Query psy14634
Match_columns 388
No_of_seqs 259 out of 337
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 16:43:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14634hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2402|consensus 100.0 1.6E-48 3.5E-53 400.8 15.2 230 92-325 219-461 (525)
2 COG5296 Transcription factor i 100.0 1.4E-41 3E-46 337.7 19.3 217 92-308 211-435 (521)
3 smart00719 Plus3 Short conserv 100.0 1.2E-28 2.5E-33 209.6 9.9 98 90-187 3-109 (109)
4 PF03126 Plus-3: Plus-3 domain 99.9 6.4E-28 1.4E-32 204.1 6.3 97 93-189 2-108 (108)
5 KOG2402|consensus 99.7 5.6E-19 1.2E-23 183.0 3.9 56 333-388 214-269 (525)
6 smart00719 Plus3 Short conserv 99.7 1.3E-18 2.7E-23 148.2 5.3 54 335-388 2-56 (109)
7 PF03126 Plus-3: Plus-3 domain 99.6 7.5E-17 1.6E-21 136.5 4.2 51 338-388 1-53 (108)
8 COG5296 Transcription factor i 99.5 1E-14 2.2E-19 146.6 3.3 55 333-387 206-260 (521)
9 PF08858 IDEAL: IDEAL domain; 82.7 3.1 6.7E-05 29.3 4.5 30 237-266 8-37 (37)
10 PRK03057 hypothetical protein; 82.2 2.5 5.5E-05 39.6 5.2 34 238-271 144-177 (180)
11 PRK03636 hypothetical protein; 82.2 2.4 5.2E-05 39.7 5.0 34 238-271 145-178 (179)
12 PRK11020 hypothetical protein; 73.6 15 0.00033 32.3 7.0 37 240-276 14-50 (118)
13 PF06476 DUF1090: Protein of u 72.3 32 0.0007 30.0 8.9 37 236-272 22-58 (115)
14 PF02151 UVR: UvrB/uvrC motif; 71.7 9.1 0.0002 26.5 4.3 31 241-271 5-35 (36)
15 PF08231 SYF2: SYF2 splicing f 66.3 7.8 0.00017 35.0 3.9 49 255-303 90-139 (153)
16 KOG2609|consensus 64.3 12 0.00025 36.4 4.8 48 254-301 159-207 (228)
17 PF09312 SurA_N: SurA N-termin 58.8 1E+02 0.0022 26.3 9.3 64 167-230 6-83 (118)
18 PF06476 DUF1090: Protein of u 55.5 1.4E+02 0.0029 26.1 9.5 34 239-272 78-111 (115)
19 PF14257 DUF4349: Domain of un 53.7 54 0.0012 31.7 7.6 79 174-276 102-181 (262)
20 KOG4403|consensus 50.4 1.2E+02 0.0026 32.7 9.7 56 195-253 240-295 (575)
21 PF08317 Spc7: Spc7 kinetochor 45.8 3E+02 0.0065 27.7 11.7 28 247-274 199-226 (325)
22 PF11464 Rbsn: Rabenosyn Rab b 45.0 72 0.0016 23.4 5.1 31 243-273 8-38 (42)
23 PRK10884 SH3 domain-containing 41.8 83 0.0018 30.1 6.6 43 116-161 32-76 (206)
24 COG5582 Uncharacterized conser 39.6 53 0.0011 30.9 4.7 35 237-271 145-179 (182)
25 COG3880 Modulator of heat shoc 38.0 67 0.0014 30.2 5.1 62 212-273 99-171 (176)
26 COG1579 Zn-ribbon protein, pos 36.6 1.4E+02 0.003 29.5 7.4 39 333-374 173-211 (239)
27 PF04420 CHD5: CHD5-like prote 36.3 51 0.0011 30.0 4.2 38 239-276 48-85 (161)
28 PF06102 DUF947: Domain of unk 36.1 2E+02 0.0044 26.5 8.1 61 239-316 64-125 (168)
29 PF03902 Gal4_dimer: Gal4-like 36.0 55 0.0012 25.5 3.6 31 196-226 5-35 (57)
30 PF07106 TBPIP: Tat binding pr 35.4 2.6E+02 0.0057 25.2 8.6 37 206-253 9-45 (169)
31 KOG0994|consensus 34.5 3.3E+02 0.0071 33.1 10.7 32 195-226 1202-1234(1758)
32 PF02403 Seryl_tRNA_N: Seryl-t 34.5 64 0.0014 26.8 4.2 80 197-276 5-93 (108)
33 TIGR01461 greB transcription e 32.9 1.1E+02 0.0025 27.7 5.8 46 213-264 4-49 (156)
34 TIGR00470 sepS O-phosphoseryl- 32.5 1.3E+02 0.0028 32.9 6.9 101 189-294 98-204 (533)
35 PF14265 DUF4355: Domain of un 32.3 2.8E+02 0.006 23.7 7.9 16 212-227 6-21 (125)
36 cd07963 Anticodon_Ia_Cys Antic 31.3 61 0.0013 28.7 3.7 32 240-271 112-143 (156)
37 PF05278 PEARLI-4: Arabidopsis 30.1 5.9E+02 0.013 25.7 11.1 81 151-251 103-183 (269)
38 COG1422 Predicted membrane pro 29.4 1.2E+02 0.0026 29.2 5.5 35 242-276 83-117 (201)
39 PF03449 GreA_GreB_N: Transcri 29.3 1.4E+02 0.003 24.0 5.1 41 214-260 6-46 (74)
40 PF02696 UPF0061: Uncharacteri 29.0 2.3E+02 0.0051 30.6 8.2 52 213-267 433-484 (487)
41 PRK10884 SH3 domain-containing 28.9 2.7E+02 0.0058 26.7 7.8 8 138-145 40-47 (206)
42 PHA02277 hypothetical protein 28.0 4.6E+02 0.01 23.8 11.1 54 173-228 11-64 (150)
43 COG5126 FRQ1 Ca2+-binding prot 27.5 2.1E+02 0.0046 26.4 6.6 57 168-228 8-67 (160)
44 KOG3032|consensus 27.4 95 0.0021 30.7 4.5 51 174-230 164-214 (264)
45 cd00454 Trunc_globin Truncated 27.2 1.1E+02 0.0023 25.4 4.3 38 172-209 71-112 (116)
46 PRK05431 seryl-tRNA synthetase 27.1 1.4E+02 0.0031 31.3 6.1 35 238-272 49-88 (425)
47 PRK05892 nucleoside diphosphat 26.6 2.5E+02 0.0055 25.6 6.9 46 212-264 6-51 (158)
48 COG0216 PrfA Protein chain rel 26.3 3.7E+02 0.008 28.1 8.6 75 196-272 9-91 (363)
49 PF13779 DUF4175: Domain of un 24.6 1E+03 0.022 27.6 12.6 125 180-304 454-610 (820)
50 PF04380 BMFP: Membrane fusoge 23.8 2.4E+02 0.0051 22.8 5.6 71 194-276 6-76 (79)
51 TIGR01462 greA transcription e 23.4 2.9E+02 0.0064 24.7 6.7 20 239-258 21-40 (151)
52 COG1842 PspA Phage shock prote 23.0 4.8E+02 0.011 25.3 8.5 94 218-311 46-150 (225)
53 PRK10869 recombination and rep 23.0 8.6E+02 0.019 26.5 11.3 59 213-273 292-357 (553)
54 TIGR00414 serS seryl-tRNA synt 22.7 1.8E+02 0.004 30.4 5.9 35 238-272 51-91 (418)
55 PRK01885 greB transcription el 22.6 2.8E+02 0.0062 25.2 6.5 46 213-264 6-51 (157)
56 PF10453 NUFIP1: Nuclear fragi 21.7 1.6E+02 0.0034 22.8 3.9 17 215-231 19-35 (56)
57 PF11338 DUF3140: Protein of u 21.5 1E+02 0.0022 26.2 3.0 50 174-223 8-63 (92)
58 PF13758 Prefoldin_3: Prefoldi 21.0 5.4E+02 0.012 22.2 8.4 86 176-272 11-97 (99)
59 PF08912 Rho_Binding: Rho Bind 21.0 1.7E+02 0.0037 23.6 4.1 18 235-252 7-24 (69)
60 PF08537 NBP1: Fungal Nap bind 20.8 3.2E+02 0.007 28.2 7.0 41 256-296 174-214 (323)
61 PLN03229 acetyl-coenzyme A car 20.8 7.1E+02 0.015 28.7 10.1 51 175-225 434-486 (762)
62 PF02661 Fic: Fic/DOC family; 20.6 18 0.00039 28.5 -1.5 28 54-81 58-85 (97)
63 TIGR03185 DNA_S_dndD DNA sulfu 20.6 7.7E+02 0.017 27.2 10.5 34 197-230 401-434 (650)
64 PRK13729 conjugal transfer pil 20.5 2.1E+02 0.0046 31.0 5.8 45 256-300 75-119 (475)
65 PRK10698 phage shock protein P 20.4 4.6E+02 0.01 25.1 7.7 57 217-273 45-108 (222)
66 PRK00260 cysS cysteinyl-tRNA s 20.3 1.2E+02 0.0025 32.2 4.0 33 239-271 417-449 (463)
67 KOG1029|consensus 20.0 4.5E+02 0.0097 30.6 8.3 22 279-300 424-445 (1118)
No 1
>KOG2402|consensus
Probab=100.00 E-value=1.6e-48 Score=400.80 Aligned_cols=230 Identities=39% Similarity=0.572 Sum_probs=215.8
Q ss_pred ccccEEEechHHHHhccc--cCccccccceeec------CCCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCceee
Q psy14634 92 PEIVEVVYKKDLISSAMF--YGSVCDLTSWHIF------SSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERV 163 (388)
Q Consensus 92 ~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~------g~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~eR~ 163 (388)
.|++.|+|+|+.|++||+ ||+..|+|||||+ |.++||||+|+||.+++|+|.+++++||+||.|.||.++++
T Consensus 219 ~dln~~rlsR~~vak~~~~P~Fe~~V~gCfvRv~ig~~~~~p~YRv~~I~gV~es~k~Y~l~~~~Tnk~l~~~~G~s~r~ 298 (525)
T KOG2402|consen 219 SDLNALRLSRHKVAKWLFSPFFESTVTGCFVRVGIGGEGSKPVYRVAEIVGVLESDKPYKLEGVKTNKYLRVRHGRSERV 298 (525)
T ss_pred HHHHHHHhhHHHHHHHHhhhHHHHHhhhheEEeeecCcCCCCceeEEEEeeecccCccccccceeecceeeeecCcchhh
Confidence 579999999999999999 8999999999997 47899999999999999999999999999999999999999
Q ss_pred eeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHH
Q psy14634 164 FRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQL 243 (388)
Q Consensus 164 f~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL 243 (388)
|+|++|||++||++||++|+.+|...++.+||++.|.+|..+|.++++|+|++++|++||++|.+++..|.|+||+|++|
T Consensus 299 f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~sd~~v~~~v~~k~~~~~~p~N~ameK~~l 378 (525)
T KOG2402|consen 299 FRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRLSDKEVDQMVAEKFEASPRPRNVAMEKTGL 378 (525)
T ss_pred cchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCccCcccHHHHHHhhhhcCcCcchHHHHHHhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHhhHHHHHHHHHhhhhh-----hcCCCc
Q psy14634 244 MKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMVSCCC-----CCSGFS 318 (388)
Q Consensus 244 ~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l~k~~~~~~~~La~IN~RNRk~N~e~irKA~l~E~k~-----~~~gfs 318 (388)
++++++|...||.+.+++|+.||.+||+++.++++.+++.+..+++||+|||++ |++|+....+. +.++|+
T Consensus 379 ~k~r~~A~~~~d~~~a~~~~~qi~elE~~a~~~~~~~~s~i~~~~~lN~rNR~~----~~~a~~~~~~~~~~~~~~dpfT 454 (525)
T KOG2402|consen 379 RKERDLAQLLGDAKSAEEIQRQINELEARAEELDKARASPILKLAELNRRNRRR----IAKAELSGGAVAKNLSAPDPFT 454 (525)
T ss_pred HHHHHHHHhcccHhHHHHHHHHHHHHHHHHhhhccccccccccccccchhHHHH----hhhhhhhhhhhhhcCCCCCCcc
Confidence 999999999999999999999999999999889988999999999999999999 44444444332 227799
Q ss_pred ccccccc
Q psy14634 319 YRSVKSS 325 (388)
Q Consensus 319 ~rs~kss 325 (388)
.|++.++
T Consensus 455 Rr~~~~~ 461 (525)
T KOG2402|consen 455 RRKTRTS 461 (525)
T ss_pred ccccccc
Confidence 9998765
No 2
>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
Probab=100.00 E-value=1.4e-41 Score=337.67 Aligned_cols=217 Identities=20% Similarity=0.269 Sum_probs=202.8
Q ss_pred ccccEEEechHHHHhccc--cCccccccceeec------CCCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCceee
Q psy14634 92 PEIVEVVYKKDLISSAMF--YGSVCDLTSWHIF------SSHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERV 163 (388)
Q Consensus 92 ~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~------g~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~eR~ 163 (388)
.||+.|+|.|+++.++|+ -|++.|.|||+|+ |+.+||||+|.++....|||.+++..||+||.|.||++.|+
T Consensus 211 ~Dfn~~rvgR~~VA~~~f~P~Fed~v~Gcf~Rv~Ig~R~g~~vyRiv~V~~~~~~~kpy~~~~v~Tn~yl~v~~Gr~~kv 290 (521)
T COG5296 211 YDFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVGKGSTYSKPYGRKEVKTNRYLDVSTGRTYKV 290 (521)
T ss_pred hhhhhhhhhHHHHHHHhcccchhhhhcceeeEEEecccCCeeEEEEEEeccceeccccccccceeeeeeEeeecCcceee
Confidence 469999999999999999 4888999999985 68899999999998789999999999999999999999999
Q ss_pred eeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHH
Q psy14634 164 FRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQL 243 (388)
Q Consensus 164 f~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL 243 (388)
|+|+++||+||.++||+||...+......+|++..|.+|.+++-.+++++||+++|++||++|..+.+.+.|++++|++|
T Consensus 291 F~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d~~~~~LSdkeis~~V~~k~e~~~k~sNvi~eKt~L 370 (521)
T COG5296 291 FRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEISKMVACKDEVHPKRSNVIHEKTEL 370 (521)
T ss_pred eEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHhCCcCchhHHHHHHHHHHhcCccchhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHhhHHHHHHHHHh
Q psy14634 244 MKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKAIMV 308 (388)
Q Consensus 244 ~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l~k~~~~~~~~La~IN~RNRk~N~e~irKA~l~ 308 (388)
++.|+.|...||.+.|.+++.||++||..........++.+..|+++|+|||++|+.+||-|+..
T Consensus 371 rqkrq~A~e~~n~k~~~ey~~qL~~~E~~~~~~~hN~ns~~~~L~~v~~rNRr~N~t~IR~AE~~ 435 (521)
T COG5296 371 RQKRQRAIELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVNERNRRRNHTEIRLAEQR 435 (521)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHhhhccccccccchHHHHHhhhhhhhccchhhhhHHHH
Confidence 99999999999999999999999999997522211225678999999999999999999987654
No 3
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=99.95 E-value=1.2e-28 Score=209.62 Aligned_cols=98 Identities=29% Similarity=0.418 Sum_probs=92.0
Q ss_pred ccccccEEEechHHHHhccc--cCccccccceeecC-------CCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCc
Q psy14634 90 IEPEIVEVVYKKDLISSAMF--YGSVCDLTSWHIFS-------SHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNS 160 (388)
Q Consensus 90 ~~~~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~g-------~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~ 160 (388)
.-.||++|+|+|+.|++||+ +|++++.|||||++ +++||||+|+||.+++++|+++++.||+||.|+||+.
T Consensus 3 ~l~~l~~i~L~R~~l~~~~~~p~Fe~~v~GcFVRv~ig~~~~~~~~Yrl~qI~gv~~~~k~Y~~~~~~t~~~L~v~~g~~ 82 (109)
T smart00719 3 VFDNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKQPIYRLVQVTGVKEADKPYELGGKTTNVLLEVLNGDS 82 (109)
T ss_pred ChHHhheEEEEHHHHHHHhcCCchhHhceEeEEEEEECCCCCCCCeEEEEEEeeEEecCcceecCCceeeEEEEEecCCc
Confidence 33569999999999999999 89999999999972 3899999999999889999999999999999999999
Q ss_pred eeeeeeeeccCCcCCHHHHHHHHHHHH
Q psy14634 161 ERVFRLEFISNQEFTESEFIRWKDQCM 187 (388)
Q Consensus 161 eR~f~m~~VSNspfTe~EF~Rw~~~~~ 187 (388)
++.|+|+.||||||||+||++|+++|.
T Consensus 83 ~~~~~i~~iSn~~fte~E~~~w~~~~~ 109 (109)
T smart00719 83 EKVVQINFISNQDFTEEEFQRWKQAIK 109 (109)
T ss_pred eEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence 999999999999999999999999884
No 4
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=99.94 E-value=6.4e-28 Score=204.06 Aligned_cols=97 Identities=35% Similarity=0.567 Sum_probs=82.9
Q ss_pred cccEEEechHHHHhccc--cCccccccceeec--C------CCceEEEEEEeeeecCceeecCCeeeeeEEEEeecCcee
Q psy14634 93 EIVEVVYKKDLISSAMF--YGSVCDLTSWHIF--S------SHPQEIGEISGVCETGKIYSLGKTRTNKGLKLRHGNSER 162 (388)
Q Consensus 93 ~i~~I~l~Rd~L~k~~~--yfe~~v~G~fvR~--g------~~vYRm~eI~gV~e~~K~Y~lg~~~TnkyL~L~hG~~eR 162 (388)
||++|+|+|++|++||+ +|+.+++|||||+ | .++||||+|+||.+..|+|++++..||++|.|+||+..|
T Consensus 2 ~i~~i~l~Rs~l~~~~~~P~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~v~~~~k~Y~~~~~~t~~~L~l~~g~~~r 81 (108)
T PF03126_consen 2 DIKRIRLSRSQLEKWLFKPFFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVGVKEGKKPYKLGSKKTNKYLVLRHGNSER 81 (108)
T ss_dssp HHHHTBE-HHHHHHHTTSTTHHHHHTT-EEEEEEETTSSS-E--EEEEEEEEEEEEEEEEEETTEEEEEEEEEEETTEEE
T ss_pred chHeEEEEHHHHHHHHcCCChhHheeEEEEEEEecCCCCCCceeEEEEEEEEEecccccEecCCeEEEEEEEEEECCcee
Confidence 68999999999999999 9999999999997 2 236999999999987789999999999999999999999
Q ss_pred eeeeeeccCCcCCHHHHHHHHHHHHhc
Q psy14634 163 VFRLEFISNQEFTESEFIRWKDQCMTE 189 (388)
Q Consensus 163 ~f~m~~VSNspfTe~EF~Rw~~~~~~~ 189 (388)
.|+|+.|||||||++||++|+++|+++
T Consensus 82 ~~~i~~vSn~~~te~E~~~w~~~~~~~ 108 (108)
T PF03126_consen 82 DFPIDMVSNSPFTEEEFERWKQSCEKD 108 (108)
T ss_dssp EEEGGGBBSS---HHHHHHHHHHH---
T ss_pred EEEeEeeECCCCCHHHHHHHHHHhccC
Confidence 999999999999999999999999863
No 5
>KOG2402|consensus
Probab=99.74 E-value=5.6e-19 Score=183.01 Aligned_cols=56 Identities=43% Similarity=0.774 Sum_probs=54.8
Q ss_pred ccccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCCCCceEEEEecC
Q psy14634 333 YIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENFC 388 (388)
Q Consensus 333 ~~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g~~~YR~~~I~~ 388 (388)
++++++||+++|||||+||+|||+|||+++|+||||||+||.++|+|+||||+|+|
T Consensus 214 ~v~~~~dln~~rlsR~~vak~~~~P~Fe~~V~gCfvRv~ig~~~~~p~YRv~~I~g 269 (525)
T KOG2402|consen 214 RVPSISDLNALRLSRHKVAKWLFSPFFESTVTGCFVRVGIGGEGSKPVYRVAEIVG 269 (525)
T ss_pred CCCCHHHHHHHHhhHHHHHHHHhhhHHHHHhhhheEEeeecCcCCCCceeEEEEee
Confidence 78999999999999999999999999999999999999999999999999999986
No 6
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=99.74 E-value=1.3e-18 Score=148.15 Aligned_cols=54 Identities=39% Similarity=0.663 Sum_probs=50.3
Q ss_pred ccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCC-CCceEEEEecC
Q psy14634 335 ETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTG-IPLYRVSENFC 388 (388)
Q Consensus 335 ~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g-~~~YR~~~I~~ 388 (388)
++++||++|+|+|+.|++||++|+|+++|.||||||+||++.. +|+||||+|+|
T Consensus 2 ~~l~~l~~i~L~R~~l~~~~~~p~Fe~~v~GcFVRv~ig~~~~~~~~Yrl~qI~g 56 (109)
T smart00719 2 IVFDNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKQPIYRLVQVTG 56 (109)
T ss_pred CChHHhheEEEEHHHHHHHhcCCchhHhceEeEEEEEECCCCCCCCeEEEEEEee
Confidence 6899999999999999999999999999999999999999633 39999999986
No 7
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=99.65 E-value=7.5e-17 Score=136.55 Aligned_cols=51 Identities=47% Similarity=0.866 Sum_probs=43.2
Q ss_pred hhhcceeechhhhhhhhcCCchhhhhccceEEEeecCC--CCCCceEEEEecC
Q psy14634 338 EELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNN--TGIPLYRVSENFC 388 (388)
Q Consensus 338 ~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~--~g~~~YR~~~I~~ 388 (388)
+||++|+|+|+.|++||++|+|+++|.||||||+||+. ++.++||||+|++
T Consensus 1 e~i~~i~l~Rs~l~~~~~~P~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~ 53 (108)
T PF03126_consen 1 EDIKRIRLSRSQLEKWLFKPFFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVG 53 (108)
T ss_dssp HHHHHTBE-HHHHHHHTTSTTHHHHHTT-EEEEEEETTSSS-E--EEEEEEEE
T ss_pred CchHeEEEEHHHHHHHHcCCChhHheeEEEEEEEecCCCCCCceeEEEEEEEE
Confidence 68999999999999999999999999999999999996 4455799999975
No 8
>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
Probab=99.49 E-value=1e-14 Score=146.62 Aligned_cols=55 Identities=33% Similarity=0.535 Sum_probs=51.9
Q ss_pred ccccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecCCCCCCceEEEEec
Q psy14634 333 YIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGIPLYRVSENF 387 (388)
Q Consensus 333 ~~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~~~g~~~YR~~~I~ 387 (388)
.-+.|-|||+|||||+++|+|||+|+|+++|+|||+||+||.++|+.+||||.|-
T Consensus 206 ~~a~l~Dfn~~rvgR~~VA~~~f~P~Fed~v~Gcf~Rv~Ig~R~g~~vyRiv~V~ 260 (521)
T COG5296 206 DFAELYDFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVG 260 (521)
T ss_pred hhhhhhhhhhhhhhHHHHHHHhcccchhhhhcceeeEEEecccCCeeEEEEEEec
Confidence 3566899999999999999999999999999999999999999999999999974
No 9
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=82.71 E-value=3.1 Score=29.28 Aligned_cols=30 Identities=27% Similarity=0.256 Sum_probs=26.7
Q ss_pred hHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Q psy14634 237 AMKKTQLMKERDMAQSKGDDEEASILQRKI 266 (388)
Q Consensus 237 a~eK~rL~~ere~A~~~GD~eev~~L~~qL 266 (388)
..+|.+|..+++.|.+.||.+.-.+|.++|
T Consensus 8 ~~~~~~L~~~ID~ALd~~D~e~F~~Ls~eL 37 (37)
T PF08858_consen 8 EFRKEQLLELIDEALDNRDKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHhhC
Confidence 478999999999999999999999998886
No 10
>PRK03057 hypothetical protein; Provisional
Probab=82.25 E-value=2.5 Score=39.65 Aligned_cols=34 Identities=29% Similarity=0.293 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634 238 MKKTQLMKERDMAQSKGDDEEASILQRKIDDLEE 271 (388)
Q Consensus 238 ~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~ 271 (388)
.++.+|++++|.|.++||.+.-.+|..+|.+|+.
T Consensus 144 ~~~~~L~~~ID~ALd~~D~e~F~~Lt~~L~~l~~ 177 (180)
T PRK03057 144 NEVSRLRMQIDQALDRKDMEEFQRLTEKLKKLEG 177 (180)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 6899999999999999999999999999999965
No 11
>PRK03636 hypothetical protein; Provisional
Probab=82.22 E-value=2.4 Score=39.73 Aligned_cols=34 Identities=24% Similarity=0.419 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634 238 MKKTQLMKERDMAQSKGDDEEASILQRKIDDLEE 271 (388)
Q Consensus 238 ~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~ 271 (388)
.+|.+|+.++|.|.++||.+.-.+|..+|++|+.
T Consensus 145 ~r~~~L~~~ID~ALd~~D~e~F~~Ls~~l~~L~~ 178 (179)
T PRK03636 145 FRREKLLKQIDEALDRRDKEAFHRLSDELNQLRT 178 (179)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhc
Confidence 6889999999999999999999999999999864
No 12
>PRK11020 hypothetical protein; Provisional
Probab=73.57 E-value=15 Score=32.29 Aligned_cols=37 Identities=19% Similarity=0.271 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhh
Q psy14634 240 KTQLMKERDMAQSKGDDEEASILQRKIDDLEERANEL 276 (388)
Q Consensus 240 K~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l 276 (388)
=..+.+.++.|..+||.+.+.+...+++.|+...+.+
T Consensus 14 LD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~l 50 (118)
T PRK11020 14 LDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIARL 50 (118)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788999999999999999999999999876544
No 13
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=72.33 E-value=32 Score=29.99 Aligned_cols=37 Identities=14% Similarity=0.374 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q psy14634 236 YAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEER 272 (388)
Q Consensus 236 ~a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~ 272 (388)
-+.+...|.++++.|+..||...|..|+.-|.++..-
T Consensus 22 C~~K~~~Ie~qI~~Ak~~gN~~rv~GLe~AL~~v~~~ 58 (115)
T PF06476_consen 22 CEAKEQAIEKQIEYAKAHGNQHRVAGLEKALEEVKAH 58 (115)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhh
Confidence 4568889999999999999999999999999999763
No 14
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=71.71 E-value=9.1 Score=26.47 Aligned_cols=31 Identities=26% Similarity=0.321 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634 241 TQLMKERDMAQSKGDDEEASILQRKIDDLEE 271 (388)
Q Consensus 241 ~rL~~ere~A~~~GD~eev~~L~~qL~eLE~ 271 (388)
..|..++..|....|.++++.|..+|..|+.
T Consensus 5 ~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~ 35 (36)
T PF02151_consen 5 KELEEKMEEAVENEDFEKAARLRDQIKALKK 35 (36)
T ss_dssp HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCHHHHHHHHHHHHHHHc
Confidence 4688899999999999999999999999875
No 15
>PF08231 SYF2: SYF2 splicing factor; InterPro: IPR013260 Proteins in this entry are involved in cell cycle progression and pre-mRNA splicing [, ].
Probab=66.30 E-value=7.8 Score=35.04 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHHHHHHHHhhhhhcccc-chHHHHHHHHHHHHhhHHHHH
Q psy14634 255 DDEEASILQRKIDDLEERANELDKARTS-TISSISYINNRNRRKNVEEAE 303 (388)
Q Consensus 255 D~eev~~L~~qL~eLE~~~~~l~k~~~~-~~~~La~IN~RNRk~N~e~ir 303 (388)
..+.|.+|...|.+-........+.+.. ...-+.+||+||+..|..--|
T Consensus 90 ~~e~vdrlv~~l~k~~~kR~k~sRrR~~~d~~dv~YINerNk~FN~KL~R 139 (153)
T PF08231_consen 90 SPEAVDRLVNDLEKQIEKRKKFSRRRKFDDDADVDYINERNKQFNKKLER 139 (153)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhHhcccccCCCcCchhhhhHHHHHHHHH
Confidence 4556777777777665543333333322 222688999999999976433
No 16
>KOG2609|consensus
Probab=64.29 E-value=12 Score=36.43 Aligned_cols=48 Identities=21% Similarity=0.336 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHhhhhhcc-ccchHHHHHHHHHHHHhhHHH
Q psy14634 254 GDDEEASILQRKIDDLEERANELDKAR-TSTISSISYINNRNRRKNVEE 301 (388)
Q Consensus 254 GD~eev~~L~~qL~eLE~~~~~l~k~~-~~~~~~La~IN~RNRk~N~e~ 301 (388)
-|.+.|.+|-..|..-..+..+..+.+ .....-|..||+||++.|-.-
T Consensus 159 ~~~~~idKl~~~L~~q~kkR~k~srRR~~n~d~~idfINerN~kFNkKl 207 (228)
T KOG2609|consen 159 PDTEAIDKLVKDLEKQIKKRYKYSRRRMYNEDADIDFINERNKKFNKKL 207 (228)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhccCCcccchhHHHHhHHHHHHHH
Confidence 366777777777766666544454444 233445789999999999543
No 17
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=58.76 E-value=1e+02 Score=26.27 Aligned_cols=64 Identities=14% Similarity=0.336 Sum_probs=36.6
Q ss_pred eeccCCcCCHHHHHHHHHHHH----hcCCCCCCHHHHHHHHH--------HHHHh--hcCCCCHHHHHHHHHHHhhcC
Q psy14634 167 EFISNQEFTESEFIRWKDQCM----TEGVALPTKDEVERKSK--------EIQNG--MMYQWKEEDVEQIVREKERFK 230 (388)
Q Consensus 167 ~~VSNspfTe~EF~Rw~~~~~----~~~~~lPT~~~V~~K~~--------dI~k~--~n~~~TeeDI~~mI~~K~~~~ 230 (388)
.+|-|.+||.+|++.....+. ..+...|....+.++.- .++.+ .+...|++||+..|+.-.+..
T Consensus 6 AvVn~eiIt~sel~~~~~~~~~~~~~~~~~~~~~~~l~~qvLd~LI~e~L~~q~ak~~gI~vsd~evd~~i~~ia~~n 83 (118)
T PF09312_consen 6 AVVNDEIITQSELEQRLAQLKAQIQQQGQQIPPRNQLRKQVLDQLIDEKLQLQEAKRLGIKVSDEEVDEAIANIAKQN 83 (118)
T ss_dssp EEESSSEEEHHHHHHHHHHHHHHHHTTT-----HHHHHHHHHHHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHT
T ss_pred EEECCcCcCHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHc
Confidence 468899999999999877654 44667776555443221 12222 466778999999998755443
No 18
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=55.45 E-value=1.4e+02 Score=26.15 Aligned_cols=34 Identities=26% Similarity=0.339 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q psy14634 239 KKTQLMKERDMAQSKGDDEEASILQRKIDDLEER 272 (388)
Q Consensus 239 eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~ 272 (388)
+-.....+|+.|++.||.+++...+.+|++-...
T Consensus 78 kV~ere~eL~eA~~~G~~~KI~K~~~KL~ea~~e 111 (115)
T PF06476_consen 78 KVAEREAELKEAQAKGDSDKIAKRQKKLAEAKAE 111 (115)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 3445667788888888888888888887775543
No 19
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=53.73 E-value=54 Score=31.66 Aligned_cols=79 Identities=16% Similarity=0.252 Sum_probs=44.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHH-HhhcCCCCCchhHHHHHHHHHHHHHHh
Q psy14634 174 FTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVRE-KERFKPTPYNYAMKKTQLMKERDMAQS 252 (388)
Q Consensus 174 fTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~-K~~~~~~~~N~a~eK~rL~~ere~A~~ 252 (388)
+..+.|+.+...+...| ...++..+.+||..-... ..++. |.-.++.||...++ .
T Consensus 102 VP~~~~~~~l~~l~~~g-----------------~v~~~~~~~~DvT~~y~D~~arl~----~l~~~~~rl~~ll~---k 157 (262)
T PF14257_consen 102 VPADKFDSFLDELSELG-----------------KVTSRNISSEDVTEQYVDLEARLK----NLEAEEERLLELLE---K 157 (262)
T ss_pred ECHHHHHHHHHHHhccC-----------------ceeeeeccccchHHHHHHHHHHHH----HHHHHHHHHHHHHH---h
Confidence 44566777776665333 334455555555544322 11111 11134455544444 5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhhh
Q psy14634 253 KGDDEEASILQRKIDDLEERANEL 276 (388)
Q Consensus 253 ~GD~eev~~L~~qL~eLE~~~~~l 276 (388)
.++.+++-+++.+|.+++.....+
T Consensus 158 a~~~~d~l~ie~~L~~v~~eIe~~ 181 (262)
T PF14257_consen 158 AKTVEDLLEIERELSRVRSEIEQL 181 (262)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHH
Confidence 669999999999998888765444
No 20
>KOG4403|consensus
Probab=50.42 E-value=1.2e+02 Score=32.66 Aligned_cols=56 Identities=20% Similarity=0.231 Sum_probs=38.2
Q ss_pred CHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhC
Q psy14634 195 TKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSK 253 (388)
Q Consensus 195 T~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~ 253 (388)
.+..|++=.++|..+..-.=+=+|+.++|.+-+. ...|+|.||..|++.++.|-..
T Consensus 240 akehv~km~kdle~Lq~aEqsl~dlQk~Lekar~---e~rnvavek~~lerkl~ea~rl 295 (575)
T KOG4403|consen 240 AKEHVNKMMKDLEGLQRAEQSLEDLQKRLEKARE---EQRNVAVEKLDLERKLDEAPRL 295 (575)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhchhhhhhhHHHHHhhhhhh
Confidence 3455655566666655544555788888866444 3468999999999999966543
No 21
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=45.79 E-value=3e+02 Score=27.69 Aligned_cols=28 Identities=18% Similarity=0.209 Sum_probs=20.6
Q ss_pred HHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q psy14634 247 RDMAQSKGDDEEASILQRKIDDLEERAN 274 (388)
Q Consensus 247 re~A~~~GD~eev~~L~~qL~eLE~~~~ 274 (388)
+.......|.++++.+..+|.+++....
T Consensus 199 ~~~e~~~~D~~eL~~lr~eL~~~~~~i~ 226 (325)
T PF08317_consen 199 LVEEIESCDQEELEALRQELAEQKEEIE 226 (325)
T ss_pred HHhhhhhcCHHHHHHHHHHHHHHHHHHH
Confidence 3333456788899999999988887654
No 22
>PF11464 Rbsn: Rabenosyn Rab binding domain; InterPro: IPR021565 Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively []. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking []. ; PDB: 1Z0K_B 1YZM_A 1Z0J_B.
Probab=45.04 E-value=72 Score=23.40 Aligned_cols=31 Identities=13% Similarity=0.229 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q psy14634 243 LMKERDMAQSKGDDEEASILQRKIDDLEERA 273 (388)
Q Consensus 243 L~~ere~A~~~GD~eev~~L~~qL~eLE~~~ 273 (388)
+..=++.|++.|..|+|+-|+.=|.+|....
T Consensus 8 I~~~I~qAk~~~r~dEV~~L~~NL~EL~~e~ 38 (42)
T PF11464_consen 8 IESYIKQAKAARRFDEVATLEENLRELQDEI 38 (42)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHH
Confidence 4455889999999999999999999998754
No 23
>PRK10884 SH3 domain-containing protein; Provisional
Probab=41.83 E-value=83 Score=30.10 Aligned_cols=43 Identities=14% Similarity=0.195 Sum_probs=24.5
Q ss_pred ccceeecC-CCceEEEEEEeeeecCceeecCCeee-eeEEEEeecCce
Q psy14634 116 LTSWHIFS-SHPQEIGEISGVCETGKIYSLGKTRT-NKGLKLRHGNSE 161 (388)
Q Consensus 116 ~G~fvR~g-~~vYRm~eI~gV~e~~K~Y~lg~~~T-nkyL~L~hG~~e 161 (388)
+.-++|.| ..-||+. +..+.|.+..+=.... ..|..|+..+..
T Consensus 32 l~v~lRsGPg~~y~Iv---~~l~~G~~v~vl~~~~~~~w~~Vr~~~G~ 76 (206)
T PRK10884 32 LNTYVRSGPGDQYRIV---GTLNAGEEVTLLQVNANTNYAQIRDSKGR 76 (206)
T ss_pred eeEEEEcCCCCCCceE---EEEcCCCEEEEEEEcCCCCEEEEEeCCCC
Confidence 34456665 5688665 4544555555433332 468888765543
No 24
>COG5582 Uncharacterized conserved protein [Function unknown]
Probab=39.56 E-value=53 Score=30.89 Aligned_cols=35 Identities=23% Similarity=0.308 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634 237 AMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEE 271 (388)
Q Consensus 237 a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~ 271 (388)
++++..|.+.+|.|.+..|.+.-..|..+|++|..
T Consensus 145 ~f~~~~LL~~IDeALd~~Dk~~F~~L~q~Lq~L~~ 179 (182)
T COG5582 145 AFERKKLLQQIDEALDMRDKERFYQLVQILQQLDL 179 (182)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHh
Confidence 57999999999999999999999999999999875
No 25
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=38.04 E-value=67 Score=30.23 Aligned_cols=62 Identities=18% Similarity=0.181 Sum_probs=48.1
Q ss_pred CCCCHHHHHHHHHHHhhcC-----CC------CCchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q psy14634 212 YQWKEEDVEQIVREKERFK-----PT------PYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERA 273 (388)
Q Consensus 212 ~~~TeeDI~~mI~~K~~~~-----~~------~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~ 273 (388)
|..-+++|.-++.+=+.-+ +. ..|+..+=..|...|+.+..+-|.|+|+.+.+||..|++..
T Consensus 99 Y~tf~~~i~pi~~rvq~g~~~H~GK~P~~~~~~i~~~~~I~~L~e~Lq~~i~~EefEeAA~iRDqIr~Lk~k~ 171 (176)
T COG3880 99 YKTFESQISPIITRVQGGYVEHVGKVPKRIGRKINPKRKIIALKEALQDLIEREEFEEAAVIRDQIRALKAKN 171 (176)
T ss_pred HHHHHHHhhHHHHHhhCCceeecCcCcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4446778888887755432 23 34556777889999999999999999999999999999753
No 26
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=36.63 E-value=1.4e+02 Score=29.45 Aligned_cols=39 Identities=23% Similarity=0.366 Sum_probs=29.4
Q ss_pred ccccHhhhcceeechhhhhhhhcCCchhhhhccceEEEeecC
Q psy14634 333 YIETKEELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGN 374 (388)
Q Consensus 333 ~~~~l~d~~~irl~R~~l~k~~~~P~F~~~v~gcfvRv~iG~ 374 (388)
||..+.-+.+||-+-.- ..-.|.=..+..||++.++.+.
T Consensus 173 ~~ell~~yeri~~~~kg---~gvvpl~g~~C~GC~m~l~~~~ 211 (239)
T COG1579 173 DPELLSEYERIRKNKKG---VGVVPLEGRVCGGCHMKLPSQT 211 (239)
T ss_pred CHHHHHHHHHHHhcCCC---ceEEeecCCcccCCeeeecHHH
Confidence 67788888888754311 2346888899999999999886
No 27
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=36.32 E-value=51 Score=30.01 Aligned_cols=38 Identities=29% Similarity=0.376 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhh
Q psy14634 239 KKTQLMKERDMAQSKGDDEEASILQRKIDDLEERANEL 276 (388)
Q Consensus 239 eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l 276 (388)
|..+|.+|+..=-++.+..+-++|+.+++++++.++++
T Consensus 48 Ei~~l~~E~~~iS~qDeFAkwaKl~Rk~~kl~~el~~~ 85 (161)
T PF04420_consen 48 EILQLKRELNAISAQDEFAKWAKLNRKLDKLEEELEKL 85 (161)
T ss_dssp HHHHHHHHHTTS-TTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444455667777777777777777765443
No 28
>PF06102 DUF947: Domain of unknown function (DUF947); InterPro: IPR009292 This is a family of eukaryotic proteins with unknown function.
Probab=36.14 E-value=2e+02 Score=26.52 Aligned_cols=61 Identities=20% Similarity=0.232 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHhhH-HHHHHHHHhhhhhhcCC
Q psy14634 239 KKTQLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNV-EEAEKAIMVSCCCCCSG 316 (388)
Q Consensus 239 eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l~k~~~~~~~~La~IN~RNRk~N~-e~irKA~l~E~k~~~~g 316 (388)
|...|..+|..+. |.++.++|+.+|..++.+.. ....+.+..++ ...++.+.+-.+.|.-+
T Consensus 64 E~~~Lk~~lk~~k---~~~~~e~lk~~L~~~~~q~~--------------~~~~~~~~~e~~~~~kk~E~e~v~~GKkP 125 (168)
T PF06102_consen 64 EIKELKKQLKKTK---DPEEREELKRELQRMESQLK--------------ARKRKDREREVKKEHKKEEREKVKQGKKP 125 (168)
T ss_pred HHHHHHHHHHHcC---CHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 4445544444444 77888888888888887542 23334444442 33445555555555554
No 29
>PF03902 Gal4_dimer: Gal4-like dimerisation domain; InterPro: IPR005600 The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of alpha-helix), is essential for dimerisation []. ; PDB: 1HBW_B 1D66_A 3COQ_A.
Probab=36.00 E-value=55 Score=25.54 Aligned_cols=31 Identities=16% Similarity=0.398 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHH
Q psy14634 196 KDEVERKSKEIQNGMMYQWKEEDVEQIVREK 226 (388)
Q Consensus 196 ~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K 226 (388)
+-+|+.+...+..++.+-+.+.||+.+++.+
T Consensus 5 LTeVE~Rl~~lE~ll~~lfP~~did~lL~~~ 35 (57)
T PF03902_consen 5 LTEVENRLEKLEQLLRELFPGEDIDDLLNDR 35 (57)
T ss_dssp HHHHHHHHHHHHHHHCCCSSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHCCCcCHHHHHHcc
Confidence 3579999999999999999999999999775
No 30
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=35.43 E-value=2.6e+02 Score=25.18 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=22.4
Q ss_pred HHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhC
Q psy14634 206 IQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSK 253 (388)
Q Consensus 206 I~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~ 253 (388)
--+-.|+||+..||-.-+..+ +-|+.+.+-|+.....
T Consensus 9 y~~~qNRPys~~di~~nL~~~-----------~~K~~v~k~Ld~L~~~ 45 (169)
T PF07106_consen 9 YMKEQNRPYSAQDIFDNLHNK-----------VGKTAVQKALDSLVEE 45 (169)
T ss_pred HHHHcCCCCcHHHHHHHHHhh-----------ccHHHHHHHHHHHHhC
Confidence 334458888888888877652 3455555555554443
No 31
>KOG0994|consensus
Probab=34.47 E-value=3.3e+02 Score=33.07 Aligned_cols=32 Identities=22% Similarity=0.221 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHHhh-cCCCCHHHHHHHHHHH
Q psy14634 195 TKDEVERKSKEIQNGM-MYQWKEEDVEQIVREK 226 (388)
Q Consensus 195 T~~~V~~K~~dI~k~~-n~~~TeeDI~~mI~~K 226 (388)
+..++++|+++|++++ +...|.+||.+|...=
T Consensus 1202 ~f~~me~kl~~ir~il~~~svs~~~i~~l~~~~ 1234 (1758)
T KOG0994|consen 1202 RFLDMEEKLEEIRAILSAPSVSAEDIAQLASAT 1234 (1758)
T ss_pred HHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHH
Confidence 4567889999999998 8888999998887653
No 32
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=34.47 E-value=64 Score=26.85 Aligned_cols=80 Identities=24% Similarity=0.395 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHhhcCC-CCHHHHHHHHHH---HhhcCCCCCchhHHHHHHHHHHHHHHhCC-CH----HHHHHHHHHHH
Q psy14634 197 DEVERKSKEIQNGMMYQ-WKEEDVEQIVRE---KERFKPTPYNYAMKKTQLMKERDMAQSKG-DD----EEASILQRKID 267 (388)
Q Consensus 197 ~~V~~K~~dI~k~~n~~-~TeeDI~~mI~~---K~~~~~~~~N~a~eK~rL~~ere~A~~~G-D~----eev~~L~~qL~ 267 (388)
..|..-.+.+.+.+... ....+|++++.- ++.+...--++-.++-.+.+++..+...| |. +++..|.++|.
T Consensus 5 k~ir~n~e~v~~~l~~R~~~~~~vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~ 84 (108)
T PF02403_consen 5 KLIRENPEEVRENLKKRGGDEEDVDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIK 84 (108)
T ss_dssp HHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHH
T ss_pred HHHHhCHHHHHHHHHHcCCCHhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHH
Confidence 33444444555444333 566666666643 33333222233467777888888888877 22 25666667777
Q ss_pred HHHHHHhhh
Q psy14634 268 DLEERANEL 276 (388)
Q Consensus 268 eLE~~~~~l 276 (388)
+++..+..+
T Consensus 85 ~le~~~~~~ 93 (108)
T PF02403_consen 85 ELEEQLKEL 93 (108)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 777655443
No 33
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=32.91 E-value=1.1e+02 Score=27.73 Aligned_cols=46 Identities=20% Similarity=0.180 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHH
Q psy14634 213 QWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQR 264 (388)
Q Consensus 213 ~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~ 264 (388)
.+|.+-.+++-++=..+. ..++.++.+++..|.+.||..+-++++.
T Consensus 4 ~lT~~G~~~L~~El~~L~------~~~r~~~~~~i~~Ar~~GDlsENaeY~a 49 (156)
T TIGR01461 4 LITPEGYEKLKQELNYLW------REERPEVTQKVTWAASLGDRSENADYQY 49 (156)
T ss_pred ccCHHHHHHHHHHHHHHH------hcccHHHHHHHHHHHHcCCcchhhhhHH
Confidence 355555555555544432 1367788889999999999776665544
No 34
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.
Probab=32.52 E-value=1.3e+02 Score=32.85 Aligned_cols=101 Identities=18% Similarity=0.245 Sum_probs=70.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHH---H
Q psy14634 189 EGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQR---K 265 (388)
Q Consensus 189 ~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~---q 265 (388)
.|.|.|.+.-=.+|+++|++ +...+++++++..-+-=....+ + .++=..|--++..|..-.|..-+.-|++ +
T Consensus 98 ~glprp~vgis~~~~~~i~~-~g~~~~~~~~e~lr~~lh~ykk-g---~idgddl~~eia~~l~~~d~~~~~ild~vfpe 172 (533)
T TIGR00470 98 AGLPRPDVGLGNEKIEIIEN-LGIDIDDEKKERLREVFHLYKK-G---AIDGDDLVFEIAKALNVSNEMGLKVLETVFPE 172 (533)
T ss_pred cCCCCCCcCcCHHHHHHHHH-hCCCCChhHHHHHHHHHHHhhc-C---CCccchhHHHHHHhhCCchHHHHHHHHHhChh
Confidence 57999999999999999999 9999999987764333223222 2 2566778888888888888888887776 6
Q ss_pred HHHHHHHHhhhh-hcc--ccchHHHHHHHHHH
Q psy14634 266 IDDLEERANELD-KAR--TSTISSISYINNRN 294 (388)
Q Consensus 266 L~eLE~~~~~l~-k~~--~~~~~~La~IN~RN 294 (388)
+++|......+- ..+ +.++..|+.||.++
T Consensus 173 fk~l~p~s~~~lLRTHTTpgqirtL~~L~~~~ 204 (533)
T TIGR00470 173 FKDLKPESTTLTLRSHMTSGWFITLSSIIDKR 204 (533)
T ss_pred hhhcChHhhCcccccCChhHHHHHHHHHhhcC
Confidence 677765432221 122 22466777777744
No 35
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=32.34 E-value=2.8e+02 Score=23.69 Aligned_cols=16 Identities=19% Similarity=0.586 Sum_probs=12.7
Q ss_pred CCCCHHHHHHHHHHHh
Q psy14634 212 YQWKEEDVEQIVREKE 227 (388)
Q Consensus 212 ~~~TeeDI~~mI~~K~ 227 (388)
..+|.+||+.+|+.+.
T Consensus 6 kt~tq~ev~~~i~k~~ 21 (125)
T PF14265_consen 6 KTFTQEEVDKIIKKRL 21 (125)
T ss_pred hhhHHHHHHHHHHHHH
Confidence 4689999999997543
No 36
>cd07963 Anticodon_Ia_Cys Anticodon-binding domain of cysteinyl tRNA synthetases. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA.
Probab=31.34 E-value=61 Score=28.71 Aligned_cols=32 Identities=19% Similarity=0.207 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634 240 KTQLMKERDMAQSKGDDEEASILQRKIDDLEE 271 (388)
Q Consensus 240 K~rL~~ere~A~~~GD~eev~~L~~qL~eLE~ 271 (388)
=..|..+|..|+..+|.+.+.+|..+|.++.=
T Consensus 112 v~~Ll~~R~~aR~~Kdf~~AD~IRd~L~~~Gi 143 (156)
T cd07963 112 IEALIAQRNQARKAKDWAEADRIRDELAAQGI 143 (156)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHHCCc
Confidence 55788999999999999999999999988653
No 37
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=30.09 E-value=5.9e+02 Score=25.66 Aligned_cols=81 Identities=14% Similarity=0.291 Sum_probs=52.6
Q ss_pred eEEEEeecCceeeeeeeeccCCcCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcC
Q psy14634 151 KGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFK 230 (388)
Q Consensus 151 kyL~L~hG~~eR~f~m~~VSNspfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~ 230 (388)
+.+.-+||. ..||..++-.-|.-+.-+|-. .=+..|+..--+.+|++|+..|++-=.-+.
T Consensus 103 q~If~KHGD--------IAsNc~lkS~~~RS~yLe~Lc------------~IIqeLq~t~~~~LS~~dl~e~~~~l~DLe 162 (269)
T PF05278_consen 103 QKIFEKHGD--------IASNCKLKSQQFRSYYLECLC------------DIIQELQSTPLKELSESDLKEMIATLKDLE 162 (269)
T ss_pred HHHHHhCcc--------HhhccccCcHHHHHHHHHHHH------------HHHHHHhcCcHhhhhHHHHHHHHHHHHHHH
Confidence 334456675 446677777777665544432 225666665567899999999988876666
Q ss_pred CCCCchhHHHHHHHHHHHHHH
Q psy14634 231 PTPYNYAMKKTQLMKERDMAQ 251 (388)
Q Consensus 231 ~~~~N~a~eK~rL~~ere~A~ 251 (388)
..+.++.--|.+|..-++..+
T Consensus 163 sa~vkV~WLR~~L~Ei~Ea~e 183 (269)
T PF05278_consen 163 SAKVKVDWLRSKLEEILEAKE 183 (269)
T ss_pred HcCcchHHHHHHHHHHHHHHH
Confidence 677777767777766555433
No 38
>COG1422 Predicted membrane protein [Function unknown]
Probab=29.41 E-value=1.2e+02 Score=29.21 Aligned_cols=35 Identities=31% Similarity=0.343 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhh
Q psy14634 242 QLMKERDMAQSKGDDEEASILQRKIDDLEERANEL 276 (388)
Q Consensus 242 rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l 276 (388)
.+.++...|+.+||.+++++|+++=.++-....++
T Consensus 83 efq~e~~eA~~~~d~~~lkkLq~~qmem~~~Q~el 117 (201)
T COG1422 83 EFQKEFREAQESGDMKKLKKLQEKQMEMMDDQREL 117 (201)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 56778899999999999999998776665533333
No 39
>PF03449 GreA_GreB_N: Transcription elongation factor, N-terminal; InterPro: IPR022691 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A 2ETN_C 2P4V_B.
Probab=29.29 E-value=1.4e+02 Score=23.98 Aligned_cols=41 Identities=24% Similarity=0.366 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHH
Q psy14634 214 WKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEAS 260 (388)
Q Consensus 214 ~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~ 260 (388)
+|.+-..++.++=..+. -.++..+..++..|.+.||..+=+
T Consensus 6 lT~~g~~~L~~EL~~L~------~~~rpe~~~~i~~Ar~~GDlsENa 46 (74)
T PF03449_consen 6 LTPEGYEKLQAELEHLK------NVERPEIAEEIAEAREQGDLSENA 46 (74)
T ss_dssp EEHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHCCSSSTSSH
T ss_pred cCHHHHHHHHHHHHHHH------HhhhHHHHHHHHHHHHcCCcccch
Confidence 55555555444433322 257889999999999999985433
No 40
>PF02696 UPF0061: Uncharacterized ACR, YdiU/UPF0061 family; InterPro: IPR003846 The proteins in this entry are functionally uncharacterised.
Probab=29.05 E-value=2.3e+02 Score=30.58 Aligned_cols=52 Identities=15% Similarity=0.265 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Q psy14634 213 QWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKID 267 (388)
Q Consensus 213 ~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~qL~ 267 (388)
..+++++....+.-++.++. ++++--.+.+.++.|++.||...+.+|.+-|.
T Consensus 433 ~~~~~~~a~r~~~M~~vNP~---yIlRN~l~e~AI~~Ae~~GD~s~~~~Ll~~l~ 484 (487)
T PF02696_consen 433 ALSDEEIAARQARMRSVNPK---YILRNHLAEEAIEAAEEDGDFSEVHRLLEVLQ 484 (487)
T ss_pred cCChhhHHHHHHHHHHhCCC---ccCcHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Confidence 35566666555554455442 24455566777999999999999999877654
No 41
>PRK10884 SH3 domain-containing protein; Provisional
Probab=28.95 E-value=2.7e+02 Score=26.68 Aligned_cols=8 Identities=25% Similarity=0.517 Sum_probs=3.9
Q ss_pred cCceeecC
Q psy14634 138 TGKIYSLG 145 (388)
Q Consensus 138 ~~K~Y~lg 145 (388)
|+..|.+=
T Consensus 40 Pg~~y~Iv 47 (206)
T PRK10884 40 PGDQYRIV 47 (206)
T ss_pred CCCCCceE
Confidence 44555543
No 42
>PHA02277 hypothetical protein
Probab=28.00 E-value=4.6e+02 Score=23.78 Aligned_cols=54 Identities=13% Similarity=0.200 Sum_probs=39.7
Q ss_pred cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhh
Q psy14634 173 EFTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKER 228 (388)
Q Consensus 173 pfTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~ 228 (388)
.+++.....|...+....+.- +.-=++..++|+++-++..+=+|+..++.-=..
T Consensus 11 ~iS~~Dm~~W~e~V~tg~v~g--K~v~ek~~KqL~Ri~~RsVSledaT~Ia~~L~~ 64 (150)
T PHA02277 11 GISQADMEKWIEAVVQGTVDG--KQVDEKTAKQLDRIGSRSVSLEEATRIAKVLNA 64 (150)
T ss_pred hccHHHHHHHHHHHHhCcccc--cccchhhHHHHHHHhcccccHHHHHHHHHHHHH
Confidence 578999999999887654432 222234568999999999999999988865443
No 43
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=27.52 E-value=2.1e+02 Score=26.43 Aligned_cols=57 Identities=14% Similarity=0.264 Sum_probs=44.3
Q ss_pred eccCCcCCHHHHHHHHHHHHhcCC---CCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhh
Q psy14634 168 FISNQEFTESEFIRWKDQCMTEGV---ALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKER 228 (388)
Q Consensus 168 ~VSNspfTe~EF~Rw~~~~~~~~~---~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~ 228 (388)
...++.||++|.++|+.+-..-.. -..+..++ ..|-+++.++.|+++|.+|+..=..
T Consensus 8 ~~~~~~~t~~qi~~lkeaF~l~D~d~~G~I~~~el----~~ilr~lg~~~s~~ei~~l~~~~d~ 67 (160)
T COG5126 8 LLTFTQLTEEQIQELKEAFQLFDRDSDGLIDRNEL----GKILRSLGFNPSEAEINKLFEEIDA 67 (160)
T ss_pred hhhcccCCHHHHHHHHHHHHHhCcCCCCCCcHHHH----HHHHHHcCCCCcHHHHHHHHHhccC
Confidence 456789999999999998765432 34455666 5566689999999999999988665
No 44
>KOG3032|consensus
Probab=27.42 E-value=95 Score=30.70 Aligned_cols=51 Identities=12% Similarity=0.235 Sum_probs=41.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcC
Q psy14634 174 FTESEFIRWKDQCMTEGVALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFK 230 (388)
Q Consensus 174 fTe~EF~Rw~~~~~~~~~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~ 230 (388)
--++||+||.+.+..+. -.+..+.++.+...+...-.++|++.+..++++.
T Consensus 164 ~~d~Ey~rfqkeI~~~~------tesd~iveEeeed~~l~reieeidEQi~~~kkve 214 (264)
T KOG3032|consen 164 DIDDEYKRFQKEIQDDL------TESDSIVEEEEEDAALTREIEEIDEQISYKKKVE 214 (264)
T ss_pred hHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44789999999999875 3566778888888888888888998888887764
No 45
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=27.25 E-value=1.1e+02 Score=25.38 Aligned_cols=38 Identities=24% Similarity=0.319 Sum_probs=27.3
Q ss_pred CcCCHHHHHHHHHH----HHhcCCCCCCHHHHHHHHHHHHHh
Q psy14634 172 QEFTESEFIRWKDQ----CMTEGVALPTKDEVERKSKEIQNG 209 (388)
Q Consensus 172 spfTe~EF~Rw~~~----~~~~~~~lPT~~~V~~K~~dI~k~ 209 (388)
-+||+++|++|... ++..+.+-+..+++......+...
T Consensus 71 ~~I~~~~f~~~l~~l~~al~~~~~~~~~~~~~~~~~~~~~~~ 112 (116)
T cd00454 71 FPITEEEFDAWLELLRDALDELGVPAELADALLARAERIADH 112 (116)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 38999999999874 455566666777777776666544
No 46
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=27.13 E-value=1.4e+02 Score=31.33 Aligned_cols=35 Identities=37% Similarity=0.491 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHhCC-CHH----HHHHHHHHHHHHHHH
Q psy14634 238 MKKTQLMKERDMAQSKG-DDE----EASILQRKIDDLEER 272 (388)
Q Consensus 238 ~eK~rL~~ere~A~~~G-D~e----ev~~L~~qL~eLE~~ 272 (388)
.++..+.+++..+...+ |.+ ++.+|.++|++|++.
T Consensus 49 ~~rn~~sk~i~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~ 88 (425)
T PRK05431 49 AERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEAE 88 (425)
T ss_pred HHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555554433333 211 334444444444443
No 47
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=26.65 E-value=2.5e+02 Score=25.58 Aligned_cols=46 Identities=13% Similarity=0.160 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHH
Q psy14634 212 YQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQR 264 (388)
Q Consensus 212 ~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~ 264 (388)
..+|.+-.+++-++=..+. -+|..+.+++..|.+.||..+=+++..
T Consensus 6 ~~lT~eg~~~L~~EL~~L~-------~~r~~i~~~i~~Ar~~GDlsENaey~a 51 (158)
T PRK05892 6 KGLAPAARDHLEAELARLR-------ARRDRLAVEVNDRGMIGDHGDQAEAIQ 51 (158)
T ss_pred CccCHHHHHHHHHHHHHHH-------HHhHHHHHHHHHHHhCCCcchhhhHHH
Confidence 4577777777777666553 268889999999999999876555443
No 48
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=26.28 E-value=3.7e+02 Score=28.13 Aligned_cols=75 Identities=13% Similarity=0.251 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHhhcCCC---CHHHHHHHHHHHhhcCCCCCchh-----HHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Q psy14634 196 KDEVERKSKEIQNGMMYQW---KEEDVEQIVREKERFKPTPYNYA-----MKKTQLMKERDMAQSKGDDEEASILQRKID 267 (388)
Q Consensus 196 ~~~V~~K~~dI~k~~n~~~---TeeDI~~mI~~K~~~~~~~~N~a-----~eK~rL~~ere~A~~~GD~eev~~L~~qL~ 267 (388)
++.|..+.++|.+++..+= ..+...+.-++-..+. +...+ --...|....++.....|.+..+-.+.+|.
T Consensus 9 l~~~~~r~~el~~~L~~p~v~~d~~~~~~lske~a~l~--~iv~~~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~ 86 (363)
T COG0216 9 LESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELE--PIVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIK 86 (363)
T ss_pred HHHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence 5678888899999887773 3333444444443333 22212 223345555556666667654444444444
Q ss_pred HHHHH
Q psy14634 268 DLEER 272 (388)
Q Consensus 268 eLE~~ 272 (388)
+++..
T Consensus 87 ~~~~~ 91 (363)
T COG0216 87 ELEAK 91 (363)
T ss_pred HHHHH
Confidence 44443
No 49
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=24.56 E-value=1e+03 Score=27.59 Aligned_cols=125 Identities=14% Similarity=0.252 Sum_probs=78.8
Q ss_pred HHHHHHHHhcCCCCCC-HHHHHHHHHHHHHhhcCCCCHHHHHHHHHH-Hhhc-------------CC----CC---Cch-
Q psy14634 180 IRWKDQCMTEGVALPT-KDEVERKSKEIQNGMMYQWKEEDVEQIVRE-KERF-------------KP----TP---YNY- 236 (388)
Q Consensus 180 ~Rw~~~~~~~~~~lPT-~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~-K~~~-------------~~----~~---~N~- 236 (388)
.-|--++.-+...+-. ...+..-.+.|.+++.+.-+++||++.+++ |..+ .. .| .|.
T Consensus 454 ~LW~lAl~iEdG~ls~A~~~Lr~AQe~L~eAL~~gAs~eEI~rLm~eLR~A~~~ym~~LAeq~~~~~~~~~~p~~~~~~~ 533 (820)
T PF13779_consen 454 LLWDLALRIEDGDLSDAERRLRAAQEALREALERGASDEEIARLMQELREAMQDYMQALAEQAQRNPQQQDQPPDQGNSQ 533 (820)
T ss_pred HHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhHhCcccccCcccchhhh
Confidence 3477777766653211 123444556778888999999999997766 3222 11 12 121
Q ss_pred ---hHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhhhhc------cccchHHHHHHHHHHHHhhHHHHHH
Q psy14634 237 ---AMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKA------RTSTISSISYINNRNRRKNVEEAEK 304 (388)
Q Consensus 237 ---a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l~k~------~~~~~~~La~IN~RNRk~N~e~irK 304 (388)
.-.=.+++++++.+...|+.+++..+-++|+++-+.+..-..+ ..+.++.|.++=++=+.+--+.-|.
T Consensus 534 ~~~~~dL~~mmd~ie~la~~G~~~~A~q~L~qlq~mmenmq~~~~q~~~~~~~~q~m~~L~dl~r~Qq~L~D~tfr~ 610 (820)
T PF13779_consen 534 MMSQQDLQRMMDRIEELARSGRMDEARQLLEQLQQMMENMQNAQPQQQQQQEMQQAMEELGDLLRRQQQLMDETFRQ 610 (820)
T ss_pred ccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhccccCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2344577889999999999999999999988887744211111 1234667777777766666555443
No 50
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=23.85 E-value=2.4e+02 Score=22.83 Aligned_cols=71 Identities=15% Similarity=0.249 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q psy14634 194 PTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERA 273 (388)
Q Consensus 194 PT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~ 273 (388)
+..+++.++..+.-... .=.-+|++..++..-.-.-+..++ +.|....-.. +.+.++.++|+.||+++
T Consensus 6 ~~~d~~~~~~~~~~~~~--~~~~~e~e~~~r~~l~~~l~kldl-VtREEFd~q~---------~~L~~~r~kl~~LEarl 73 (79)
T PF04380_consen 6 KIFDDLAKQISEALPAA--QGPREEIEKNIRARLQSALSKLDL-VTREEFDAQK---------AVLARTREKLEALEARL 73 (79)
T ss_pred hHHHHHHHHHHHHHHhh--hhhHHHHHHHHHHHHHHHHHHCCC-CcHHHHHHHH---------HHHHHHHHHHHHHHHHH
Confidence 45566666655554444 233456777776543321122222 1222222222 23445566666666665
Q ss_pred hhh
Q psy14634 274 NEL 276 (388)
Q Consensus 274 ~~l 276 (388)
..|
T Consensus 74 ~~L 76 (79)
T PF04380_consen 74 AAL 76 (79)
T ss_pred HHH
Confidence 544
No 51
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=23.42 E-value=2.9e+02 Score=24.65 Aligned_cols=20 Identities=30% Similarity=0.418 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHhCCCHHH
Q psy14634 239 KKTQLMKERDMAQSKGDDEE 258 (388)
Q Consensus 239 eK~rL~~ere~A~~~GD~ee 258 (388)
++..+..++..|.+.||..+
T Consensus 21 ~r~~~~~~~~~a~~~gDl~E 40 (151)
T TIGR01462 21 KRPEISEEIAEAREHGDLSE 40 (151)
T ss_pred ccHHHHHHHHHHHHCCChhh
Confidence 45566677777777777444
No 52
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=23.03 E-value=4.8e+02 Score=25.29 Aligned_cols=94 Identities=15% Similarity=0.164 Sum_probs=56.4
Q ss_pred HHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhhhhcccc----------c-hHH
Q psy14634 218 DVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERANELDKARTS----------T-ISS 286 (388)
Q Consensus 218 DI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~~~l~k~~~~----------~-~~~ 286 (388)
.+.+.+.+++.+...-.........|...=..|.+.||++-+.+.-.+.+.||..+..++..-+. . ...
T Consensus 46 ~~A~~~a~~k~~e~~~~~~~~~~~k~e~~A~~Al~~g~E~LAr~al~~~~~le~~~~~~~~~~~~~~~~~~~l~~~~~~L 125 (225)
T COG1842 46 ALAQAIARQKQLERKLEEAQARAEKLEEKAELALQAGNEDLAREALEEKQSLEDLAKALEAELQQAEEQVEKLKKQLAAL 125 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555666666554333344567778888889999999998888888888887765433321100 1 111
Q ss_pred HHHHHHHHHHhhHHHHHHHHHhhhh
Q psy14634 287 ISYINNRNRRKNVEEAEKAIMVSCC 311 (388)
Q Consensus 287 La~IN~RNRk~N~e~irKA~l~E~k 311 (388)
=.+|-+.+.+++.-.+|.+..+-..
T Consensus 126 e~Ki~e~~~~~~~l~ar~~~akA~~ 150 (225)
T COG1842 126 EQKIAELRAKKEALKARKAAAKAQE 150 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2345555666776666655444433
No 53
>PRK10869 recombination and repair protein; Provisional
Probab=22.96 E-value=8.6e+02 Score=26.49 Aligned_cols=59 Identities=10% Similarity=0.286 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHH-------HhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q psy14634 213 QWKEEDVEQIVRE-------KERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERA 273 (388)
Q Consensus 213 ~~TeeDI~~mI~~-------K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~~~ 273 (388)
.+.++.++++-.+ |++++.+.-.+...+..+..+++.. .+..+..++|+++++++...+
T Consensus 292 ~~dp~~l~~ie~Rl~~l~~L~rKyg~~~~~~~~~~~~l~~eL~~L--~~~e~~l~~Le~e~~~l~~~l 357 (553)
T PRK10869 292 DLDPNRLAELEQRLSKQISLARKHHVSPEELPQHHQQLLEEQQQL--DDQEDDLETLALAVEKHHQQA 357 (553)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHh--hCCHHHHHHHHHHHHHHHHHH
Confidence 5666444444333 4455544444445666666666554 445777888888888887765
No 54
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=22.69 E-value=1.8e+02 Score=30.43 Aligned_cols=35 Identities=23% Similarity=0.366 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHhCCCH------HHHHHHHHHHHHHHHH
Q psy14634 238 MKKTQLMKERDMAQSKGDD------EEASILQRKIDDLEER 272 (388)
Q Consensus 238 ~eK~rL~~ere~A~~~GD~------eev~~L~~qL~eLE~~ 272 (388)
.+|-.+.+++..+...++. +++.+|.++|.+|++.
T Consensus 51 ~erN~~sk~i~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~ 91 (418)
T TIGR00414 51 AKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSAA 91 (418)
T ss_pred HHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555554444432 1334444455555443
No 55
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=22.65 E-value=2.8e+02 Score=25.19 Aligned_cols=46 Identities=15% Similarity=0.143 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHHHHH
Q psy14634 213 QWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQR 264 (388)
Q Consensus 213 ~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~L~~ 264 (388)
.+|.+-.+++-++=..+. ..+|..+.+++..|.+.||..+-++++.
T Consensus 6 ~lT~~g~~~L~~EL~~L~------~~~r~e~~~~i~~Ar~~GDl~ENaeY~a 51 (157)
T PRK01885 6 YITREGYARLKQELDYLW------REERPEVTQKVSWAASLGDRSENADYIY 51 (157)
T ss_pred ccCHHHHHHHHHHHHHHH------hhhhHHHHHHHHHHHHcCCcchhhcHHH
Confidence 355555555555544432 2467788888999999998887665554
No 56
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=21.67 E-value=1.6e+02 Score=22.75 Aligned_cols=17 Identities=18% Similarity=0.472 Sum_probs=8.3
Q ss_pred CHHHHHHHHHHHhhcCC
Q psy14634 215 KEEDVEQIVREKERFKP 231 (388)
Q Consensus 215 TeeDI~~mI~~K~~~~~ 231 (388)
|++||.+-+++|++.-+
T Consensus 19 t~eeI~~W~eERrk~~P 35 (56)
T PF10453_consen 19 TPEEIAKWIEERRKNYP 35 (56)
T ss_pred CHHHHHHHHHHHHHcCC
Confidence 45555555555444433
No 57
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=21.49 E-value=1e+02 Score=26.22 Aligned_cols=50 Identities=20% Similarity=0.251 Sum_probs=38.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCCC------HHHHHHHHHHHHHhhcCCCCHHHHHHHH
Q psy14634 174 FTESEFIRWKDQCMTEGVALPT------KDEVERKSKEIQNGMMYQWKEEDVEQIV 223 (388)
Q Consensus 174 fTe~EF~Rw~~~~~~~~~~lPT------~~~V~~K~~dI~k~~n~~~TeeDI~~mI 223 (388)
.|..|...|+.+=.....-.+. -.+-=+|+-+|-.-..-.||++|++-|=
T Consensus 8 Mt~~EL~~WL~t~~S~~~g~~~~~~es~Gh~sGRrIv~IL~K~k~dltddD~~hMr 63 (92)
T PF11338_consen 8 MTPAELEDWLRTDESKSVGEKKDGGESVGHESGRRIVEILRKRKTDLTDDDYEHMR 63 (92)
T ss_pred CCHHHHHHHHcCccccccccCCCCCcccCcchhhHHHHHHhcCcccCCHHHHHHHH
Confidence 5889999999987766555444 2455677888888888999999999874
No 58
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=21.02 E-value=5.4e+02 Score=22.16 Aligned_cols=86 Identities=16% Similarity=0.191 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCC
Q psy14634 176 ESEFIRWKDQCMTEGV-ALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKG 254 (388)
Q Consensus 176 e~EF~Rw~~~~~~~~~-~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~G 254 (388)
+.||+-.+.++..--. ..|+.+++.+=.. .+-..-+|+.||+.++-.+....+++. -=-.-|-+.++.-++
T Consensus 11 ~aEYe~LKEEi~~l~~~~~~~~e~l~~i~r---~f~g~lv~~kEi~~ilG~~~~i~Rt~~---Qvv~~l~RRiDYV~~-- 82 (99)
T PF13758_consen 11 EAEYEGLKEEIEALPEDDDATREDLLRIRR---DFGGSLVTEKEIKEILGEGQGITRTRE---QVVDVLSRRIDYVQQ-- 82 (99)
T ss_pred HHHHHHHHHHHHhccccCCCCHHHHHHHHH---hcCcccccHHHHHHHhCCCCCCCcCHH---HHHHHHHHHHHHHHH--
Confidence 6788888888877532 3456666644322 233678899999999987654332221 111223333343332
Q ss_pred CHHHHHHHHHHHHHHHHH
Q psy14634 255 DDEEASILQRKIDDLEER 272 (388)
Q Consensus 255 D~eev~~L~~qL~eLE~~ 272 (388)
-++.|+++|+..|.+
T Consensus 83 ---Ni~tleKql~~aE~k 97 (99)
T PF13758_consen 83 ---NIETLEKQLEAAENK 97 (99)
T ss_pred ---HHHHHHHHHHHHHHh
Confidence 255566666665553
No 59
>PF08912 Rho_Binding: Rho Binding; InterPro: IPR015008 Rho is responsible for the recognition and binding of Rho binding domain-containing proteins (such as ROCK) to Rho, resulting in activation of the GTPase which in turn modulates the phosphorylation of various signalling proteins. This domain is within an amphipathic alpha-helical coiled-coil and interacts with Rho through predominantly hydrophobic interactions []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0000910 cytokinesis, 0006468 protein phosphorylation; PDB: 1UIX_A 1S1C_X.
Probab=20.97 E-value=1.7e+02 Score=23.64 Aligned_cols=18 Identities=28% Similarity=0.265 Sum_probs=12.3
Q ss_pred chhHHHHHHHHHHHHHHh
Q psy14634 235 NYAMKKTQLMKERDMAQS 252 (388)
Q Consensus 235 N~a~eK~rL~~ere~A~~ 252 (388)
|++.|+..|..++..+.+
T Consensus 7 ~l~~EkeeL~~klk~~qe 24 (69)
T PF08912_consen 7 NLAKEKEELNNKLKKQQE 24 (69)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHH
Confidence 456778888777765544
No 60
>PF08537 NBP1: Fungal Nap binding protein NBP1; InterPro: IPR013743 NBP1 is a nuclear protein which has been shown in Saccharomyces cerevisiae (Bakers yeast) to be essential for the G2/M transition of the cell cycle.
Probab=20.79 E-value=3.2e+02 Score=28.18 Aligned_cols=41 Identities=34% Similarity=0.563 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHH
Q psy14634 256 DEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRR 296 (388)
Q Consensus 256 ~eev~~L~~qL~eLE~~~~~l~k~~~~~~~~La~IN~RNRk 296 (388)
.+.|--|+.++++|++++..+.+.-......|..-+++|.-
T Consensus 174 ~D~v~LLqkk~~~l~~~l~~~~~eL~~~~k~L~faqekn~L 214 (323)
T PF08537_consen 174 SDRVILLQKKIDELEERLNDLEKELEITKKDLKFAQEKNAL 214 (323)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47777778888888777655443222233455555555554
No 61
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=20.78 E-value=7.1e+02 Score=28.65 Aligned_cols=51 Identities=14% Similarity=0.240 Sum_probs=38.7
Q ss_pred CHHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q psy14634 175 TESEFIRWKDQCMTEG--VALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVRE 225 (388)
Q Consensus 175 Te~EF~Rw~~~~~~~~--~~lPT~~~V~~K~~dI~k~~n~~~TeeDI~~mI~~ 225 (388)
.+.|+...++++-+.. ..-|+...+.++++.|++-+++.||++=.-.=|+.
T Consensus 434 Le~elekLk~eilKAk~s~~~~~~~~L~e~IeKLk~E~d~e~S~A~~~~gLk~ 486 (762)
T PLN03229 434 LEGEVEKLKEQILKAKESSSKPSELALNEMIEKLKKEIDLEYTEAVIAMGLQE 486 (762)
T ss_pred HHHHHHHHHHHHHhcccccCCCCChHHHHHHHHHHHHHHHHHHHhhhhhhHHH
Confidence 3788888888888774 45666778889999999989998888765544444
No 62
>PF02661 Fic: Fic/DOC family; InterPro: IPR003812 This entry contains the Fic (filamentation induced by cAMP) protein and doc (death on curing) protein. The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism []. This family contains a central conserved motif HPFXXGNG in most members. The exact molecular function of these proteins is uncertain. P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation []. A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1 []. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family.; PDB: 3SHG_A 3N3V_A 3N3U_A 2F6S_B 2JK8_B 2VZA_D 2VY3_A 3LET_B 3EQX_A 3SE5_D ....
Probab=20.60 E-value=18 Score=28.51 Aligned_cols=28 Identities=25% Similarity=0.372 Sum_probs=21.4
Q ss_pred hhhhhhhhhhhhhhhhhccCCCcCCCCC
Q psy14634 54 AMKKTQLMKERDMAQSKIGESQPFRDGN 81 (388)
Q Consensus 54 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (388)
+.+....+..-..+-..+-..+||+|||
T Consensus 58 ~~~~~~~~~~aa~~~~~~~~iHPF~dGN 85 (97)
T PF02661_consen 58 ANSEEDPIEKAAWLHYEFVYIHPFRDGN 85 (97)
T ss_dssp HHTHCCHHHHHHHHHHHHHHHCSSSSHH
T ss_pred hcccccHHHHHHHHHHHHHhcCcccCCC
Confidence 4555666666677777788889999998
No 63
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=20.56 E-value=7.7e+02 Score=27.16 Aligned_cols=34 Identities=21% Similarity=0.263 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHhhcC
Q psy14634 197 DEVERKSKEIQNGMMYQWKEEDVEQIVREKERFK 230 (388)
Q Consensus 197 ~~V~~K~~dI~k~~n~~~TeeDI~~mI~~K~~~~ 230 (388)
..+.....+|.+-+...-.+++|..+..+.....
T Consensus 401 ~~~e~el~~l~~~l~~~~~~e~i~~l~e~l~~l~ 434 (650)
T TIGR03185 401 RELEEELAEVDKKISTIPSEEQIAQLLEELGEAQ 434 (650)
T ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHH
Confidence 3455555666666666556677777776666554
No 64
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=20.47 E-value=2.1e+02 Score=30.96 Aligned_cols=45 Identities=16% Similarity=0.259 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHhhHH
Q psy14634 256 DEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVE 300 (388)
Q Consensus 256 ~eev~~L~~qL~eLE~~~~~l~k~~~~~~~~La~IN~RNRk~N~e 300 (388)
.+++++|+++|+.|...+..+.+......+.|.++...|+.+..+
T Consensus 75 Q~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Q 119 (475)
T PRK13729 75 QVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ 119 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 456777788888776554434444455566777777777766443
No 65
>PRK10698 phage shock protein PspA; Provisional
Probab=20.41 E-value=4.6e+02 Score=25.14 Aligned_cols=57 Identities=16% Similarity=0.211 Sum_probs=35.9
Q ss_pred HHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHhCCCHHHHHH-------HHHHHHHHHHHH
Q psy14634 217 EDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASI-------LQRKIDDLEERA 273 (388)
Q Consensus 217 eDI~~mI~~K~~~~~~~~N~a~eK~rL~~ere~A~~~GD~eev~~-------L~~qL~eLE~~~ 273 (388)
..+...+..++++...-..+...-..+...=..|...|+++.+.. +..++..|+...
T Consensus 45 ~alA~~~A~~k~~er~~~~~~~~~~~~e~kA~~Al~~G~EdLAr~AL~~K~~~~~~~~~l~~~~ 108 (222)
T PRK10698 45 STSARALAEKKQLTRRIEQAEAQQVEWQEKAELALRKEKEDLARAALIEKQKLTDLIATLEHEV 108 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555443222233455666677788899999998887 777777776644
No 66
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=20.35 E-value=1.2e+02 Score=32.19 Aligned_cols=33 Identities=21% Similarity=0.240 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q psy14634 239 KKTQLMKERDMAQSKGDDEEASILQRKIDDLEE 271 (388)
Q Consensus 239 eK~rL~~ere~A~~~GD~eev~~L~~qL~eLE~ 271 (388)
+-..|.++|+.|++++|.+++.+|.++|.++.=
T Consensus 417 ~~~~li~~R~~aR~~Kdf~~AD~IRd~L~~~Gi 449 (463)
T PRK00260 417 EIEALIEERQEARKAKDFALADAIRDELAALGI 449 (463)
T ss_pred HHHHHHHHHHHHHHccCHHHHHHHHHHHHHCCc
Confidence 456788899999999999999999999987643
No 67
>KOG1029|consensus
Probab=20.03 E-value=4.5e+02 Score=30.61 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=13.8
Q ss_pred ccccchHHHHHHHHHHHHhhHH
Q psy14634 279 ARTSTISSISYINNRNRRKNVE 300 (388)
Q Consensus 279 ~~~~~~~~La~IN~RNRk~N~e 300 (388)
++...++.+-++|.+|..+|++
T Consensus 424 Qk~reqe~iv~~nak~~ql~~e 445 (1118)
T KOG1029|consen 424 QKNREQEWIVYLNAKKKQLQQE 445 (1118)
T ss_pred hhhHHHHHHHHHHHHHHHHHHH
Confidence 3344556666677777777765
Done!