i~~~Fe~~~--~~~s~~~~~gl~~Lq~~LL~~i-l~~~------~~~~~~~-----~~~~ 262 (315)
+|+|-.|+||+ +++++..+|+..| .-.-++. ..+..+.+.++..- +... .+-.... ....
T Consensus 73 ~If~~~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer~-~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~~~a~ 151 (274)
T cd01133 73 GLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGERT-REGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVALTGL 151 (274)
T ss_pred EEecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCc-HHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHH
Confidence 45688999993 4566777788777 1111221 13344555555321 1110 0000011 1222
Q ss_pred HHHHhh--C-CcEEEEEeeCCCCC
Q 039731 263 QIQRRH--I-RLKVSLLASKVDSA 283 (315)
Q Consensus 263 ~i~~rL--~-~kKvLIVLDDVd~~ 283 (315)
.+-+++ + ++.|||++||+..-
T Consensus 152 ~~AEyfr~~~g~~Vl~~~Dsltr~ 175 (274)
T cd01133 152 TMAEYFRDEEGQDVLLFIDNIFRF 175 (274)
T ss_pred HHHHHHHHhcCCeEEEEEeChhHH
Confidence 345666 3 78999999998754
No 32
>smart00382 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Probab=61.62 E-value=13 Score=28.67 Aligned_cols=28 Identities=18% Similarity=0.045 Sum_probs=18.8
Q ss_pred HHHHHHhhCCcE-EEEEeeCCCCCCCccc
Q 039731 261 SIQIQRRHIRLK-VSLLASKVDSASSPEL 288 (315)
Q Consensus 261 ~~~i~~rL~~kK-vLIVLDDVd~~~qle~ 288 (315)
...+.++.+..+ .+|++|+++....-..
T Consensus 67 ~~~~~~~~~~~~~~viiiDei~~~~~~~~ 95 (148)
T smart00382 67 LRLALALARKLKPDVLILDEITSLLDAEQ 95 (148)
T ss_pred HHHHHHHHHhcCCCEEEEECCcccCCHHH
Confidence 344555555544 9999999998765543
No 33
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=59.54 E-value=57 Score=23.23 Aligned_cols=61 Identities=18% Similarity=0.176 Sum_probs=38.3
Q ss_pred HHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHHHHhhhCCCeee
Q 039731 31 SHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKILECHKMNSQMVV 103 (315)
Q Consensus 31 ~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~Vi 103 (315)
.-|+.-|++.|+.+-... . ..++++...-.+++++|.+.-+. -.++..+.+..+.++..||
T Consensus 8 ~a~~~~L~~~g~~v~~~~------~----~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~v~~G~~lvl 68 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWR------K----PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEWVEAGNTLVL 68 (70)
T ss_pred HHHHHHHHHCCCeeEEec------c----cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHHHHcCCEEEE
Confidence 457788888898874322 1 12244557888999999966553 3455555555555655554
No 34
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=58.78 E-value=35 Score=25.19 Aligned_cols=59 Identities=17% Similarity=0.222 Sum_probs=38.0
Q ss_pred eeEEEccccc---cCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeec
Q 039731 14 YDVFLSFRGE---DTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSK 76 (315)
Q Consensus 14 ydVFIS~~~~---D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (315)
++|+|-.-+. .. ...+-.+...|++.|+.+.+|. .+..+...+..|-..---+++++.+
T Consensus 2 ~~v~ii~~~~~~~~~-~~~a~~~~~~Lr~~g~~v~~~~---~~~~~~k~~~~a~~~g~~~~iiig~ 63 (94)
T cd00738 2 IDVAIVPLTDPRVEA-REYAQKLLNALLANGIRVLYDD---RERKIGKKFREADLRGVPFAVVVGE 63 (94)
T ss_pred eEEEEEECCCCcHHH-HHHHHHHHHHHHHCCCEEEecC---CCcCHhHHHHHHHhCCCCEEEEECC
Confidence 6776665443 22 4577888999999999998875 2345555555554443345666665
No 35
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=58.16 E-value=29 Score=26.06 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=32.2
Q ss_pred cchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeec
Q 039731 27 DNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSK 76 (315)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (315)
..++.+|...|.+.|+++.+|. .+..+...+..|-..=--+++|+.+
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~---~~~~~~k~~~~a~~~g~p~~iiiG~ 61 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDD---SDKSLGKQIKYADKLGIPFIIIIGE 61 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEES---SSSTHHHHHHHHHHTTESEEEEEEH
T ss_pred HHHHHHHHHHHHHCCCEEEEEC---CCCchhHHHHHHhhcCCeEEEEECc
Confidence 4688999999999999999986 3455555666665433334444443
No 36
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=55.26 E-value=90 Score=23.62 Aligned_cols=74 Identities=19% Similarity=0.241 Sum_probs=48.4
Q ss_pred EEEccccccCccchHHHHHHHHhhCCCeEEeeC-ccC-------CCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHH
Q 039731 16 VFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDE-ELN-------RGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDE 87 (315)
Q Consensus 16 VFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~-~~~-------~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~E 87 (315)
+|.|..|---+..++.+|...|.++|.++..-+ |.. -+-.+.+....++..|+..|+++.+... .+..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~----s~~~ 78 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL----DLDG 78 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH----HHHH
Confidence 466766555556788899999998998876533 321 1122344455788999999999877644 4555
Q ss_pred HHHHHH
Q 039731 88 LVKILE 93 (315)
Q Consensus 88 l~~i~~ 93 (315)
+..+++
T Consensus 79 ~~~~~~ 84 (104)
T cd02042 79 LEKLLE 84 (104)
T ss_pred HHHHHH
Confidence 555544
No 37
>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=52.47 E-value=19 Score=33.51 Aligned_cols=61 Identities=10% Similarity=-0.052 Sum_probs=32.2
Q ss_pred ccccCCCccchhcccccc---ccceeeccccCCccCHHHHHHHHHHHhcCCCCCcCChhHHHHHHHHhhCCcEEEEEeeC
Q 039731 203 NVGTSGNSESIDRSGELE---VESICREQINAPQQQRSSLFSHIIAKGGGLYAFLAPSDHASIQIQRRHIRLKVSLLASK 279 (315)
Q Consensus 203 ~~GmGGiGK~vy~~i~~~---Fe~~~~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~~~~~~~i~~rL~~kKvLIVLDD 279 (315)
++|+||.||....++... ++..-.+.++. |++.+....|- ..+.+.-+.++++.+++.|
T Consensus 36 LvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~--y~~~~f~~dLk----------------~~~~~ag~~~~~~vfll~d 97 (268)
T PF12780_consen 36 LVGVGGSGRQSLARLAAFICGYEVFQIEITKG--YSIKDFKEDLK----------------KALQKAGIKGKPTVFLLTD 97 (268)
T ss_dssp EECTTTSCHHHHHHHHHHHTTEEEE-TTTSTT--THHHHHHHHHH----------------HHHHHHHCS-S-EEEEEEC
T ss_pred EecCCCccHHHHHHHHHHHhccceEEEEeeCC--cCHHHHHHHHH----------------HHHHHHhccCCCeEEEecC
Confidence 359999999555554432 22111333333 36655443332 1234567778888888887
Q ss_pred CC
Q 039731 280 VD 281 (315)
Q Consensus 280 Vd 281 (315)
-.
T Consensus 98 ~q 99 (268)
T PF12780_consen 98 SQ 99 (268)
T ss_dssp CC
T ss_pred cc
Confidence 43
No 38
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=50.81 E-value=46 Score=26.58 Aligned_cols=60 Identities=8% Similarity=-0.009 Sum_probs=40.5
Q ss_pred ceeEEEcccc--ccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeecc
Q 039731 13 KYDVFLSFRG--EDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKN 77 (315)
Q Consensus 13 ~ydVFIS~~~--~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (315)
.+||||-.-+ .+. ...+..|+..|++.|+++-+|.. ..+...+..|-+.---+++++.++
T Consensus 26 p~~v~Ii~~~~~~~~-~~~a~~la~~LR~~gi~v~~d~~----~sl~kqlk~A~k~g~~~~iiiG~~ 87 (121)
T cd00858 26 PIKVAVLPLVKRDEL-VEIAKEISEELRELGFSVKYDDS----GSIGRRYARQDEIGTPFCVTVDFD 87 (121)
T ss_pred CcEEEEEecCCcHHH-HHHHHHHHHHHHHCCCEEEEeCC----CCHHHHHHHhHhcCCCEEEEECcC
Confidence 5788887766 332 45777899999999999988752 466666666644444455665544
No 39
>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=48.72 E-value=23 Score=35.70 Aligned_cols=76 Identities=11% Similarity=0.072 Sum_probs=39.6
Q ss_pred ccCCCccc-hhcccccccccee--------eccccCCccCHHHHHHHHHHHhcC-CCCCcCChhHHHHHHHHhhCC-c-E
Q 039731 205 GTSGNSES-IDRSGELEVESIC--------REQINAPQQQRSSLFSHIIAKGGG-LYAFLAPSDHASIQIQRRHIR-L-K 272 (315)
Q Consensus 205 GmGGiGK~-vy~~i~~~Fe~~~--------~~~s~~~~~gl~~Lq~~LL~~il~-~~~~~~~~~~~~~~i~~rL~~-k-K 272 (315)
|-.|.||+ ...++..+|.... .+.+- .....+.+++++.++. .... .+..+....+.+.... + -
T Consensus 182 G~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl---~~~~aiF~kI~~~~~q~~~s~-~~~~~~~~~~~~h~~q~k~~ 257 (529)
T KOG2227|consen 182 GQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSL---TEASAIFKKIFSSLLQDLVSP-GTGMQHLEKFEKHTKQSKFM 257 (529)
T ss_pred CCCCcchHHHHHHHHHhhhhhcccceeEEEeeccc---cchHHHHHHHHHHHHHHhcCC-chhHHHHHHHHHHHhcccce
Confidence 99999993 3333444433222 22110 1335677788777743 1111 1112223344455544 3 5
Q ss_pred EEEEeeCCCCCC
Q 039731 273 VSLLASKVDSAS 284 (315)
Q Consensus 273 vLIVLDDVd~~~ 284 (315)
+|||||.+|..-
T Consensus 258 ~llVlDEmD~L~ 269 (529)
T KOG2227|consen 258 LLLVLDEMDHLI 269 (529)
T ss_pred EEEEechhhHHh
Confidence 999999988653
No 40
>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein. This is thought to be an ATPase involved in viral DNA packaging [].
Probab=48.67 E-value=13 Score=34.07 Aligned_cols=11 Identities=0% Similarity=0.259 Sum_probs=9.9
Q ss_pred EEEEEeeCCCC
Q 039731 272 KVSLLASKVDS 282 (315)
Q Consensus 272 KvLIVLDDVd~ 282 (315)
++||||||+-+
T Consensus 99 ~~LiIlDD~~~ 109 (241)
T PF04665_consen 99 RFLIILDDLGD 109 (241)
T ss_pred CeEEEEeCCCC
Confidence 89999999965
No 41
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=47.38 E-value=12 Score=29.34 Aligned_cols=17 Identities=12% Similarity=0.141 Sum_probs=13.0
Q ss_pred cEEEEEeeCCCCCCCcc
Q 039731 271 LKVSLLASKVDSASSPE 287 (315)
Q Consensus 271 kKvLIVLDDVd~~~qle 287 (315)
++.+|++||+|...+-.
T Consensus 58 ~~~vl~iDe~d~l~~~~ 74 (132)
T PF00004_consen 58 KPCVLFIDEIDKLFPKS 74 (132)
T ss_dssp TSEEEEEETGGGTSHHC
T ss_pred cceeeeeccchhccccc
Confidence 47999999998765443
No 42
>PTZ00202 tuzin; Provisional
Probab=46.98 E-value=1.5e+02 Score=30.27 Aligned_cols=96 Identities=10% Similarity=-0.038 Sum_probs=47.1
Q ss_pred ccCCCCCCceeeeeCCCC-CcccceeeeeeeccccccccCCCccchh-cccccccccee-eccccCCccCHHHHHHHHHH
Q 039731 169 HPNGTKPNTFTVNVLPPN-EEECTQIRKLHYDFHDNVGTSGNSESID-RSGELEVESIC-REQINAPQQQRSSLFSHIIA 245 (315)
Q Consensus 169 ~~Vg~~~r~~~v~~Ll~~-~~~~~~l~~i~~d~~~~~GmGGiGK~vy-~~i~~~Fe~~~-~~~s~~~~~gl~~Lq~~LL~ 245 (315)
.-+|+....-.+..++.. +..-..+..| .|+.|.||++. ..+...-...+ .-+ -. |..++.+.++.
T Consensus 263 ~FVGReaEla~Lr~VL~~~d~~~privvL-------tG~~G~GKTTLlR~~~~~l~~~qL~vN--pr--g~eElLr~LL~ 331 (550)
T PTZ00202 263 QFVSREAEESWVRQVLRRLDTAHPRIVVF-------TGFRGCGKSSLCRSAVRKEGMPAVFVD--VR--GTEDTLRSVVK 331 (550)
T ss_pred CCCCcHHHHHHHHHHHhccCCCCceEEEE-------ECCCCCCHHHHHHHHHhcCCceEEEEC--CC--CHHHHHHHHHH
Confidence 345555444444444432 2222334444 49999999543 33332222112 221 22 66788888888
Q ss_pred HhcCCCCCcCChhHHHHHHHHhh------CCcEEEEEe
Q 039731 246 KGGGLYAFLAPSDHASIQIQRRH------IRLKVSLLA 277 (315)
Q Consensus 246 ~il~~~~~~~~~~~~~~~i~~rL------~~kKvLIVL 277 (315)
.+.-.. .....+....|.+.| ++++++||+
T Consensus 332 ALGV~p--~~~k~dLLrqIqeaLl~~~~e~GrtPVLII 367 (550)
T PTZ00202 332 ALGVPN--VEACGDLLDFISEACRRAKKMNGETPLLVL 367 (550)
T ss_pred HcCCCC--cccHHHHHHHHHHHHHHHHHhCCCCEEEEE
Confidence 875321 112233334444333 256777776
No 43
>PRK13342 recombination factor protein RarA; Reviewed
Probab=44.33 E-value=26 Score=34.41 Aligned_cols=15 Identities=7% Similarity=0.109 Sum_probs=12.0
Q ss_pred CCcEEEEEeeCCCCC
Q 039731 269 IRLKVSLLASKVDSA 283 (315)
Q Consensus 269 ~~kKvLIVLDDVd~~ 283 (315)
.+++.+|++|+|+..
T Consensus 90 ~g~~~vL~IDEi~~l 104 (413)
T PRK13342 90 AGRRTILFIDEIHRF 104 (413)
T ss_pred cCCceEEEEechhhh
Confidence 447788999999865
No 44
>PRK04841 transcriptional regulator MalT; Provisional
Probab=43.94 E-value=63 Score=34.64 Aligned_cols=80 Identities=10% Similarity=-0.077 Sum_probs=39.0
Q ss_pred cccCCCccch-hccccccccceeeccc-cCCccCHHHHHHHHHHHhcC---C--C--------CCcCChhHHHHHHHHhh
Q 039731 204 VGTSGNSESI-DRSGELEVESICREQI-NAPQQQRSSLFSHIIAKGGG---L--Y--------AFLAPSDHASIQIQRRH 268 (315)
Q Consensus 204 ~GmGGiGK~v-y~~i~~~Fe~~~~~~s-~~~~~gl~~Lq~~LL~~il~---~--~--------~~~~~~~~~~~~i~~rL 268 (315)
.|.+|.||++ ..+...++. .+.+.+ ...+++...+...|+..+.. . . ....+.......+-..|
T Consensus 38 ~apaG~GKTtl~~~~~~~~~-~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 116 (903)
T PRK04841 38 TSPAGYGKTTLISQWAAGKN-NLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIEL 116 (903)
T ss_pred ECCCCCCHHHHHHHHHHhCC-CeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHH
Confidence 3999999954 344445555 332211 11122444444555555421 1 0 00011122222222333
Q ss_pred C--CcEEEEEeeCCCCCC
Q 039731 269 I--RLKVSLLASKVDSAS 284 (315)
Q Consensus 269 ~--~kKvLIVLDDVd~~~ 284 (315)
. ..+++|||||+...+
T Consensus 117 ~~~~~~~~lvlDD~h~~~ 134 (903)
T PRK04841 117 ADWHQPLYLVIDDYHLIT 134 (903)
T ss_pred hcCCCCEEEEEeCcCcCC
Confidence 2 578999999998875
No 45
>PRK08116 hypothetical protein; Validated
Probab=42.20 E-value=37 Score=31.41 Aligned_cols=17 Identities=18% Similarity=0.272 Sum_probs=11.5
Q ss_pred HHHhhCCcEEEEEeeCCC
Q 039731 264 IQRRHIRLKVSLLASKVD 281 (315)
Q Consensus 264 i~~rL~~kKvLIVLDDVd 281 (315)
+.+.+.+-. ||||||+.
T Consensus 172 ~~~~l~~~d-lLviDDlg 188 (268)
T PRK08116 172 IIRSLVNAD-LLILDDLG 188 (268)
T ss_pred HHHHhcCCC-EEEEeccc
Confidence 345566544 78999994
No 46
>PRK04195 replication factor C large subunit; Provisional
Probab=40.04 E-value=36 Score=34.25 Aligned_cols=14 Identities=21% Similarity=0.275 Sum_probs=11.3
Q ss_pred cEEEEEeeCCCCCC
Q 039731 271 LKVSLLASKVDSAS 284 (315)
Q Consensus 271 kKvLIVLDDVd~~~ 284 (315)
++-+||+|+||...
T Consensus 98 ~~kvIiIDEaD~L~ 111 (482)
T PRK04195 98 RRKLILLDEVDGIH 111 (482)
T ss_pred CCeEEEEecCcccc
Confidence 56789999998764
No 47
>cd02426 Pol_gamma_b_Cterm C-terminal domain of mitochondrial DNA polymerase gamma B subunit, which is required for processivity. Polymerase gamma replicates and repairs mitochondrial DNA. The c-terminal domain of its B subunit is strikingly similar to the anticodon-binding domain of glycyl tRNA synthetase.
Probab=39.08 E-value=22 Score=29.18 Aligned_cols=31 Identities=10% Similarity=0.111 Sum_probs=24.1
Q ss_pred cchHHHHHHHHhhCCCeEEeeC-cc---CCCCcch
Q 039731 27 DNFTSHLHAALCRKKIKTFIDE-EL---NRGDEIS 57 (315)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~D~-~~---~~G~~i~ 57 (315)
..++..|+..|+..|+.++.|+ +- .+|..+.
T Consensus 43 ~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~~ 77 (128)
T cd02426 43 RDLCQGLKNELREAGLSVWPGYLETQHSSLEQLLD 77 (128)
T ss_pred HHHHHHHHHHHHHcCCEEEeccCcccccCHHHHHH
Confidence 5678899999999999999988 32 4555543
No 48
>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []. The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=38.02 E-value=9 Score=31.04 Aligned_cols=14 Identities=14% Similarity=0.143 Sum_probs=10.9
Q ss_pred cEEEEEeeCCCCCC
Q 039731 271 LKVSLLASKVDSAS 284 (315)
Q Consensus 271 kKvLIVLDDVd~~~ 284 (315)
+..++|||+++...
T Consensus 65 ~~~il~lDEin~a~ 78 (139)
T PF07728_consen 65 KGGILVLDEINRAP 78 (139)
T ss_dssp EEEEEEESSCGG--
T ss_pred ceeEEEECCcccCC
Confidence 78999999999543
No 49
>PRK12289 GTPase RsgA; Reviewed
Probab=37.91 E-value=89 Score=30.26 Aligned_cols=46 Identities=9% Similarity=0.307 Sum_probs=26.2
Q ss_pred HHhhcCeEEEEeecccc-CChHhHHHHHHHHHHhhhCCCeeeeEEEecCCccc
Q 039731 63 AIEGSKITVIIFSKNYA-SSKWCLDELVKILECHKMNSQMVVPVFYRIDPSDV 114 (315)
Q Consensus 63 aI~~S~~~Ivv~S~~y~-~S~wcl~El~~i~~~~~~~~~~ViPIfy~v~ps~V 114 (315)
++.+++.+++|++-.=. -+.|=++.+.... ...+ +|+++=++..|+
T Consensus 86 ~~aNvD~vLlV~d~~~p~~~~~~LdR~L~~a---~~~~---ip~ILVlNK~DL 132 (352)
T PRK12289 86 PVANADQILLVFALAEPPLDPWQLSRFLVKA---ESTG---LEIVLCLNKADL 132 (352)
T ss_pred hhhcCCEEEEEEECCCCCCCHHHHHHHHHHH---HHCC---CCEEEEEEchhc
Confidence 68999999999996522 2555444433322 2233 344444566665
No 50
>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
Probab=37.86 E-value=64 Score=30.96 Aligned_cols=22 Identities=18% Similarity=0.093 Sum_probs=15.5
Q ss_pred HHHhh--CCcEEEEEeeCCCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSASS 285 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~~q 285 (315)
+-+++ ++|.|||++||+...-|
T Consensus 150 ~AEyfr~~g~~Vll~~Dsltr~a~ 173 (326)
T cd01136 150 IAEYFRDQGKDVLLLMDSLTRFAM 173 (326)
T ss_pred HHHHHHHcCCCeEEEeccchHHHH
Confidence 44444 46899999999775433
No 51
>PRK05922 type III secretion system ATPase; Validated
Probab=35.49 E-value=37 Score=33.91 Aligned_cols=21 Identities=10% Similarity=0.048 Sum_probs=15.7
Q ss_pred HHHhh--CCcEEEEEeeCCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSAS 284 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~~ 284 (315)
|-+++ +++.||+++||+..--
T Consensus 238 iAEyfrd~G~~VLl~~DslTR~A 260 (434)
T PRK05922 238 IAEYFRDQGHRVLFIMDSLSRWI 260 (434)
T ss_pred HHHHHHHcCCCEEEeccchhHHH
Confidence 44555 5699999999997653
No 52
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=34.84 E-value=25 Score=37.45 Aligned_cols=14 Identities=14% Similarity=0.145 Sum_probs=11.2
Q ss_pred CcEEEEEeeCCCCC
Q 039731 270 RLKVSLLASKVDSA 283 (315)
Q Consensus 270 ~kKvLIVLDDVd~~ 283 (315)
+++.+|+||||+..
T Consensus 108 ~~~~IL~IDEIh~L 121 (725)
T PRK13341 108 GKRTILFIDEVHRF 121 (725)
T ss_pred CCceEEEEeChhhC
Confidence 45678999999865
No 53
>PRK08149 ATP synthase SpaL; Validated
Probab=34.77 E-value=39 Score=33.68 Aligned_cols=85 Identities=6% Similarity=-0.026 Sum_probs=41.7
Q ss_pred cccccccCCCccc-hhccccccccc--ee-eccccCCccCHHHHHHHHHHHhcCCC-------CCcCCh-----hHHHHH
Q 039731 200 FHDNVGTSGNSES-IDRSGELEVES--IC-REQINAPQQQRSSLFSHIIAKGGGLY-------AFLAPS-----DHASIQ 263 (315)
Q Consensus 200 ~~~~~GmGGiGK~-vy~~i~~~Fe~--~~-~~~s~~~~~gl~~Lq~~LL~~il~~~-------~~~~~~-----~~~~~~ 263 (315)
..+++|-.|.||+ +.+.+..+-+. .| ..+.... ..+..+.++++......+ .+.... ......
T Consensus 153 ~i~I~G~sG~GKTTLl~~i~~~~~~dv~v~g~Ig~rg-~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~~~a~t 231 (428)
T PRK08149 153 RMGIFASAGCGKTSLMNMLIEHSEADVFVIGLIGERG-REVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAALVATT 231 (428)
T ss_pred EEEEECCCCCChhHHHHHHhcCCCCCeEEEEEEeeCC-ccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHHHHHHH
Confidence 5567799999994 44545443322 12 1111111 144455555655321110 111110 012223
Q ss_pred HHHhh--CCcEEEEEeeCCCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSASS 285 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~~q 285 (315)
+-+++ ++|.|||++||+...-+
T Consensus 232 iAE~fr~~G~~Vll~~DslTr~A~ 255 (428)
T PRK08149 232 VAEYFRDQGKRVVLFIDSMTRYAR 255 (428)
T ss_pred HHHHHHHcCCCEEEEccchHHHHH
Confidence 44444 57999999999976543
No 54
>PRK02551 flavoprotein NrdI; Provisional
Probab=34.29 E-value=2.2e+02 Score=24.19 Aligned_cols=119 Identities=17% Similarity=0.280 Sum_probs=61.6
Q ss_pred eEEEccccccCccchHHHHHHHHhhC--CCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeeccc-cCC--------hH
Q 039731 15 DVFLSFRGEDTRDNFTSHLHAALCRK--KIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNY-ASS--------KW 83 (315)
Q Consensus 15 dVFIS~~~~D~r~~fv~~L~~~L~~~--gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y-~~S--------~w 83 (315)
=+|+|-+|.- +.|+..|-..+.++ ++.+.. +...+.+.++- ..++...- .+++.|.| --. .|
T Consensus 6 I~Y~S~TGNt--~rFv~kL~~~~~~~~~~~~~~~---i~~~~~i~~~~-~~~~~~~p-~vli~pTY~~gG~~~~~~~~~~ 78 (154)
T PRK02551 6 LVYISLSGNT--RSFVKRLSDYLATQHKDIEVNP---INIKDLIHETT-DFFPETEP-FVAFLPTYLEGGNGIDNGDVEI 78 (154)
T ss_pred EEEEeCChhH--HHHHHHHhcHHhhcccccccee---cccccccCccc-cccccCCC-EEEEEeeecCCCCCcccCcccc
Confidence 3688887775 47999997666542 333321 11122221100 00122223 34555888 322 56
Q ss_pred hHHHHHHHHHHhhhCCCeeeeEEEecCCcccccccCchhHHHHHHHHhhc--------------CChHHHHHHHHHHHHH
Q 039731 84 CLDELVKILECHKMNSQMVVPVFYRIDPSDVRKQSGRFKDAFVKHEEQFK--------------DMPEKIQIWRAFSVQY 149 (315)
Q Consensus 84 cl~El~~i~~~~~~~~~~ViPIfy~v~ps~V~~q~g~f~~~f~~~~~~~~--------------~~~e~v~~W~~aL~~v 149 (315)
--+.+..++..... ...+.=|+ -+ -...||+.|....+.+. .+.+.+++-++.|.+.
T Consensus 79 vp~~v~dFL~~~~N-~~~~~gVi----gs----GNrNfg~~F~~aa~~ia~~~~vP~L~~fEl~GT~~Dv~~v~~~~~~~ 149 (154)
T PRK02551 79 LTTPLGDFIAYHDN-AKRCLGII----GS----GNRNFNNQYCLTAKQYAKRFGFPMLADFELRGTPSDIERIAAIIAEL 149 (154)
T ss_pred chHHHHHHHcchhh-hhheEEEE----ee----cccHHHHHHHHHHHHHHHHcCCCEEEEeeccCCHHHHHHHHHHHHHH
Confidence 66676666643322 34555555 11 12368888888776542 3456666666665554
No 55
>PRK07261 topology modulation protein; Provisional
Probab=33.86 E-value=51 Score=28.08 Aligned_cols=20 Identities=20% Similarity=0.112 Sum_probs=13.5
Q ss_pred cccccCCCccchhc-cccccc
Q 039731 202 DNVGTSGNSESIDR-SGELEV 221 (315)
Q Consensus 202 ~~~GmGGiGK~vy~-~i~~~F 221 (315)
.++|++|.||+++. ++...+
T Consensus 4 ~i~G~~GsGKSTla~~l~~~~ 24 (171)
T PRK07261 4 AIIGYSGSGKSTLARKLSQHY 24 (171)
T ss_pred EEEcCCCCCHHHHHHHHHHHh
Confidence 45699999996654 344444
No 56
>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP.; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.
Probab=33.68 E-value=40 Score=29.10 Aligned_cols=14 Identities=14% Similarity=0.173 Sum_probs=12.0
Q ss_pred cEEEEEeeCCCCCC
Q 039731 271 LKVSLLASKVDSAS 284 (315)
Q Consensus 271 kKvLIVLDDVd~~~ 284 (315)
++++||+||++...
T Consensus 118 ~~~iiviDe~~~~~ 131 (234)
T PF01637_consen 118 KKVIIVIDEFQYLA 131 (234)
T ss_dssp CCEEEEEETGGGGG
T ss_pred CcEEEEEecHHHHh
Confidence 45999999998777
No 57
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=33.61 E-value=14 Score=31.67 Aligned_cols=62 Identities=16% Similarity=0.289 Sum_probs=38.7
Q ss_pred ChHhHHHHHHHHHHhhhCCCeeeeEEEecCCcccccccCchhHHHHHHHHhhcCChHHHHHHHHHHHHHhc
Q 039731 81 SKWCLDELVKILECHKMNSQMVVPVFYRIDPSDVRKQSGRFKDAFVKHEEQFKDMPEKIQIWRAFSVQYRC 151 (315)
Q Consensus 81 S~wcl~El~~i~~~~~~~~~~ViPIfy~v~ps~V~~q~g~f~~~f~~~~~~~~~~~e~v~~W~~aL~~v~~ 151 (315)
|.|.+.||..-++..+-+.=.=+-+.++|+|-++.+... .++.+...-+++||+.|+.-=|-
T Consensus 54 s~~~Lf~LI~k~~~keikTW~~La~~LGVepp~~ek~qS---------tQKvqQYaVRLKRWM~aMHVDAF 115 (175)
T PF09441_consen 54 STFTLFELIRKLESKEIKTWAQLALELGVEPPDPEKGQS---------TQKVQQYAVRLKRWMRAMHVDAF 115 (175)
T ss_pred hHHHHHHHHHHHhhhhHhHHHHHHHHhCCCCCCcccccc---------hHHHHHHHHHHHHHHHHhhHHHH
Confidence 578888888776654433323345667899988765221 12222335678899999875554
No 58
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=33.17 E-value=37 Score=34.03 Aligned_cols=20 Identities=25% Similarity=0.215 Sum_probs=15.2
Q ss_pred HHHhh--CCcEEEEEeeCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSA 283 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~ 283 (315)
+-+++ +++.|||++||+..-
T Consensus 243 iAEyfrd~G~~VLl~~DslTR~ 264 (444)
T PRK08972 243 IAEYFRDQGLNVLLLMDSLTRY 264 (444)
T ss_pred HHHHHHHcCCCEEEEEcChHHH
Confidence 44555 579999999998754
No 59
>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=31.57 E-value=1.2e+02 Score=32.46 Aligned_cols=72 Identities=14% Similarity=0.038 Sum_probs=39.0
Q ss_pred ceeeeeeeccccccccCCCccchhcccccccccee-eccccCCccCHHHHHHHHHHHhcCCCCCcCChhHHHHHHHHhhC
Q 039731 191 TQIRKLHYDFHDNVGTSGNSESIDRSGELEVESIC-REQINAPQQQRSSLFSHIIAKGGGLYAFLAPSDHASIQIQRRHI 269 (315)
Q Consensus 191 ~~l~~i~~d~~~~~GmGGiGK~vy~~i~~~Fe~~~-~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~~~~~~~i~~rL~ 269 (315)
.+|.-++ |..|+||++.+.+.-+=-+.. .|+--..+.....+.+++..-+. ...-|.
T Consensus 326 kKilLL~-------GppGlGKTTLAHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq---------------~~s~l~ 383 (877)
T KOG1969|consen 326 KKILLLC-------GPPGLGKTTLAHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQ---------------NHSVLD 383 (877)
T ss_pred cceEEee-------cCCCCChhHHHHHHHHhcCceEEEecccccccHHHHHHHHHHHHh---------------hccccc
Confidence 3555566 999999988776543322222 33211111234445555544332 122332
Q ss_pred --CcEEEEEeeCCCCCC
Q 039731 270 --RLKVSLLASKVDSAS 284 (315)
Q Consensus 270 --~kKvLIVLDDVd~~~ 284 (315)
.+.+-||+|.+|-..
T Consensus 384 adsrP~CLViDEIDGa~ 400 (877)
T KOG1969|consen 384 ADSRPVCLVIDEIDGAP 400 (877)
T ss_pred cCCCcceEEEecccCCc
Confidence 567788999888654
No 60
>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional
Probab=30.58 E-value=96 Score=30.69 Aligned_cols=14 Identities=14% Similarity=0.161 Sum_probs=11.4
Q ss_pred CCcEEEEEeeCCCC
Q 039731 269 IRLKVSLLASKVDS 282 (315)
Q Consensus 269 ~~kKvLIVLDDVd~ 282 (315)
+.+...|++||||.
T Consensus 210 ~~aPcVLFIDEIDA 223 (413)
T PLN00020 210 KGKMSCLFINDLDA 223 (413)
T ss_pred cCCCeEEEEehhhh
Confidence 45789999999984
No 61
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=30.14 E-value=58 Score=30.10 Aligned_cols=28 Identities=18% Similarity=0.134 Sum_probs=20.6
Q ss_pred HHHHHhhCCcEEEEEeeCCCCCCCcccc
Q 039731 262 IQIQRRHIRLKVSLLASKVDSASSPELS 289 (315)
Q Consensus 262 ~~i~~rL~~kKvLIVLDDVd~~~qle~~ 289 (315)
..+...+.+.++.+|+|+..+..|++..
T Consensus 99 e~l~~~~~~~~~~~v~~~~~~~~~~~~~ 126 (305)
T TIGR00635 99 ELLYPAMEDFRLDIVIGKGPSARSVRLD 126 (305)
T ss_pred HHhhHHHhhhheeeeeccCccccceeec
Confidence 4456666777888999988888777654
No 62
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=29.74 E-value=53 Score=32.98 Aligned_cols=21 Identities=19% Similarity=0.124 Sum_probs=15.2
Q ss_pred HHHhh--CCcEEEEEeeCCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSAS 284 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~~ 284 (315)
|-+++ +++.||+++||+...-
T Consensus 245 iAEyfrd~G~~Vll~~DslTr~A 267 (450)
T PRK06002 245 IAEYFRDRGENVLLIVDSVTRFA 267 (450)
T ss_pred HHHHHHHcCCCEEEeccchHHHH
Confidence 44444 4689999999987653
No 63
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=29.68 E-value=49 Score=32.29 Aligned_cols=24 Identities=25% Similarity=0.440 Sum_probs=13.5
Q ss_pred EEEEeeccccCChHhHHHHHHHHH
Q 039731 70 TVIIFSKNYASSKWCLDELVKILE 93 (315)
Q Consensus 70 ~Ivv~S~~y~~S~wcl~El~~i~~ 93 (315)
.+++.-||-..-.|-...+...++
T Consensus 32 ~l~l~~Pn~F~~~wi~~~y~~~i~ 55 (405)
T TIGR00362 32 TLIISVPNEFAKDWIEKNYLDLIE 55 (405)
T ss_pred EEEEEeCCHHHHHHHHHHHHHHHH
Confidence 345555776666777665544333
No 64
>PF03720 UDPG_MGDP_dh_C: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; InterPro: IPR014027 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the C-terminal substrate-binding domain of these enzymes. Structural studies indicate that this domain forms an incomplete dinucleotide binding fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3GG2_D 1DLI_A 1DLJ_A 2Y0E_D 2Y0D_B 2Y0C_D 1MV8_B 1MUU_A 1MFZ_C 3TDK_B ....
Probab=29.08 E-value=69 Score=25.00 Aligned_cols=56 Identities=16% Similarity=0.284 Sum_probs=34.3
Q ss_pred cccCccchHHHHHHHHhhCCCeEEeeC-ccC----------CCCcchHHHHHHHhhcCeEEEEeecc
Q 039731 22 GEDTRDNFTSHLHAALCRKKIKTFIDE-ELN----------RGDEISPAILKAIEGSKITVIIFSKN 77 (315)
Q Consensus 22 ~~D~r~~fv~~L~~~L~~~gi~~f~D~-~~~----------~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (315)
..|+|.+=+-.|++.|.+.|+.+.+.+ -+. .+-.+.+.+.++++.++..|+.-...
T Consensus 11 ~~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~h~ 77 (106)
T PF03720_consen 11 TDDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATDHD 77 (106)
T ss_dssp SS--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS--G
T ss_pred CcccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEecCH
Confidence 357899999999999999999987765 221 12223345678888888876664433
No 65
>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.
Probab=28.85 E-value=41 Score=30.04 Aligned_cols=15 Identities=27% Similarity=0.435 Sum_probs=11.2
Q ss_pred ccCCCcc-----chhccccc
Q 039731 205 GTSGNSE-----SIDRSGEL 219 (315)
Q Consensus 205 GmGGiGK-----~vy~~i~~ 219 (315)
|-.|.|| ++++.+..
T Consensus 41 G~~G~GKTHLL~Ai~~~~~~ 60 (219)
T PF00308_consen 41 GPSGLGKTHLLQAIANEAQK 60 (219)
T ss_dssp ESTTSSHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHh
Confidence 9999999 56665543
No 66
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=28.67 E-value=53 Score=32.66 Aligned_cols=24 Identities=13% Similarity=0.364 Sum_probs=14.4
Q ss_pred eEEEEeeccccCChHhHHHHHHHH
Q 039731 69 ITVIIFSKNYASSKWCLDELVKIL 92 (315)
Q Consensus 69 ~~Ivv~S~~y~~S~wcl~El~~i~ 92 (315)
-.+++.-||-....|-...+...+
T Consensus 37 ~~l~l~vPn~F~~~wi~~~y~~~I 60 (450)
T PRK00149 37 NTLTLYVPNRFVKDWIEKNYLDLI 60 (450)
T ss_pred CEEEEEECCHHHHHHHHHHHHHHH
Confidence 356666677666678765444433
No 67
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.20 E-value=2.6e+02 Score=21.25 Aligned_cols=57 Identities=11% Similarity=0.155 Sum_probs=34.3
Q ss_pred chHHHHHHHHhhCCCeEEeeCccCCCC-cchHHHHHHHhhcCeEEEEeeccccCChHhH
Q 039731 28 NFTSHLHAALCRKKIKTFIDEELNRGD-EISPAILKAIEGSKITVIIFSKNYASSKWCL 85 (315)
Q Consensus 28 ~fv~~L~~~L~~~gi~~f~D~~~~~G~-~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl 85 (315)
.....+...+++.|...-++. -..|. .-...|...|.+++++|++.+----...|..
T Consensus 10 ~~~~~~~~~~~~~G~~~~~hg-~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~v 67 (97)
T PF10087_consen 10 DRERRYKRILEKYGGKLIHHG-RDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKV 67 (97)
T ss_pred ccHHHHHHHHHHcCCEEEEEe-cCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHH
Confidence 356678888899999854441 11121 1122477889999998888644443444443
No 68
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=28.17 E-value=2.4e+02 Score=21.80 Aligned_cols=69 Identities=16% Similarity=0.138 Sum_probs=43.4
Q ss_pred HHHHHHHHhhCCCeE-EeeCccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHHHHhhhCCCeeeeEE
Q 039731 30 TSHLHAALCRKKIKT-FIDEELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKILECHKMNSQMVVPVF 106 (315)
Q Consensus 30 v~~L~~~L~~~gi~~-f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~ViPIf 106 (315)
...|...|++.|+.+ ++|-.... +++.+++.+.+--++.+|-.+. |...+...+.+..+.....+.-|+
T Consensus 17 l~~la~~l~~~G~~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~---~~~~~~~~l~~~~k~~~p~~~iv~ 86 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDANVPP-----EELVEALRAERPDVVGISVSMT---PNLPEAKRLARAIKERNPNIPIVV 86 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSS---THHHHHHHHHHHHHTTCTTSEEEE
T ss_pred HHHHHHHHHHCCCeEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCc---CcHHHHHHHHHHHHhcCCCCEEEE
Confidence 456888999999987 45543322 6777888888888888876543 445555555555444433333333
No 69
>cd07363 45_DOPA_Dioxygenase The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine. This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine (4,5-DOPA). The reaction results in the opening of the cyclic ring between carbons 4 and 5 and producing an unstable seco-DOPA that rearranges to betalamic acid. 4,5-DOPA Dioxygenase is a key enzyme in the biosynthetic pathway of the plant pigment betalain. Homologs of DODA are present not only in betalain-producing plants but also in bacteria and archaea. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated ca
Probab=28.09 E-value=2.7e+02 Score=25.40 Aligned_cols=69 Identities=14% Similarity=0.083 Sum_probs=48.4
Q ss_pred cchHHHHHHHHhhCCCeEEeeC--ccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHHHHhhh
Q 039731 27 DNFTSHLHAALCRKKIKTFIDE--ELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKILECHKM 97 (315)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~D~--~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~~~~~ 97 (315)
..++.+|.+.|...|+.+-.+. .+.-|--+. +.-...+.++-||.+|.+...+..-..+|-++++..+.
T Consensus 80 ~eLa~~i~~~l~~~gi~~~~~~~~~lDHG~~vP--L~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l~~ 150 (253)
T cd07363 80 PELAERVAELLKAAGIPARLDPERGLDHGAWVP--LKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPLRD 150 (253)
T ss_pred HHHHHHHHHHHHhcCCCccccCCcCCcccHHHH--HHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhhhh
Confidence 4699999999999999876543 343443322 22223345788999999988777777899998876543
No 70
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=27.57 E-value=2.8e+02 Score=21.33 Aligned_cols=60 Identities=13% Similarity=0.058 Sum_probs=40.8
Q ss_pred HHHHHHhhCCCeEEeeCcc--CCCCcchHHH---HHHHhhcCeEEEEeeccccCChHhHHHHHHHHH
Q 039731 32 HLHAALCRKKIKTFIDEEL--NRGDEISPAI---LKAIEGSKITVIIFSKNYASSKWCLDELVKILE 93 (315)
Q Consensus 32 ~L~~~L~~~gi~~f~D~~~--~~G~~i~~~i---~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~ 93 (315)
...+.|+.+|..+.---.+ ..|.++.+-+ ...+..|+..+++ |++-.|.=|.-|+..+..
T Consensus 20 ~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i~~l--~gWe~S~GA~~E~~~A~~ 84 (92)
T PF14359_consen 20 AAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAIYML--PGWENSRGARLEHELAKK 84 (92)
T ss_pred HHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEEEEc--CCcccCcchHHHHHHHHH
Confidence 4667889999766533233 5565555433 3456677754443 999999999999988854
No 71
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=26.96 E-value=3.3e+02 Score=24.25 Aligned_cols=98 Identities=17% Similarity=0.258 Sum_probs=56.9
Q ss_pred EEEccccccC--ccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhh---------------------------
Q 039731 16 VFLSFRGEDT--RDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEG--------------------------- 66 (315)
Q Consensus 16 VFIS~~~~D~--r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~--------------------------- 66 (315)
.||.+-|-|- +.+.+..|++.|+.+|+.|.+=.+ +.|.++.+.|.+.+-+
T Consensus 4 ~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~trE-P~~~~ige~iR~~ll~~~~~~~~~~e~lLfaadR~~h~~~~i~ 82 (208)
T COG0125 4 MFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTRE-PGGTPIGEKIRELLLNGEEKLSPKAEALLFAADRAQHLEEVIK 82 (208)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC-CCCChHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5888866663 356889999999999988655431 1122222222221111
Q ss_pred --cCeEEEEeeccccCChHhHH--------HHHHHHHHh-hhCCCeeeeEEEecCCccc
Q 039731 67 --SKITVIIFSKNYASSKWCLD--------ELVKILECH-KMNSQMVVPVFYRIDPSDV 114 (315)
Q Consensus 67 --S~~~Ivv~S~~y~~S~wcl~--------El~~i~~~~-~~~~~~ViPIfy~v~ps~V 114 (315)
-.-.-+|++..|.-|..+.. ++...+... ..+-.+-+-+|++|+|..-
T Consensus 83 pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~a 141 (208)
T COG0125 83 PALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVA 141 (208)
T ss_pred HhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHH
Confidence 01124888999999988866 233333222 1222466778889999653
No 72
>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=26.95 E-value=95 Score=33.30 Aligned_cols=22 Identities=9% Similarity=0.063 Sum_probs=16.2
Q ss_pred HHHhhCCcEEEEEeeCCCCCCC
Q 039731 264 IQRRHIRLKVSLLASKVDSASS 285 (315)
Q Consensus 264 i~~rL~~kKvLIVLDDVd~~~q 285 (315)
.-+.+....-+|||||+|-.-.
T Consensus 487 fse~~~~~PSiIvLDdld~l~~ 508 (952)
T KOG0735|consen 487 FSEALWYAPSIIVLDDLDCLAS 508 (952)
T ss_pred HHHHHhhCCcEEEEcchhhhhc
Confidence 3456677889999999975543
No 73
>TIGR00418 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..
Probab=26.85 E-value=1.4e+02 Score=30.52 Aligned_cols=61 Identities=13% Similarity=0.207 Sum_probs=42.3
Q ss_pred CceeEEEccccccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeec
Q 039731 12 SKYDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSK 76 (315)
Q Consensus 12 ~~ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (315)
..++|||-.-+++. ...+..|...|+++|++|-+|. .+..+...+..|-..---.++|+.+
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~---~~~sl~~q~k~A~~~g~~~~iiiG~ 529 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDD---RNERLGKKIREAQKQKIPYMLVVGD 529 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEEC---CCCCHHHHHHHHHhcCCCEEEEEch
Confidence 45788887766554 4688899999999999999985 2456666666664433334555543
No 74
>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]
Probab=26.45 E-value=56 Score=30.38 Aligned_cols=9 Identities=22% Similarity=0.619 Sum_probs=8.2
Q ss_pred ccCCCccch
Q 039731 205 GTSGNSESI 213 (315)
Q Consensus 205 GmGGiGK~v 213 (315)
||.|+||++
T Consensus 55 GpPG~GKTT 63 (333)
T KOG0991|consen 55 GPPGTGKTT 63 (333)
T ss_pred CCCCCchhh
Confidence 999999965
No 75
>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].
Probab=26.43 E-value=1.1e+02 Score=29.13 Aligned_cols=79 Identities=18% Similarity=0.109 Sum_probs=42.3
Q ss_pred ccccCCCccc-hhcccccc----ccce---e----eccccCCccCHHHHHHHHHHHhcCCCCCcCChhHHHHHHHHhhCC
Q 039731 203 NVGTSGNSES-IDRSGELE----VESI---C----REQINAPQQQRSSLFSHIIAKGGGLYAFLAPSDHASIQIQRRHIR 270 (315)
Q Consensus 203 ~~GmGGiGK~-vy~~i~~~----Fe~~---~----~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~~~~~~~~~i~~rL~~ 270 (315)
+||-.|+||+ +.+++... ++.- | ++.-... +...+-..||..+.--...-.+.......+..-|+.
T Consensus 66 ivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p--~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~ 143 (302)
T PF05621_consen 66 IVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEP--DERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRR 143 (302)
T ss_pred EecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCC--ChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHH
Confidence 4599999994 44444332 2211 1 1211222 667888888888764211223444444454455544
Q ss_pred -cEEEEEeeCCCCC
Q 039731 271 -LKVSLLASKVDSA 283 (315)
Q Consensus 271 -kKvLIVLDDVd~~ 283 (315)
+-=+||+|.|.+.
T Consensus 144 ~~vrmLIIDE~H~l 157 (302)
T PF05621_consen 144 LGVRMLIIDEFHNL 157 (302)
T ss_pred cCCcEEEeechHHH
Confidence 2236778888653
No 76
>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=25.99 E-value=17 Score=33.83 Aligned_cols=16 Identities=13% Similarity=0.121 Sum_probs=12.0
Q ss_pred CCcEEEEEeeCCCCCC
Q 039731 269 IRLKVSLLASKVDSAS 284 (315)
Q Consensus 269 ~~kKvLIVLDDVd~~~ 284 (315)
.+||.++.+||++-..
T Consensus 98 ~~k~lv~fiDDlN~p~ 113 (272)
T PF12775_consen 98 GGKKLVLFIDDLNMPQ 113 (272)
T ss_dssp SSSEEEEEEETTT-S-
T ss_pred CCcEEEEEecccCCCC
Confidence 4689999999998654
No 77
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=24.77 E-value=1.1e+02 Score=25.37 Aligned_cols=54 Identities=15% Similarity=0.173 Sum_probs=38.0
Q ss_pred eeEEEccccccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcC
Q 039731 14 YDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSK 68 (315)
Q Consensus 14 ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~ 68 (315)
.++|+-..+.=....++..|..++..+|+-++.|-|. +|+.|...|.+.+.++.
T Consensus 30 ~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D~-~Ge~Irk~l~~~l~~~~ 83 (127)
T COG1658 30 AGVIITNGSAINSLETIELIKKAQKYKGVIILTDPDR-KGERIRKKLKEYLPGAK 83 (127)
T ss_pred CceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCCc-chHHHHHHHHHHhcccc
Confidence 4566665443111568888888888999999888764 58888877777776633
No 78
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=24.63 E-value=2e+02 Score=21.14 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=29.8
Q ss_pred cchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeecc
Q 039731 27 DNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKN 77 (315)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (315)
..++..|...|+..|+++.+|.. +..+...+..|-..---+++++.++
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~---~~~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDR---NERPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCCcccchhHHHhcCCCEEEEECCc
Confidence 35788899999999999999861 2344444444433333345555443
No 79
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=24.16 E-value=75 Score=31.68 Aligned_cols=24 Identities=17% Similarity=0.271 Sum_probs=13.8
Q ss_pred EEEEeeccccCChHhHHHHHHHHH
Q 039731 70 TVIIFSKNYASSKWCLDELVKILE 93 (315)
Q Consensus 70 ~Ivv~S~~y~~S~wcl~El~~i~~ 93 (315)
.+++.-|+-....|-...+...++
T Consensus 34 ~~~l~~p~~f~~~~i~~~~~~~i~ 57 (440)
T PRK14088 34 KVVFSVGNLFIKEWLEKKYGSVLS 57 (440)
T ss_pred EEEEEeCCHHHHHHHHHHHHHHHH
Confidence 355555766666787665544433
No 80
>TIGR01287 nifH nitrogenase iron protein. This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.
Probab=23.85 E-value=36 Score=31.08 Aligned_cols=10 Identities=30% Similarity=0.435 Sum_probs=8.2
Q ss_pred cccCCCccch
Q 039731 204 VGTSGNSESI 213 (315)
Q Consensus 204 ~GmGGiGK~v 213 (315)
.|-||+||++
T Consensus 6 ~gKGGVGKTT 15 (275)
T TIGR01287 6 YGKGGIGKST 15 (275)
T ss_pred eCCCcCcHHH
Confidence 3999999954
No 81
>PRK12608 transcription termination factor Rho; Provisional
Probab=23.69 E-value=1.8e+02 Score=28.61 Aligned_cols=81 Identities=7% Similarity=-0.088 Sum_probs=41.5
Q ss_pred cccccCCCccchhc-c----ccccc-ccee--eccccCCccCHHHHHHHHHHHhcCCCCCcC------ChhHHHHHHHHh
Q 039731 202 DNVGTSGNSESIDR-S----GELEV-ESIC--REQINAPQQQRSSLFSHIIAKGGGLYAFLA------PSDHASIQIQRR 267 (315)
Q Consensus 202 ~~~GmGGiGK~vy~-~----i~~~F-e~~~--~~~s~~~~~gl~~Lq~~LL~~il~~~~~~~------~~~~~~~~i~~r 267 (315)
.|+|-.|.||++.- . +..+- +..| .-+.+.. ..+.++++.++..+........ -...+..+.+..
T Consensus 137 LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~-~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~Ae~f 215 (380)
T PRK12608 137 LIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERP-EEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERAKRL 215 (380)
T ss_pred EEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCC-CCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHHHHH
Confidence 35699999995432 2 22222 3334 1222222 2667788888765542111111 111222333222
Q ss_pred -hCCcEEEEEeeCCCCC
Q 039731 268 -HIRLKVSLLASKVDSA 283 (315)
Q Consensus 268 -L~~kKvLIVLDDVd~~ 283 (315)
=.++.|+||+|++...
T Consensus 216 ~~~GkdVVLvlDsltr~ 232 (380)
T PRK12608 216 VEQGKDVVILLDSLTRL 232 (380)
T ss_pred HHcCCCEEEEEeCcHHH
Confidence 2468999999999854
No 82
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=23.43 E-value=59 Score=30.01 Aligned_cols=39 Identities=8% Similarity=0.004 Sum_probs=23.6
Q ss_pred hhHHHHHHHHhhCCcEEEEEeeCCCC------CCCcccccCCCCCcc
Q 039731 257 SDHASIQIQRRHIRLKVSLLASKVDS------ASSPELSTSDKIEPK 297 (315)
Q Consensus 257 ~~~~~~~i~~rL~~kKvLIVLDDVd~------~~qle~~~~~~~~~~ 297 (315)
.......|+. +..|++|.+||..= -..|+.+....+|.+
T Consensus 94 l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~ 138 (249)
T PF05673_consen 94 LPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEAR 138 (249)
T ss_pred HHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccC
Confidence 3333444442 44789999999751 235666666777654
No 83
>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=23.42 E-value=2e+02 Score=28.55 Aligned_cols=79 Identities=13% Similarity=0.210 Sum_probs=54.2
Q ss_pred ccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHHHHhhhCCCeeeeEEEecCCcccccccCchhHHHHHH
Q 039731 49 ELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKILECHKMNSQMVVPVFYRIDPSDVRKQSGRFKDAFVKH 128 (315)
Q Consensus 49 ~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~~~~~~~~~ViPIfy~v~ps~V~~q~g~f~~~f~~~ 128 (315)
.+.+|-.+...+..-++.++..|++|-++=.. .-+|+..++...+.....+=-|+=+.+.-+-.+....||...+..
T Consensus 164 risR~ydF~~v~~WFaeR~D~IiLlfD~hKLD---IsdEf~~vi~aLkG~EdkiRVVLNKADqVdtqqLmRVyGALmWsl 240 (532)
T KOG1954|consen 164 RISRGYDFTGVLEWFAERVDRIILLFDAHKLD---ISDEFKRVIDALKGHEDKIRVVLNKADQVDTQQLMRVYGALMWSL 240 (532)
T ss_pred cccccCChHHHHHHHHHhccEEEEEechhhcc---ccHHHHHHHHHhhCCcceeEEEeccccccCHHHHHHHHHHHHHhh
Confidence 36678888889999999999999999998775 347999988887665554444444433333333445666555554
Q ss_pred HH
Q 039731 129 EE 130 (315)
Q Consensus 129 ~~ 130 (315)
.+
T Consensus 241 gk 242 (532)
T KOG1954|consen 241 GK 242 (532)
T ss_pred hh
Confidence 43
No 84
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=23.34 E-value=85 Score=31.43 Aligned_cols=20 Identities=15% Similarity=0.140 Sum_probs=12.8
Q ss_pred HHHHhhCCcEEEEEeeCCCCC
Q 039731 263 QIQRRHIRLKVSLLASKVDSA 283 (315)
Q Consensus 263 ~i~~rL~~kKvLIVLDDVd~~ 283 (315)
.++++++. --+|||||+...
T Consensus 199 ~~~~~~~~-~dvLiIDDiq~l 218 (450)
T PRK14087 199 QFKNEICQ-NDVLIIDDVQFL 218 (450)
T ss_pred HHHHHhcc-CCEEEEeccccc
Confidence 34555554 457888999654
No 85
>PRK13236 nitrogenase reductase; Reviewed
Probab=23.26 E-value=46 Score=31.12 Aligned_cols=9 Identities=33% Similarity=0.523 Sum_probs=7.8
Q ss_pred ccCCCccch
Q 039731 205 GTSGNSESI 213 (315)
Q Consensus 205 GmGGiGK~v 213 (315)
|-|||||++
T Consensus 13 GKGGVGKTt 21 (296)
T PRK13236 13 GKGGIGKST 21 (296)
T ss_pred CCCcCCHHH
Confidence 999999943
No 86
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=23.17 E-value=89 Score=31.26 Aligned_cols=18 Identities=17% Similarity=0.093 Sum_probs=14.1
Q ss_pred CCcEEEEEeeCCCCCCCc
Q 039731 269 IRLKVSLLASKVDSASSP 286 (315)
Q Consensus 269 ~~kKvLIVLDDVd~~~ql 286 (315)
+++.|||++||+..--+-
T Consensus 243 ~g~~Vll~~Dsltr~a~A 260 (434)
T PRK07196 243 KGHDVLLLVDSLTRYAMA 260 (434)
T ss_pred ccCCEEEeecchhHHHhh
Confidence 468999999999765443
No 87
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=23.12 E-value=77 Score=31.88 Aligned_cols=20 Identities=20% Similarity=0.109 Sum_probs=15.1
Q ss_pred HHHhh--CCcEEEEEeeCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSA 283 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~ 283 (315)
+-+++ +++.|||++||+..-
T Consensus 249 iAEyfrd~G~~VLl~~DslTR~ 270 (451)
T PRK05688 249 IAEYFRDKGKNVLLLMDSLTRF 270 (451)
T ss_pred HHHHHHHCCCCEEEEecchhHH
Confidence 44544 568999999998754
No 88
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=22.95 E-value=59 Score=26.85 Aligned_cols=35 Identities=26% Similarity=0.520 Sum_probs=22.9
Q ss_pred cchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHH
Q 039731 55 EISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKI 91 (315)
Q Consensus 55 ~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i 91 (315)
.+...+.++|..-...|++++..|-.+ |+.||...
T Consensus 59 ~~~~~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~ 93 (130)
T PF11074_consen 59 ELIEALIKAIGSIYGSIVVYNKSFEKT--RLKELAEL 93 (130)
T ss_pred HHHHHHHHHhhhhcCeEEEechHHHHH--HHHHHHHH
Confidence 344455556655546778887777655 78887766
No 89
>cd00859 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=22.64 E-value=2.7e+02 Score=19.68 Aligned_cols=59 Identities=22% Similarity=0.193 Sum_probs=33.8
Q ss_pred eeEEEccccccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeec
Q 039731 14 YDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSK 76 (315)
Q Consensus 14 ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (315)
.||||-..+.+. ..-+-.+...|+..|+++.++.. +..+...+..|-...-..++++.+
T Consensus 2 ~~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~---~~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 2 VDVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYG---GRKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred CcEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecC---CCCHHHHHHHHHHcCCCEEEEEcH
Confidence 367766544432 23466788999999999988651 123444444443332234555544
No 90
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=22.27 E-value=31 Score=31.68 Aligned_cols=11 Identities=27% Similarity=0.302 Sum_probs=8.8
Q ss_pred ccccCCCccch
Q 039731 203 NVGTSGNSESI 213 (315)
Q Consensus 203 ~~GmGGiGK~v 213 (315)
++|-||+||++
T Consensus 6 ~~gKGGVGKTT 16 (279)
T PRK13230 6 FYGKGGIGKST 16 (279)
T ss_pred EECCCCCcHHH
Confidence 44999999954
No 91
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=22.10 E-value=3.3e+02 Score=24.85 Aligned_cols=69 Identities=17% Similarity=0.176 Sum_probs=42.7
Q ss_pred cchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeeccccCChHhHHHHHHHHHHhhhCC
Q 039731 27 DNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNYASSKWCLDELVKILECHKMNS 99 (315)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wcl~El~~i~~~~~~~~ 99 (315)
......|.+..+.++ .-|+|=++..++....++.+.-.+-. +|+|-+...++|.++|+..++......+
T Consensus 78 ~~~i~ll~~la~~~~-~d~iDiEl~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~ 146 (231)
T COG0710 78 EEYIELLKKLAELNG-PDYIDIELSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLG 146 (231)
T ss_pred HHHHHHHHHHHhhcC-CCEEEEEccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhC
Confidence 345556655555555 45666444433332223332222222 8999999999999999999998875544
No 92
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=22.10 E-value=1.3e+02 Score=29.98 Aligned_cols=20 Identities=15% Similarity=0.124 Sum_probs=14.8
Q ss_pred HHHhh--CCcEEEEEeeCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSA 283 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~ 283 (315)
+-+++ .+++||+++||+..-
T Consensus 226 ~AE~f~~~g~~Vl~~~Dsltr~ 247 (422)
T TIGR02546 226 IAEYFRDQGKRVLLMMDSLTRF 247 (422)
T ss_pred HHHHHHHCCCcEEEEEeCchHH
Confidence 44554 458999999999854
No 93
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=21.96 E-value=2e+02 Score=22.32 Aligned_cols=61 Identities=23% Similarity=0.329 Sum_probs=34.3
Q ss_pred eEEEccccccCccchHHHHHHHHhhCCCeEEeeC---------cc-----CCCCcchHHHHHHHhhcCeEEEEeecc
Q 039731 15 DVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDE---------EL-----NRGDEISPAILKAIEGSKITVIIFSKN 77 (315)
Q Consensus 15 dVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~---------~~-----~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (315)
.||+|.+..|. . -...+.+.|.+.|+++|--. .+ .....-.+++.+.|++-.+.++|-.++
T Consensus 2 ~vl~s~~~~~k-~-~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn~~~ 76 (110)
T cd01424 2 TVFISVADRDK-P-EAVEIAKRLAELGFKLVATEGTAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVINTPS 76 (110)
T ss_pred eEEEEEEcCcH-h-HHHHHHHHHHHCCCEEEEchHHHHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEECCC
Confidence 37899987763 3 34466678888888875421 00 000011245666666666666665443
No 94
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=21.93 E-value=44 Score=26.00 Aligned_cols=22 Identities=14% Similarity=-0.022 Sum_probs=15.5
Q ss_pred ccccCCCccchhc-cccccccce
Q 039731 203 NVGTSGNSESIDR-SGELEVESI 224 (315)
Q Consensus 203 ~~GmGGiGK~vy~-~i~~~Fe~~ 224 (315)
+.|..|.||+++. .+..+|...
T Consensus 4 I~G~~gsGKST~a~~La~~~~~~ 26 (121)
T PF13207_consen 4 ISGPPGSGKSTLAKELAERLGFP 26 (121)
T ss_dssp EEESTTSSHHHHHHHHHHHHTCE
T ss_pred EECCCCCCHHHHHHHHHHHHCCe
Confidence 4599999996665 466666543
No 95
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=21.65 E-value=1.1e+02 Score=26.82 Aligned_cols=21 Identities=5% Similarity=-0.070 Sum_probs=13.2
Q ss_pred HHHHhhCCcEEEEEeeCCCCC
Q 039731 263 QIQRRHIRLKVSLLASKVDSA 283 (315)
Q Consensus 263 ~i~~rL~~kKvLIVLDDVd~~ 283 (315)
.+...+..+-=+||+|.+...
T Consensus 99 ~~~~~~~~~~~lvVIDsi~al 119 (225)
T PRK09361 99 KAEKLAKENVGLIVLDSATSL 119 (225)
T ss_pred HHHHHHHhcccEEEEeCcHHH
Confidence 333334355668999998644
No 96
>PLN03025 replication factor C subunit; Provisional
Probab=21.60 E-value=87 Score=29.47 Aligned_cols=14 Identities=14% Similarity=0.188 Sum_probs=10.6
Q ss_pred cEEEEEeeCCCCCC
Q 039731 271 LKVSLLASKVDSAS 284 (315)
Q Consensus 271 kKvLIVLDDVd~~~ 284 (315)
+.-+|+||++|...
T Consensus 99 ~~kviiiDE~d~lt 112 (319)
T PLN03025 99 RHKIVILDEADSMT 112 (319)
T ss_pred CeEEEEEechhhcC
Confidence 45678999998763
No 97
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=21.16 E-value=2.1e+02 Score=28.29 Aligned_cols=62 Identities=18% Similarity=0.209 Sum_probs=41.3
Q ss_pred CCceeEEEccccccCccchHHHHHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeec
Q 039731 11 QSKYDVFLSFRGEDTRDNFTSHLHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSK 76 (315)
Q Consensus 11 ~~~ydVFIS~~~~D~r~~fv~~L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (315)
....||||-+-+.+. ...+-.+.+.|+++|+++-+|. .+..+...+..|-+.--..++|+.+
T Consensus 323 ~~~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~---~~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 323 KQSIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDL---SSSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEee---CCCCHHHHHHHHHHcCCCEEEEEec
Confidence 345789998755543 3567789999999999988764 2345666666665544445666554
No 98
>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=21.04 E-value=1.3e+02 Score=29.79 Aligned_cols=20 Identities=20% Similarity=0.107 Sum_probs=14.9
Q ss_pred HHHhh--CCcEEEEEeeCCCCC
Q 039731 264 IQRRH--IRLKVSLLASKVDSA 283 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~ 283 (315)
+-+++ +++.|||++||+..-
T Consensus 218 iAEyfr~~G~~Vll~~Dsltr~ 239 (411)
T TIGR03496 218 IAEYFRDQGKDVLLLMDSLTRF 239 (411)
T ss_pred HHHHHHHCCCCEEEEEeChHHH
Confidence 34444 578999999998754
No 99
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=20.96 E-value=3.6e+02 Score=20.44 Aligned_cols=47 Identities=11% Similarity=0.187 Sum_probs=35.2
Q ss_pred HHHHHhhCCCeEEeeCccCCCCcchHHHHHHHhhcCeEEEEeeccccCC
Q 039731 33 LHAALCRKKIKTFIDEELNRGDEISPAILKAIEGSKITVIIFSKNYASS 81 (315)
Q Consensus 33 L~~~L~~~gi~~f~D~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S 81 (315)
+...|+-.|+..+... ...+.+...+.+.++...+.|++++++++..
T Consensus 9 ~v~gFrLaGv~~~~~~--~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~ 55 (95)
T PF01990_consen 9 TVLGFRLAGVEGVYVN--TDPEEAEEALKELLKDEDVGIIIITEDLAEK 55 (95)
T ss_dssp HHHHHHHTTSEEEEES--HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT
T ss_pred HHHHHHHcCCCCccCC--CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH
Confidence 4456778899988764 1234556677777889999999999998874
No 100
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=20.50 E-value=55 Score=31.48 Aligned_cols=13 Identities=8% Similarity=0.238 Sum_probs=10.7
Q ss_pred cEEEEEeeCCCCC
Q 039731 271 LKVSLLASKVDSA 283 (315)
Q Consensus 271 kKvLIVLDDVd~~ 283 (315)
...+|+|||+|..
T Consensus 215 ~p~il~iDEiD~l 227 (364)
T TIGR01242 215 APSIIFIDEIDAI 227 (364)
T ss_pred CCcEEEhhhhhhh
Confidence 4579999999875
No 101
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=20.45 E-value=1.3e+02 Score=28.36 Aligned_cols=27 Identities=15% Similarity=0.118 Sum_probs=18.3
Q ss_pred HHHHHhhCCcEEEEEeeCCCCCCCccc
Q 039731 262 IQIQRRHIRLKVSLLASKVDSASSPEL 288 (315)
Q Consensus 262 ~~i~~rL~~kKvLIVLDDVd~~~qle~ 288 (315)
+.+...+...++.+|+|+..+..++..
T Consensus 120 e~l~~~~e~~~~~~~l~~~~~~~~~~~ 146 (328)
T PRK00080 120 EILYPAMEDFRLDIMIGKGPAARSIRL 146 (328)
T ss_pred HHHHHHHHhcceeeeeccCccccceee
Confidence 345556666778888888777766543
No 102
>cd07373 2A5CPDO_A The alpha subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO) catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the alpha subunit, which does not contain a potential metal binding site and may not possess catalytic activity.
Probab=20.18 E-value=6.5e+02 Score=23.10 Aligned_cols=76 Identities=14% Similarity=0.108 Sum_probs=51.9
Q ss_pred cchHHHHHHHHhhCCCeEE-eeC-c--cCCCCcchHHHHHHH-h-hcCeEEEEeeccccCChHhHHHHHHHHHH-hhhCC
Q 039731 27 DNFTSHLHAALCRKKIKTF-IDE-E--LNRGDEISPAILKAI-E-GSKITVIIFSKNYASSKWCLDELVKILEC-HKMNS 99 (315)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f-~D~-~--~~~G~~i~~~i~~aI-~-~S~~~Ivv~S~~y~~S~wcl~El~~i~~~-~~~~~ 99 (315)
..++..+.+.|.+.||.+- .|. . +.-|--+. ..-+ . ..++-||.+|.+...+.....+|-+++.. .+..+
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA---CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH---HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 4689999999999999885 655 2 33443322 2223 2 46777888999887777788899998884 44444
Q ss_pred CeeeeE
Q 039731 100 QMVVPV 105 (315)
Q Consensus 100 ~~ViPI 105 (315)
++|+-|
T Consensus 167 ~rV~iI 172 (271)
T cd07373 167 KRVAVV 172 (271)
T ss_pred CeEEEE
Confidence 566633
No 103
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=20.12 E-value=1.4e+02 Score=29.76 Aligned_cols=23 Identities=17% Similarity=0.118 Sum_probs=16.1
Q ss_pred HHHhh--CCcEEEEEeeCCCCCCCc
Q 039731 264 IQRRH--IRLKVSLLASKVDSASSP 286 (315)
Q Consensus 264 i~~rL--~~kKvLIVLDDVd~~~ql 286 (315)
+-+++ +++.|||++||+..--+-
T Consensus 237 iAEyfr~~G~~VLlilDslTr~a~A 261 (432)
T PRK06793 237 IAEYFRDQGNNVLLMMDSVTRFADA 261 (432)
T ss_pred HHHHHHHcCCcEEEEecchHHHHHH
Confidence 44444 468999999998765443
Done!