Query gi|254780412|ref|YP_003064825.1| hypothetical protein CLIBASIA_01485 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 94 No_of_seqs 106 out of 392 Neff 5.2 Searched_HMMs 39220 Date Sun May 29 19:02:05 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780412.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG2960 Uncharacterized protei 99.8 9.1E-20 2.3E-24 146.3 9.7 82 1-82 9-90 (103) 2 pfam04380 DUF526 Protein of un 99.8 2.8E-19 7.1E-24 143.2 9.1 70 10-79 1-70 (70) 3 pfam05597 Phasin Poly(hydroxya 97.0 0.0081 2.1E-07 38.9 8.8 50 23-79 81-130 (132) 4 COG3937 Uncharacterized conser 96.8 0.0098 2.5E-07 38.4 8.3 62 14-82 46-107 (108) 5 TIGR01837 PHA_granule_1 poly(h 96.2 0.073 1.9E-06 32.8 9.4 63 9-78 57-119 (121) 6 TIGR01834 PHA_synth_III_E poly 93.3 0.45 1.2E-05 27.8 7.0 65 12-80 266-330 (332) 7 pfam09712 PHA_synth_III_E Poly 92.8 0.92 2.3E-05 25.9 8.0 58 10-71 235-292 (293) 8 pfam12126 DUF3583 Protein of u 90.9 1.5 3.8E-05 24.5 10.9 78 5-85 11-88 (284) 9 KOG4797 consensus 81.4 4 0.0001 21.8 5.2 51 30-87 46-96 (123) 10 pfam01166 TSC22 TSC-22/dip/bun 78.0 5.3 0.00014 21.1 4.9 33 49-88 12-44 (57) 11 pfam11853 DUF3373 Protein of u 77.4 3.5 8.9E-05 22.2 3.8 28 65-92 31-58 (485) 12 PRK13182 racA polar chromosome 75.5 5.7 0.00015 20.9 4.5 36 55-90 118-153 (178) 13 pfam11642 Blo-t-5 Mite allerge 71.1 8.7 0.00022 19.7 4.5 36 44-79 76-111 (112) 14 pfam10805 DUF2730 Protein of u 70.3 6 0.00015 20.7 3.6 55 27-81 34-95 (106) 15 pfam06698 DUF1192 Protein of u 70.1 6 0.00015 20.7 3.5 27 66-92 21-47 (58) 16 TIGR01462 greA transcription e 69.3 6.6 0.00017 20.5 3.6 45 32-83 23-67 (155) 17 KOG3684 consensus 65.6 12 0.00031 18.7 5.8 37 53-89 429-465 (489) 18 PRK11239 hypothetical protein; 62.8 14 0.00035 18.4 4.2 26 63-88 188-213 (215) 19 PHA00728 hypothetical protein 62.5 11 0.00029 19.0 3.7 28 65-92 5-32 (153) 20 COG5509 Uncharacterized small 61.2 12 0.0003 18.9 3.6 28 65-92 25-52 (65) 21 PRK10636 putative ABC transpor 59.0 16 0.00041 18.0 5.2 22 65-86 563-584 (638) 22 PRK11147 ABC transporter ATPas 58.7 16 0.00042 18.0 4.2 24 65-88 568-591 (632) 23 pfam03670 UPF0184 Uncharacteri 56.4 18 0.00045 17.7 5.5 40 45-84 20-59 (83) 24 COG3132 Uncharacterized protei 55.8 14 0.00035 18.5 3.2 20 70-89 190-209 (215) 25 pfam07889 DUF1664 Protein of u 54.1 19 0.00049 17.5 9.2 86 1-86 33-124 (126) 26 pfam04966 OprB Carbohydrate-se 53.9 6.1 0.00016 20.7 1.1 38 50-87 1-38 (365) 27 PRK00846 hypothetical protein; 51.2 20 0.00051 17.4 3.4 22 67-88 9-30 (78) 28 TIGR03282 methan_mark_13 putat 49.8 23 0.00058 17.1 3.8 25 41-65 129-153 (352) 29 cd04776 HTH_GnyR Helix-Turn-He 49.7 23 0.00058 17.1 5.8 35 56-90 78-112 (118) 30 pfam07106 TBPIP Tat binding pr 48.4 24 0.00061 16.9 6.0 44 44-87 65-108 (169) 31 PRK02119 hypothetical protein; 48.1 19 0.00049 17.5 3.0 26 58-83 30-55 (73) 32 PRK04406 hypothetical protein; 47.6 20 0.00051 17.4 3.0 11 67-77 41-51 (75) 33 PRK02793 hypothetical protein; 46.7 19 0.00049 17.6 2.7 24 60-83 31-54 (72) 34 pfam01519 DUF16 Protein of unk 45.3 27 0.00068 16.6 5.5 35 45-79 7-45 (87) 35 COG1579 Zn-ribbon protein, pos 44.5 27 0.0007 16.6 6.4 52 34-85 71-123 (239) 36 pfam10458 Val_tRNA-synt_C Valy 44.3 28 0.0007 16.5 4.3 45 36-84 21-65 (66) 37 TIGR01149 mtrG tetrahydrometha 44.1 28 0.00071 16.5 4.2 30 47-83 10-39 (72) 38 pfam06447 consensus 43.0 29 0.00074 16.4 8.7 38 50-87 75-112 (407) 39 PRK00892 lpxD UDP-3-O-[3-hydro 42.2 30 0.00076 16.3 3.4 21 65-85 322-342 (343) 40 PRK00295 hypothetical protein; 42.1 22 0.00056 17.1 2.5 30 56-85 24-53 (68) 41 TIGR03007 pepcterm_ChnLen poly 41.5 30 0.00078 16.3 4.8 84 7-90 267-361 (510) 42 PRK04325 hypothetical protein; 41.1 29 0.00074 16.4 3.0 32 53-84 25-56 (74) 43 TIGR00998 8a0101 efflux pump m 41.1 27 0.00069 16.6 2.8 36 40-75 154-192 (379) 44 pfam06825 HSBP1 Heat shock fac 40.8 31 0.00079 16.2 5.2 21 65-85 28-48 (54) 45 TIGR02978 phageshock_pspC phag 40.1 22 0.00057 17.1 2.3 29 62-90 88-116 (128) 46 pfam00038 Filament Intermediat 38.8 34 0.00085 16.0 11.2 67 22-88 181-253 (312) 47 cd04171 SelB SelB subfamily. 38.2 34 0.00087 15.9 3.2 22 41-62 110-131 (164) 48 pfam10152 DUF2360 Predicted co 37.6 35 0.00089 15.9 3.4 37 40-83 10-46 (147) 49 pfam08317 Spc7 Spc7 kinetochor 36.3 37 0.00093 15.7 10.9 82 8-90 166-247 (322) 50 KOG3958 consensus 36.1 34 0.00087 16.0 2.7 17 72-88 191-207 (371) 51 TIGR02894 DNA_bind_RsfA transc 35.5 38 0.00096 15.7 5.8 37 49-85 104-140 (163) 52 PRK06664 fliD flagellar hook-a 33.9 40 0.001 15.5 7.4 61 29-90 602-666 (684) 53 COG3880 Modulator of heat shoc 33.7 27 0.00068 16.6 1.8 25 46-74 147-171 (176) 54 pfam01920 Prefoldin_2 Prefoldi 33.5 41 0.001 15.5 5.7 38 54-91 65-102 (104) 55 pfam00509 Hemagglutinin Hemagg 33.2 41 0.001 15.4 5.3 49 29-88 371-419 (550) 56 pfam01763 Herpes_UL6 Herpesvir 32.0 43 0.0011 15.3 7.8 57 19-86 343-399 (551) 57 PRK09039 hypothetical protein; 32.0 43 0.0011 15.3 9.6 43 50-92 122-164 (343) 58 TIGR02132 phaR_Bmeg polyhydrox 31.7 43 0.0011 15.3 8.4 62 10-75 35-96 (189) 59 smart00787 Spc7 Spc7 kinetocho 31.5 44 0.0011 15.3 10.3 83 8-91 162-244 (312) 60 COG3165 Uncharacterized protei 31.5 44 0.0011 15.3 10.3 59 23-81 139-202 (204) 61 COG3416 Uncharacterized protei 31.2 44 0.0011 15.2 3.8 76 1-86 1-76 (233) 62 pfam11336 DUF3138 Protein of u 29.8 47 0.0012 15.1 3.2 34 60-93 20-53 (514) 63 pfam12269 zf-CpG_bind_C CpG bi 29.7 47 0.0012 15.1 5.3 33 58-90 29-61 (236) 64 pfam10393 Matrilin_ccoil Trime 29.0 48 0.0012 15.0 5.4 28 60-87 15-42 (44) 65 PRK05729 valS valyl-tRNA synth 29.0 48 0.0012 15.0 3.9 43 39-85 834-876 (877) 66 pfam08900 DUF1845 Domain of un 28.7 49 0.0012 15.0 3.8 46 27-72 153-199 (217) 67 pfam04012 PspA_IM30 PspA/IM30 28.5 49 0.0013 14.9 6.3 36 52-87 106-141 (220) 68 COG1842 PspA Phage shock prote 28.5 49 0.0013 14.9 6.4 57 32-88 85-143 (225) 69 pfam10046 BLOC1_2 Biogenesis o 28.2 50 0.0013 14.9 5.8 49 40-88 24-82 (99) 70 KOG4571 consensus 27.7 51 0.0013 14.8 6.1 41 49-89 246-286 (294) 71 pfam09766 FimP Fms-interacting 27.6 51 0.0013 14.8 5.5 73 18-92 37-128 (352) 72 pfam07407 Seadorna_VP6 Seadorn 27.4 51 0.0013 14.8 3.6 37 44-80 25-61 (420) 73 COG2193 Bfr Bacterioferritin ( 27.3 52 0.0013 14.8 6.2 48 27-77 94-141 (157) 74 KOG0241 consensus 27.0 52 0.0013 14.8 4.6 35 50-84 370-405 (1714) 75 pfam00846 Hanta_nucleocap Hant 27.0 52 0.0013 14.8 6.5 40 48-87 32-71 (428) 76 PRK10014 DNA-binding transcrip 26.8 53 0.0013 14.7 2.4 49 1-49 1-52 (342) 77 COG2846 Regulator of cell morp 26.0 54 0.0014 14.7 3.3 45 4-48 3-47 (221) 78 KOG4643 consensus 26.0 54 0.0014 14.7 3.8 41 46-86 273-315 (1195) 79 TIGR00081 purC phosphoribosyla 25.7 55 0.0014 14.6 4.7 34 39-72 234-267 (374) 80 KOG2802 consensus 25.7 55 0.0014 14.6 2.5 77 2-84 384-491 (503) 81 pfam06962 rRNA_methylase Putat 25.6 34 0.00087 15.9 1.2 17 53-69 5-21 (140) 82 pfam09340 NuA4 Histone acetylt 25.3 56 0.0014 14.6 4.4 29 60-88 4-32 (80) 83 TIGR02169 SMC_prok_A chromosom 25.2 56 0.0014 14.6 5.6 38 52-89 787-824 (1202) 84 TIGR02231 TIGR02231 conserved 24.6 58 0.0015 14.5 5.8 76 16-91 90-177 (558) 85 pfam10234 Cluap1 Clusterin-ass 24.0 59 0.0015 14.4 8.5 69 20-93 136-206 (269) 86 PRK11578 macrolide transporter 23.5 61 0.0015 14.4 12.0 51 39-89 109-159 (347) 87 pfam11488 Lge1 Transcriptional 23.3 61 0.0016 14.3 6.0 57 33-89 156-215 (234) 88 cd01282 HTH_MerR-like_sg3 Heli 23.1 62 0.0016 14.3 5.0 31 58-88 81-111 (112) 89 pfam05278 PEARLI-4 Arabidopsis 22.8 63 0.0016 14.3 5.8 40 47-86 168-207 (234) 90 COG1566 EmrA Multidrug resista 22.6 63 0.0016 14.3 5.4 28 40-67 140-167 (352) 91 pfam07195 FliD_C Flagellar hoo 22.4 64 0.0016 14.2 8.1 61 31-92 164-229 (230) 92 PRK00591 prfA peptide chain re 22.4 58 0.0015 14.5 1.9 27 58-84 76-102 (360) 93 PRK10697 DNA-binding transcrip 22.3 64 0.0016 14.2 4.3 27 63-89 80-106 (119) 94 PRK01885 greB transcription el 21.7 66 0.0017 14.1 6.4 58 23-87 14-78 (159) 95 pfam04508 Pox_A_type_inc Viral 21.5 66 0.0017 14.1 2.7 18 67-84 3-20 (26) 96 pfam07426 Dynactin_p22 Dynacti 21.4 67 0.0017 14.1 2.8 43 2-46 27-69 (172) 97 PRK00226 greA transcription el 21.4 67 0.0017 14.1 7.8 58 23-87 12-76 (157) 98 cd00187 TOP4c DNA Topoisomeras 21.2 68 0.0017 14.1 10.9 54 35-89 374-429 (445) 99 pfam06428 Sec2p GDP/GTP exchan 20.9 68 0.0017 14.0 5.8 40 50-89 43-82 (101) 100 pfam04102 SlyX SlyX. The SlyX 20.9 69 0.0017 14.0 5.5 33 53-85 20-52 (68) 101 cd04769 HTH_MerR2 Helix-Turn-H 20.5 70 0.0018 14.0 5.1 29 61-89 82-110 (116) No 1 >COG2960 Uncharacterized protein conserved in bacteria [Function unknown] Probab=99.82 E-value=9.1e-20 Score=146.26 Aligned_cols=82 Identities=28% Similarity=0.425 Sum_probs=79.5 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99750069999999998668887799999999999999999987398569999999999999999999999999999999 Q gi|254780412|r 1 MSFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ 80 (94) Q Consensus 1 m~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k 80 (94) +|...|+|.+..+++..++++++++++.|+|..+|++++++|++||||||||||+|+.|+.+||+++++|++||++||++ T Consensus 9 ~m~~~~~~e~~~~ql~e~~a~~~~~~~~evE~~~r~~~q~~lnkLDlVsREEFdvq~qvl~rtR~kl~~Leari~~LEar 88 (103) T COG2960 9 TMIGPNRFEDIAAQLSEDAAGAAQEVRAEVEKAFRAQLQRQLNKLDLVSREEFDVQRQVLLRTREKLAALEARIEELEAR 88 (103) T ss_pred HCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 04777789999999998731000103799999999999988776022439999999999999999999999999999987 Q ss_pred HH Q ss_conf 99 Q gi|254780412|r 81 LA 82 (94) Q Consensus 81 l~ 82 (94) ++ T Consensus 89 l~ 90 (103) T COG2960 89 LA 90 (103) T ss_pred HC T ss_conf 42 No 2 >pfam04380 DUF526 Protein of unknown function (DUF526). Probab=99.80 E-value=2.8e-19 Score=143.19 Aligned_cols=70 Identities=21% Similarity=0.345 Sum_probs=68.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999866888779999999999999999998739856999999999999999999999999999999 Q gi|254780412|r 10 QQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ 79 (94) Q Consensus 10 ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~ 79 (94) ||+++++++++|+++++++|+++++|++++++|++||||||||||+|++|+.|+|+++++|++||++||+ T Consensus 1 ddla~~~~~~~~~~~~~~~e~e~~~r~~l~~~l~~lDlVtREEFD~q~~~l~rtR~k~~~Le~rl~~LE~ 70 (70) T pfam04380 1 DDLAKLITDALGGAQGLREEAETNVRAVLQSALSKLDLVTREEFDVQRAVLARTREKLEALEARVAALEA 70 (70) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 9588998876688877889999999999999987778741999999999999999999999999997609 No 3 >pfam05597 Phasin Poly(hydroxyalcanoate) granule associated protein (phasin). Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon. Probab=96.97 E-value=0.0081 Score=38.89 Aligned_cols=50 Identities=20% Similarity=0.346 Sum_probs=39.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 779999999999999999998739856999999999999999999999999999999 Q gi|254780412|r 23 FKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ 79 (94) Q Consensus 23 ~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~ 79 (94) +.+--+.+|..|-.++.++|+++++.||.|.+++ ..++++|.++|+.|.. T Consensus 81 a~~~wdklE~~fe~rV~~aL~rLGips~~di~~L-------~~rId~L~a~l~~L~~ 130 (132) T pfam05597 81 AEGQWDKLEQAFDERVAKALNRLGVPSRKEVEAL-------SARIDELTAQLEELAE 130 (132) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH-------HHHHHHHHHHHHHHHC T ss_conf 8765888999999999999985699989999999-------9999999999999753 No 4 >COG3937 Uncharacterized conserved protein [Function unknown] Probab=96.85 E-value=0.0098 Score=38.39 Aligned_cols=62 Identities=23% Similarity=0.364 Sum_probs=51.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999866888779999999999999999998739856999999999999999999999999999999999 Q gi|254780412|r 14 RLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLA 82 (94) Q Consensus 14 ~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~ 82 (94) +++.+.+.-++.-+.+++..+..+++..+++++++++-|.+++ ++++++|+.+|..||+++- T Consensus 46 ~~vddl~~q~k~~~~e~e~K~~r~i~~ml~~~~~~r~~~~~~l-------~~rvd~Lerqv~~Lenk~k 107 (108) T COG3937 46 RFVDDLLRQAKEAQGELEEKIPRKIEEMLSDLEVARQSEMDEL-------TERVDALERQVADLENKLK 107 (108) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH-------HHHHHHHHHHHHHHHHHHC T ss_conf 9999999998987602777636899999845020000248888-------9899999999999998761 No 5 >TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein; InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.. Probab=96.19 E-value=0.073 Score=32.84 Aligned_cols=63 Identities=14% Similarity=0.295 Sum_probs=49.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999986688877999999999999999999873985699999999999999999999999999999 Q gi|254780412|r 9 FQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIE 78 (94) Q Consensus 9 ~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE 78 (94) ++.....++.+=+.+..==+.++..|-.+++++|++|++.||+|.|++ +.+++.|..+|..|- T Consensus 57 ~~~~~~~~~~~~d~~~~~w~~l~~~FD~R~~~~L~rL~IPs~~e~eaL-------~~k~e~L~~~~e~l~ 119 (121) T TIGR01837 57 IEEVKTKLEQVRDKVQRNWDKLEKAFDERVEQALNRLNIPSKEEVEAL-------RAKVEQLKEQVEELR 119 (121) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH-------HHHHHHHHHHHHHHH T ss_conf 999998888779999888988999999999999985789987769999-------999999999999884 No 6 >TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit; InterPro: IPR010123 This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species.. Probab=93.32 E-value=0.45 Score=27.83 Aligned_cols=65 Identities=17% Similarity=0.334 Sum_probs=42.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999998668887799999999999999999987398569999999999999999999999999999999 Q gi|254780412|r 12 ASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ 80 (94) Q Consensus 12 la~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k 80 (94) .+++-+..+.+...+ .......++..+..|||-||-|.|....-+.-+|-++-.|..++..++++ T Consensus 266 ~~~v~G~liNA~m~l----k~~~q~~~~~~~~~LnlPtRsEl~~~h~~i~~l~r~~~~L~~~l~~~~~~ 330 (332) T TIGR01834 266 YAKVHGKLINALMRL----KKRQQEVVEELLKALNLPTRSELDEAHQRIQELRREVKELKKRLADLEKK 330 (332) T ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 678998879899999----99999999999865389976899999999999999999999875114222 No 7 >pfam09712 PHA_synth_III_E Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E). This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. Probab=92.84 E-value=0.92 Score=25.89 Aligned_cols=58 Identities=21% Similarity=0.331 Sum_probs=41.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999998668887799999999999999999987398569999999999999999999999 Q gi|254780412|r 10 QQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIG 71 (94) Q Consensus 10 ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le 71 (94) ++.+++.+....+...+|.. ....++.++..|||.||.|.|.....+..+|.++-.|. T Consensus 235 ee~~k~~g~~~nA~m~~r~~----~q~~~e~~l~~l~lPTrseld~~~kri~eLrre~r~L~ 292 (293) T pfam09712 235 EEYAQIHGRLSNAQMRLRRA----LQQVVDELLGSLGLPTRSELDTAQRRLQELRRENRALA 292 (293) T ss_pred HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 89999999999999999999----99999999863899827889999999999999998752 No 8 >pfam12126 DUF3583 Protein of unknown function (DUF3583). This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with pfam00097 and pfam00643. Most members are promyelocytic leukemia proteins, and this family lies towards the C-terminus. Probab=90.93 E-value=1.5 Score=24.52 Aligned_cols=78 Identities=14% Similarity=0.250 Sum_probs=63.4 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00699999999986688877999999999999999999873985699999999999999999999999999999999999 Q gi|254780412|r 5 SNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL 84 (94) Q Consensus 5 ~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l 84 (94) ..++|+..-..+-.|++.++..+.|.+..||++++.++. .|-..|=+.+..|-.+.+.--+.+..++.-|++-|... T Consensus 11 Q~~~F~~Ahaqm~SAv~qL~~vr~dteelIR~rVrqvve---hvqaqErELLE~V~~rYqR~yeEiAgqL~~ldAVLqRI 87 (284) T pfam12126 11 QDRTFGAAHAQMCSAIGQLGRARADTEEQIRERVRQVVA---HVQAQERELLEAVNARYQRDYEEIAGQLGRLDAVLQRI 87 (284) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 776678999999999999988776299999999999999---99999999999999998740999998887899999999 Q ss_pred H Q ss_conf 9 Q gi|254780412|r 85 E 85 (94) Q Consensus 85 e 85 (94) . T Consensus 88 r 88 (284) T pfam12126 88 R 88 (284) T ss_pred H T ss_conf 8 No 9 >KOG4797 consensus Probab=81.45 E-value=4 Score=21.81 Aligned_cols=51 Identities=18% Similarity=0.227 Sum_probs=31.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999873985699999999999999999999999999999999999996 Q gi|254780412|r 30 AESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 30 ie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) |++.+-+-++=+-+.+-+--|||.|+++ +++-.|+.|...||..=.=|+.+ T Consensus 46 IDNKIeQAMDLVKtHLmfAVREEVe~Lk-------~qI~eL~er~~~Le~EN~lLk~~ 96 (123) T KOG4797 46 IDNKIEQAMDLVKTHLMFAVREEVEVLK-------EQIRELEERNSALERENSLLKTL 96 (123) T ss_pred ECHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 2148999999999999999999999999-------99999999999999987899850 No 10 >pfam01166 TSC22 TSC-22/dip/bun family. Probab=78.03 E-value=5.3 Score=21.06 Aligned_cols=33 Identities=24% Similarity=0.361 Sum_probs=17.2 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6999999999999999999999999999999999999965 Q gi|254780412|r 49 RAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 49 tREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) -|||.|+++ +++..|+.|+..||..=+-|+.+. T Consensus 12 VREEVevLk-------~~I~eL~~~~~~le~EN~~Lk~~~ 44 (57) T pfam01166 12 VREEVEVLK-------EQIKELEEKNSQLERENTLLKSLA 44 (57) T ss_pred HHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999999999-------999999999999999999998609 No 11 >pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length. Probab=77.38 E-value=3.5 Score=22.22 Aligned_cols=28 Identities=32% Similarity=0.532 Sum_probs=19.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999999999999999999999650023 Q gi|254780412|r 65 EEITAIGKRLEKIEQQLADLELFINQKE 92 (94) Q Consensus 65 ~~~e~Le~rl~~LE~kl~~le~~~~~k~ 92 (94) .+|++|+++|++|++++.++.-.+++.+ T Consensus 31 qkI~~L~~ql~eLk~~~~~~~~~v~~~e 58 (485) T pfam11853 31 QKIEALKKELAELKAQLKDLNKRVDKTE 58 (485) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999998776655566 No 12 >PRK13182 racA polar chromosome segregation protein; Reviewed Probab=75.52 E-value=5.7 Score=20.87 Aligned_cols=36 Identities=25% Similarity=0.305 Sum_probs=29.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999999999996500 Q gi|254780412|r 55 NVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQ 90 (94) Q Consensus 55 v~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~ 90 (94) |+---|..-|-+++.+-++|..||.+|+.+|-..+. T Consensus 118 VVSyQLLqHRrEiEEm~~~lq~Le~ri~klE~~~~~ 153 (178) T PRK13182 118 VVSYQLLQHRREMEEMLERIQKLEARLKKLEPIYIT 153 (178) T ss_pred EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 001899987999999999999999999986155228 No 13 >pfam11642 Blo-t-5 Mite allergen Blo t 5. This family of proteins is Blo t 5, an allergen protein from Blomia tropicalis mites. This protein shoes strong reactivity with IgE in asthmatic and rhinitis patients. The structure of the protein contains three alpha helices which form a coiled-coil. Probab=71.10 E-value=8.7 Score=19.72 Aligned_cols=36 Identities=17% Similarity=0.312 Sum_probs=21.0 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 739856999999999999999999999999999999 Q gi|254780412|r 44 SMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ 79 (94) Q Consensus 44 kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~ 79 (94) ++|++-|=-||...+...=.-..+.+++++|.+.++ T Consensus 76 DLnilEkfNfE~al~t~~iL~kDLk~~e~kVKaI~t 111 (112) T pfam11642 76 DLNLLEKFNFEAALATGKVLLKDLKELAKKVKAIET 111 (112) T ss_pred HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 135999826999999989999889999999887714 No 14 >pfam10805 DUF2730 Protein of unknown function (DUF2730). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. Probab=70.30 E-value=6 Score=20.74 Aligned_cols=55 Identities=16% Similarity=0.379 Sum_probs=28.8 Q ss_pred HHHHHHHH------HHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999------99999999873-985699999999999999999999999999999999 Q gi|254780412|r 27 SKEAESFA------QIKIQRTLNSM-GVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQL 81 (94) Q Consensus 27 ~~Eie~~~------r~~~e~~l~kl-dLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl 81 (94) |++++... ..++...=.+. .|-|..++..++--+...|-++.++.++|..++-+. T Consensus 34 kedv~~l~~~~~~~~~Rl~~lE~~v~~lPt~~dv~~L~~~itelrGe~k~l~~~i~~i~hq~ 95 (106) T pfam10805 34 REDVEKLIDIIASNDKRLTEMETKLESLPTAKDVHALKIEITELRGELKELSAQIQSISHQL 95 (106) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH T ss_conf 98899999998877768999999985399687899999999997146999988757688899 No 15 >pfam06698 DUF1192 Protein of unknown function (DUF1192). This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown. Probab=70.11 E-value=6 Score=20.75 Aligned_cols=27 Identities=19% Similarity=0.436 Sum_probs=19.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999999999999999650023 Q gi|254780412|r 66 EITAIGKRLEKIEQQLADLELFINQKE 92 (94) Q Consensus 66 ~~e~Le~rl~~LE~kl~~le~~~~~k~ 92 (94) -+++|+.||+.|+..|+.+++-+.+|. T Consensus 21 Sv~EL~~RIa~L~~EI~R~e~~~~~K~ 47 (58) T pfam06698 21 SVEELEERIALLQAEIARLEAALAKKK 47 (58) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 799999999999999999999999988 No 16 >TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359 Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue pre-existing arrested complexes. The 2.2 Å resolution crystal structure of Escherichia coli GreA comprises an N-terminal antiparallel alpha-helical coiled coil, and a C-terminal globular domain. While the C-terminal domain binds RNAP, the N-terminal coiled coil interacts with the transcript 3' end and is responsible for stimulating the transcript cleavage reaction . Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil. Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (IPR006358 from INTERPRO) forms a plausible outgroup and the remainder of the GreA/B family, included in this family, is designated GreA. In the Chlamydias and some spirochetes, the conserved region of these proteins is found as the C-terminal region of a much larger protein. ; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=69.32 E-value=6.6 Score=20.45 Aligned_cols=45 Identities=20% Similarity=0.212 Sum_probs=35.9 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999987398569999999999999999999999999999999999 Q gi|254780412|r 32 SFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLAD 83 (94) Q Consensus 32 ~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~ 83 (94) ..+-..+..+.+.-||====|||+ ||+++..+|.||..||..|+. T Consensus 23 peI~~~I~~AR~~GDLsENAEY~A-------AKe~Q~~~E~RI~~le~~l~~ 67 (155) T TIGR01462 23 PEISEEIKEAREHGDLSENAEYHA-------AKEEQGFIEGRIAELEDLLAN 67 (155) T ss_pred HHHHHHHHHHHHCCCCCCCCHHHH-------HHHHHHHHHHHHHHHHHHHHC T ss_conf 899999999985188655600389-------999999998899999988762 No 17 >KOG3684 consensus Probab=65.56 E-value=12 Score=18.75 Aligned_cols=37 Identities=14% Similarity=0.266 Sum_probs=29.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999999999999650 Q gi|254780412|r 53 IENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 53 Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) +-..-+.+.+.+.+.++|++||+.||.++.++-..++ T Consensus 429 ~~~myd~~~~l~~~q~~le~qI~~Le~kl~~l~~~l~ 465 (489) T KOG3684 429 QNDMYDLLQELHSRQEELEKQIDTLESKLEALTASLS 465 (489) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8899999999987799999999999999999999987 No 18 >PRK11239 hypothetical protein; Provisional Probab=62.75 E-value=14 Score=18.44 Aligned_cols=26 Identities=19% Similarity=0.382 Sum_probs=15.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999965 Q gi|254780412|r 63 LREEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 63 ~R~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) ...++.+||++|++|..+++.|.+.+ T Consensus 188 l~~Rv~~LE~eVa~Lk~~l~~L~a~L 213 (215) T PRK11239 188 LQARVEALEIEVAELKQRLDSLLAHL 213 (215) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999983 No 19 >PHA00728 hypothetical protein Probab=62.55 E-value=11 Score=18.98 Aligned_cols=28 Identities=29% Similarity=0.529 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999999999999999999999650023 Q gi|254780412|r 65 EEITAIGKRLEKIEQQLADLELFINQKE 92 (94) Q Consensus 65 ~~~e~Le~rl~~LE~kl~~le~~~~~k~ 92 (94) .+++.|.+.-++|.++|+.+|+.+|--. T Consensus 5 teveql~keneelkkkla~leal~nne~ 32 (153) T PHA00728 5 TEVEQLKKENEELKKKLAKLEALLNNES 32 (153) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 6899999866999999999999974788 No 20 >COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown] Probab=61.19 E-value=12 Score=18.92 Aligned_cols=28 Identities=11% Similarity=0.319 Sum_probs=21.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999999999999999999999650023 Q gi|254780412|r 65 EEITAIGKRLEKIEQQLADLELFINQKE 92 (94) Q Consensus 65 ~~~e~Le~rl~~LE~kl~~le~~~~~k~ 92 (94) --+.+|+.||+.|...|+.+++-.++|. T Consensus 25 lsV~El~eRIalLq~EIeRlkAe~~kK~ 52 (65) T COG5509 25 LSVAELEERIALLQAEIERLKAELAKKK 52 (65) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 5188899999999999999999998610 No 21 >PRK10636 putative ABC transporter ATP-binding protein; Provisional Probab=59.03 E-value=16 Score=18.01 Aligned_cols=22 Identities=41% Similarity=0.563 Sum_probs=7.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999 Q gi|254780412|r 65 EEITAIGKRLEKIEQQLADLEL 86 (94) Q Consensus 65 ~~~e~Le~rl~~LE~kl~~le~ 86 (94) .+++.||++|+.||.+++.++. T Consensus 563 ~~~~~~e~~i~~le~~~~~l~~ 584 (638) T PRK10636 563 KEIARLEKEMEKLNAQLAQAEE 584 (638) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999 No 22 >PRK11147 ABC transporter ATPase component; Reviewed Probab=58.73 E-value=16 Score=17.98 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=9.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999965 Q gi|254780412|r 65 EEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 65 ~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) .+++.+|.+|+.||+++.++|.-+ T Consensus 568 ~~~~~~e~~i~~~e~~~~~l~~~l 591 (632) T PRK11147 568 RELEQLPQLLEDLEAEIEALQAQV 591 (632) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999998999999999999999985 No 23 >pfam03670 UPF0184 Uncharacterized protein family (UPF0184). Probab=56.38 E-value=18 Score=17.73 Aligned_cols=40 Identities=18% Similarity=0.331 Sum_probs=34.4 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3985699999999999999999999999999999999999 Q gi|254780412|r 45 MGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL 84 (94) Q Consensus 45 ldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l 84 (94) -|=..-+||+++-.||-....-+++||.|-+.|-.+|..| T Consensus 20 ~de~~~~Ey~aiNs~LDqin~~LD~lEqrnD~l~~qL~eL 59 (83) T pfam03670 20 VDEFGLQEYEAINSMLDQINSALDALEERNDDLMSQLREL 59 (83) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 5300499999999999999999999998607999999999 No 24 >COG3132 Uncharacterized protein conserved in bacteria [Function unknown] Probab=55.76 E-value=14 Score=18.47 Aligned_cols=20 Identities=30% Similarity=0.567 Sum_probs=10.8 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999650 Q gi|254780412|r 70 IGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 70 Le~rl~~LE~kl~~le~~~~ 89 (94) ||+||++||..++.|+..++ T Consensus 190 learv~aLe~eva~L~~rld 209 (215) T COG3132 190 LEARVEALEQEVAELRARLD 209 (215) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999 No 25 >pfam07889 DUF1664 Protein of unknown function (DUF1664). The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long. Probab=54.12 E-value=19 Score=17.50 Aligned_cols=86 Identities=12% Similarity=0.249 Sum_probs=51.7 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------CCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99750069999999998668887799999999999999999987398------569999999999999999999999999 Q gi|254780412|r 1 MSFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGV------VRAEEIENVKRTTSHLREEITAIGKRL 74 (94) Q Consensus 1 m~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldL------VtREEFdv~~~~l~k~R~~~e~Le~rl 74 (94) |||-+.+=+.|.-.-++--+..+.+.=....+-+-++++..=.+||- -+|+|....+.=+...-..++.+..-+ T Consensus 33 lMfvTkR~ms~Av~sv~KqLe~Vs~sl~~tKrhLsqRI~~vd~kld~~~eis~~i~~eV~e~~~~~~~i~~D~~~v~~~v 112 (126) T pfam07889 33 LMFVTKRNMSDAVASVGKQLEKVSESIAATKKHLSQRIDNLDDKLDEQKEISESTRDEVTEIREDLSNIGEDVKSVQQAV 112 (126) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 56654720889999999989999999999999999988735321999999999999999999964998876999999999 Q ss_pred HHHHHHHHHHHH Q ss_conf 999999999999 Q gi|254780412|r 75 EKIEQQLADLEL 86 (94) Q Consensus 75 ~~LE~kl~~le~ 86 (94) ..||.||..+|. T Consensus 113 ~~Le~Ki~~ie~ 124 (126) T pfam07889 113 EGLEGKLDSIEY 124 (126) T ss_pred HHHHHHHHHHHH T ss_conf 989999988860 No 26 >pfam04966 OprB Carbohydrate-selective porin, OprB family. Probab=53.88 E-value=6.1 Score=20.69 Aligned_cols=38 Identities=11% Similarity=0.114 Sum_probs=25.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999999999999996 Q gi|254780412|r 50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) ||.....+....-...+++.|..|++.||.+.+.||+. T Consensus 1 ~edl~~~~rL~~ef~~ELa~L~Grvdgle~r~~~le~~ 38 (365) T pfam04966 1 KEGLAYAGQLQLEFDLDLAKLAGWVDGGEFRTSALERH 38 (365) T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHCC T ss_conf 97078998899999999999749723722066778602 No 27 >PRK00846 hypothetical protein; Provisional Probab=51.21 E-value=20 Score=17.43 Aligned_cols=22 Identities=23% Similarity=0.235 Sum_probs=11.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999965 Q gi|254780412|r 67 ITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 67 ~e~Le~rl~~LE~kl~~le~~~ 88 (94) -.+||.||..||.+|+=-|-.| T Consensus 9 d~~LE~Rl~eLE~rlaFQEqti 30 (78) T PRK00846 9 DQALEARLVELETRVSFQEQAL 30 (78) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999999999999999989 No 28 >TIGR03282 methan_mark_13 putative methanogenesis marker 13 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This metal cluster-binding family is related to nitrogenase structural protein NifD and accessory protein NifE, among others. Probab=49.77 E-value=23 Score=17.07 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=21.3 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 9987398569999999999999999 Q gi|254780412|r 41 TLNSMGVVRAEEIENVKRTTSHLRE 65 (94) Q Consensus 41 ~l~kldLVtREEFdv~~~~l~k~R~ 65 (94) ...+.++.+.+||+-|+.||.++-+ T Consensus 129 ~A~~~G~I~~~E~eRQk~mL~~Ate 153 (352) T TIGR03282 129 SAAEAGIIDEDEVERQKELLKKATE 153 (352) T ss_pred HHHHCCCCCHHHHHHHHHHHHHHHH T ss_conf 8997598588999999999999889 No 29 >cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Probab=49.74 E-value=23 Score=17.07 Aligned_cols=35 Identities=11% Similarity=0.284 Sum_probs=28.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999999996500 Q gi|254780412|r 56 VKRTTSHLREEITAIGKRLEKIEQQLADLELFINQ 90 (94) Q Consensus 56 ~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~ 90 (94) +..++.....++..|+.++..|+.-++.|+..... T Consensus 78 l~~~l~~l~~~i~~Le~~~~~L~~~l~~L~~~~~~ 112 (118) T cd04776 78 LEKMLEKIEKRRAELEQQRRDIDAALAELDAAEER 112 (118) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999999999999 No 30 >pfam07106 TBPIP Tat binding protein 1(TBP-1)-interacting protein (TBPIP). 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=48.44 E-value=24 Score=16.94 Aligned_cols=44 Identities=20% Similarity=0.303 Sum_probs=29.9 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 73985699999999999999999999999999999999999996 Q gi|254780412|r 44 SMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 44 kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) .++.++-+|...+..-+...++++..|...+..|++.|..|... T Consensus 65 ~~~~~~~eel~~~d~~i~~L~~~l~~l~~~~~~l~~el~~L~s~ 108 (169) T pfam07106 65 QFELPSDEELNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSD 108 (169) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 13569988998769999999999999999999999999998758 No 31 >PRK02119 hypothetical protein; Provisional Probab=48.07 E-value=19 Score=17.51 Aligned_cols=26 Identities=15% Similarity=0.222 Sum_probs=10.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999 Q gi|254780412|r 58 RTTSHLREEITAIGKRLEKIEQQLAD 83 (94) Q Consensus 58 ~~l~k~R~~~e~Le~rl~~LE~kl~~ 83 (94) .++.+-...++.|..++..|-.+|.+ T Consensus 30 q~v~~Qq~~i~~l~~ql~~L~~rlk~ 55 (73) T PRK02119 30 QALIQQQFVIDKMQVQLRHMANKLKD 55 (73) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999985 No 32 >PRK04406 hypothetical protein; Provisional Probab=47.63 E-value=20 Score=17.40 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=3.4 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999999 Q gi|254780412|r 67 ITAIGKRLEKI 77 (94) Q Consensus 67 ~e~Le~rl~~L 77 (94) ++.|..++..| T Consensus 41 i~~lq~qlr~L 51 (75) T PRK04406 41 ITKMQDQMKYV 51 (75) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 33 >PRK02793 hypothetical protein; Provisional Probab=46.67 E-value=19 Score=17.55 Aligned_cols=24 Identities=13% Similarity=0.250 Sum_probs=8.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999 Q gi|254780412|r 60 TSHLREEITAIGKRLEKIEQQLAD 83 (94) Q Consensus 60 l~k~R~~~e~Le~rl~~LE~kl~~ 83 (94) +.+-...++.|..++..|-.+|.+ T Consensus 31 v~~Qq~~i~~L~~ql~~L~~rLk~ 54 (72) T PRK02793 31 VTAHEMEMAKLRDHLRLLTEKLKA 54 (72) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999985 No 34 >pfam01519 DUF16 Protein of unknown function DUF16. The function of this protein is unknown. It appears to only occur in Mycoplasma pneumoniae. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils. Probab=45.32 E-value=27 Score=16.63 Aligned_cols=35 Identities=20% Similarity=0.466 Sum_probs=20.9 Q ss_pred CCCCCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH Q ss_conf 398569999999999----99999999999999999999 Q gi|254780412|r 45 MGVVRAEEIENVKRT----TSHLREEITAIGKRLEKIEQ 79 (94) Q Consensus 45 ldLVtREEFdv~~~~----l~k~R~~~e~Le~rl~~LE~ 79 (94) -+.|||.+|+.-+.- +.|.-.++.....+|..|.. T Consensus 7 t~YVT~Kqf~efKdsn~qrltKiE~k~~~qgeqI~~l~~ 45 (87) T pfam01519 7 TGYVTHKQFDEFKDSNDQRLTKIETKLDAQGEQIRKLTQ 45 (87) T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 661209988875144226899999999999999999999 No 35 >COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only] Probab=44.50 E-value=27 Score=16.56 Aligned_cols=52 Identities=19% Similarity=0.390 Sum_probs=26.4 Q ss_pred HHHHHHHHHHHCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999873985699-9999999999999999999999999999999999 Q gi|254780412|r 34 AQIKIQRTLNSMGVVRAE-EIENVKRTTSHLREEITAIGKRLEKIEQQLADLE 85 (94) Q Consensus 34 ~r~~~e~~l~kldLVtRE-EFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le 85 (94) ++.++.+.=.+++-||.+ ||.++..=...+..+...|+..+..|...+..++ T Consensus 71 ~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~ 123 (239) T COG1579 71 IRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKLE 123 (239) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999878998861256999998788999999999999999999999999889 No 36 >pfam10458 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases. Probab=44.31 E-value=28 Score=16.54 Aligned_cols=45 Identities=20% Similarity=0.394 Sum_probs=35.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999873985699999999999999999999999999999999999 Q gi|254780412|r 36 IKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL 84 (94) Q Consensus 36 ~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l 84 (94) ..++.-|+.-++|++ |-.+|+...|.++..++.+++.|+..|+.| T Consensus 21 ~~~~~kL~N~~Fv~k----AP~~VV~~er~kl~~~~~~~~~l~~~L~~L 65 (66) T pfam10458 21 ERLQKKLSNPGFVAK----APAEVVEEEKAKLAEYEEQLEKLKERLSQL 65 (66) T ss_pred HHHHHHHCCHHHHHH----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999987787677770----989999999999999999999999999875 No 37 >TIGR01149 mtrG tetrahydromethanopterin S-methyltransferase, subunit G; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane. Probab=44.07 E-value=28 Score=16.51 Aligned_cols=30 Identities=23% Similarity=0.501 Sum_probs=19.7 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8569999999999999999999999999999999999 Q gi|254780412|r 47 VVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLAD 83 (94) Q Consensus 47 LVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~ 83 (94) +|+-+||+... +|++++|.|++---.-+++ T Consensus 10 ~~~~~ef~~~~-------~rLDeie~kveFv~~E~~Q 39 (72) T TIGR01149 10 LVEPDEFNEVK-------KRLDEIEEKVEFVNGEVAQ 39 (72) T ss_pred CCCHHHHHHHH-------HHHHHHHHHHHHHHHHHHH T ss_conf 05976699999-------8741786788789999888 No 38 >pfam06447 consensus Probab=42.99 E-value=29 Score=16.41 Aligned_cols=38 Identities=21% Similarity=0.254 Sum_probs=29.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999999999999996 Q gi|254780412|r 50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) +.|-|.+..-+...++++++|+.++..|.+++.+++.. T Consensus 75 ~~e~~~~~~~~~~~q~~l~~l~qe~~~L~~q~~~~~~~ 112 (407) T pfam06447 75 RAEREEKERDLDQNQERIASLEQENQQLREQLAAGQAN 112 (407) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999998878888999999999999999999988726 No 39 >PRK00892 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional Probab=42.16 E-value=30 Score=16.33 Aligned_cols=21 Identities=24% Similarity=0.495 Sum_probs=13.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999 Q gi|254780412|r 65 EEITAIGKRLEKIEQQLADLE 85 (94) Q Consensus 65 ~~~e~Le~rl~~LE~kl~~le 85 (94) .++..|.+|+..||+++.++| T Consensus 322 ~~Lp~l~k~~~~lek~~~~~~ 342 (343) T PRK00892 322 RRLDKMRKRLKALEKKVEKQE 342 (343) T ss_pred HHHHHHHHHHHHHHHHHHHHC T ss_conf 607999999999999998634 No 40 >PRK00295 hypothetical protein; Provisional Probab=42.12 E-value=22 Score=17.14 Aligned_cols=30 Identities=3% Similarity=0.137 Sum_probs=14.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999999999 Q gi|254780412|r 56 VKRTTSHLREEITAIGKRLEKIEQQLADLE 85 (94) Q Consensus 56 ~~~~l~k~R~~~e~Le~rl~~LE~kl~~le 85 (94) +-.++..-.-.++.|..++..|-.++.+.. T Consensus 24 LN~~l~~Qq~~id~L~~q~~~l~~rl~~~~ 53 (68) T PRK00295 24 LNDVVVEQQRVIERLQLQMAALIKRQEEMV 53 (68) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999999999988 No 41 >TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345 Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene.. Probab=41.48 E-value=30 Score=16.26 Aligned_cols=84 Identities=10% Similarity=0.124 Sum_probs=43.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HCCCCCHHH------HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6999999999866888779999999999999999998-----739856999------99999999999999999999999 Q gi|254780412|r 7 QFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLN-----SMGVVRAEE------IENVKRTTSHLREEITAIGKRLE 75 (94) Q Consensus 7 ~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~-----kldLVtREE------Fdv~~~~l~k~R~~~e~Le~rl~ 75 (94) +-+|+|-=--++--|..-.+|.+|+..=+.+-+.+-. .-+=..+.+ +.=++--+.++-.++++|++|.+ T Consensus 267 ~~Ld~L~l~YTd~HPdv~~~k~~Ia~L~~~~~~e~~~~~~Q~~~~~~~~~~~~~nPvyQql~~~l~~~eA~~asl~~r~~ 346 (510) T TIGR03007 267 KQLDALRLRYTDKHPDVIATKREIAQLEEQKEEELESYRKQNGEGGGSEKGSIYNPVYQQLQIELAEAEAEIASLEARVA 346 (510) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99998633630115589999999999999988999889873034555556678983137789999999999999999999 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999996500 Q gi|254780412|r 76 KIEQQLADLELFINQ 90 (94) Q Consensus 76 ~LE~kl~~le~~~~~ 90 (94) .++.+++.++...+- T Consensus 347 ~~~~~~~~l~~~~~~ 361 (510) T TIGR03007 347 ELTARIERLESLLRT 361 (510) T ss_pred HHHHHHHHHHHHHHH T ss_conf 999999999999753 No 42 >PRK04325 hypothetical protein; Provisional Probab=41.08 E-value=29 Score=16.39 Aligned_cols=32 Identities=19% Similarity=0.343 Sum_probs=21.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999999999 Q gi|254780412|r 53 IENVKRTTSHLREEITAIGKRLEKIEQQLADL 84 (94) Q Consensus 53 Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l 84 (94) .|.+-.++.+-..+++.|..++..|-.++... T Consensus 25 id~LN~tV~rQQqqId~L~~q~~~L~q~~~~~ 56 (74) T PRK04325 25 IDGLNATVARQQQTLDLLQAQLRLLYQQMRDA 56 (74) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999999999999999999999998732 No 43 >TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694 emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall. Probab=41.07 E-value=27 Score=16.58 Aligned_cols=36 Identities=14% Similarity=0.302 Sum_probs=29.9 Q ss_pred HHHHHCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99987398569---9999999999999999999999999 Q gi|254780412|r 40 RTLNSMGVVRA---EEIENVKRTTSHLREEITAIGKRLE 75 (94) Q Consensus 40 ~~l~kldLVtR---EEFdv~~~~l~k~R~~~e~Le~rl~ 75 (94) ..|.+.|+|+| ||||--++.+..+++.+++=-..|+ T Consensus 154 ~~L~~~G~I~~RkFE~l~~ar~a~~~a~A~L~aa~~~I~ 192 (379) T TIGR00998 154 VPLLKKGLISRRKFEELDHARKALLSAKAALNAAIQEIN 192 (379) T ss_pred HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 889847899875444347689999999987889985433 No 44 >pfam06825 HSBP1 Heat shock factor binding protein 1. Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response. Probab=40.83 E-value=31 Score=16.20 Aligned_cols=21 Identities=29% Similarity=0.639 Sum_probs=15.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999 Q gi|254780412|r 65 EEITAIGKRLEKIEQQLADLE 85 (94) Q Consensus 65 ~~~e~Le~rl~~LE~kl~~le 85 (94) .|++....||+.||+-++++- T Consensus 28 ~riDdM~~riDdLE~si~dlm 48 (54) T pfam06825 28 SKIDEMSKRIDELEKSINDLM 48 (54) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 999988836888997799999 No 45 >TIGR02978 phageshock_pspC phage shock protein C; InterPro: IPR014320 All members of this protein are the phage shock protein PspC. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor; PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin over expression, ethanol, heat shock and protein export defects.. Probab=40.14 E-value=22 Score=17.12 Aligned_cols=29 Identities=14% Similarity=0.516 Sum_probs=21.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999996500 Q gi|254780412|r 62 HLREEITAIGKRLEKIEQQLADLELFINQ 90 (94) Q Consensus 62 k~R~~~e~Le~rl~~LE~kl~~le~~~~~ 90 (94) +.+.-+..++.++..+|.+|.+.|..++= T Consensus 88 ~p~~~L~~~~~~~~~~e~RLr~mE~yVTS 116 (128) T TIGR02978 88 SPKQALREVKRELRRLERRLRNMERYVTS 116 (128) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCEEEC T ss_conf 88899999999999988898976853206 No 46 >pfam00038 Filament Intermediate filament protein. Probab=38.76 E-value=34 Score=16.00 Aligned_cols=67 Identities=25% Similarity=0.326 Sum_probs=43.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCC------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8779999999999999999998739------856999999999999999999999999999999999999965 Q gi|254780412|r 22 AFKDISKEAESFAQIKIQRTLNSMG------VVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 22 ~~~~~~~Eie~~~r~~~e~~l~kld------LVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) .+...+.|++..++..++..-.... --+++|....+.-+...+.+++.|.++.+.|+.+|.+++... T Consensus 181 ~~~~~~~e~e~~y~~k~~~l~~~~~~~~~~l~~~k~E~~~lr~~i~~L~~el~~l~~~~~~Le~~l~e~e~~~ 253 (312) T pfam00038 181 LAEKNRQEAEEWYKSKLEELQQAAARNGDALRSAKEEITELRRQIQSLEIELQSLKKQKASLERQLAELEERY 253 (312) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9998799999998878899999998745779989999999999999999999999999999998999999979 No 47 >cd04171 SelB SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo Probab=38.24 E-value=34 Score=15.94 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=16.4 Q ss_pred HHHHCCCCCHHHHHHHHHHHHH Q ss_conf 9987398569999999999999 Q gi|254780412|r 41 TLNSMGVVRAEEIENVKRTTSH 62 (94) Q Consensus 41 ~l~kldLVtREEFdv~~~~l~k 62 (94) ++||+|+|.+|+++....-+.+ T Consensus 110 vlNK~D~v~~~~~~~~~~~i~~ 131 (164) T cd04171 110 VLTKADLVDEDWLELVEEEIRE 131 (164) T ss_pred EEECCCCCCHHHHHHHHHHHHH T ss_conf 3463425797899999999999 No 48 >pfam10152 DUF2360 Predicted coiled-coil domain-containing protein (DUF2360). This is the conserved 140 amino acid region of a family of proteins conserved from nematodes to humans. One C. elegans member is annotated as a Daf-16-dependent longevity protein 1 but this could not be confirmed. The function is unknown. Probab=37.62 E-value=35 Score=15.88 Aligned_cols=37 Identities=19% Similarity=0.311 Sum_probs=20.2 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99987398569999999999999999999999999999999999 Q gi|254780412|r 40 RTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLAD 83 (94) Q Consensus 40 ~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~ 83 (94) ++||++..+--+-|-- .-.++..||..+.-||+||+- T Consensus 10 ~FLNrFs~~CE~KL~~-------~e~~LQ~lE~~l~ILEaKL~S 46 (147) T pfam10152 10 QFLNRFSAVCESKLVE-------AERSLQQLETTLSLLEAKLAS 46 (147) T ss_pred HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHCC T ss_conf 9999999999999999-------999999999999999999746 No 49 >pfam08317 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association. Probab=36.27 E-value=37 Score=15.75 Aligned_cols=82 Identities=15% Similarity=0.271 Sum_probs=49.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999986688877999999999999999999873985699999999999999999999999999999999999996 Q gi|254780412|r 8 FFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 8 ~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) .+..-..++.+..+.+..-...+..-+.. ++.....++...++|....+.-+...-.++++....+..++.++..++.. T Consensus 166 ~L~~~~~~l~~~~p~l~~~~~~L~~e~~~-l~~~~~e~~~~D~~eL~~~r~eL~~~~~~i~~~~~~l~el~~el~~l~~~ 244 (322) T pfam08317 166 LLNKDLNLINSIKPKLRKKLQALKEEIAN-LRQLADELNLCDPLELEKARQELRSLSVKISEKRKQLEELQQELQELTIA 244 (322) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99989999988899999999999999999-99736555217999999999999999999999998999999999999999 Q ss_pred HHH Q ss_conf 500 Q gi|254780412|r 88 INQ 90 (94) Q Consensus 88 ~~~ 90 (94) |.. T Consensus 245 ie~ 247 (322) T pfam08317 245 IEA 247 (322) T ss_pred HHH T ss_conf 999 No 50 >KOG3958 consensus Probab=36.13 E-value=34 Score=15.95 Aligned_cols=17 Identities=24% Similarity=0.618 Sum_probs=10.3 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999999965 Q gi|254780412|r 72 KRLEKIEQQLADLELFI 88 (94) Q Consensus 72 ~rl~~LE~kl~~le~~~ 88 (94) +|++.||++|..+|..+ T Consensus 191 akVA~LE~Rlt~lE~vv 207 (371) T KOG3958 191 AKVAELEKRLTELETVV 207 (371) T ss_pred HHHHHHHHHHHHHHHHH T ss_conf 88999999999999997 No 51 >TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243 This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. . Probab=35.52 E-value=38 Score=15.67 Aligned_cols=37 Identities=27% Similarity=0.413 Sum_probs=25.4 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6999999999999999999999999999999999999 Q gi|254780412|r 49 RAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLE 85 (94) Q Consensus 49 tREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le 85 (94) .+-|=+.++.=....+.+++.|++++..|+++..-.+ T Consensus 104 l~~E~~~L~~~~~~Lq~~ne~L~~el~~L~~~~~~~e 140 (163) T TIGR02894 104 LQKENERLKKELESLQKRNEELEKELEKLEKRQSTIE 140 (163) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9989999999999999999999999999999846789 No 52 >PRK06664 fliD flagellar hook-associated protein FliD; Validated Probab=33.94 E-value=40 Score=15.51 Aligned_cols=61 Identities=11% Similarity=0.208 Sum_probs=35.2 Q ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHH Q ss_conf 99999999999999873985699999999999999999999999999999999----999996500 Q gi|254780412|r 29 EAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQL----ADLELFINQ 90 (94) Q Consensus 29 Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl----~~le~~~~~ 90 (94) .+-..+...+..++..-+++.--. +-+..-+.+...+++.|+.|++.+|.++ +.+|..+.+ T Consensus 602 G~a~~l~~~l~~~~~~~G~i~~~~-~~l~~~i~~~~~~i~~~~~rl~~~e~ry~~QF~ame~~~~~ 666 (684) T PRK06664 602 GVAKMLLEYLKPYTQAGGIVYNKV-KSLDEKIANNNKKVEEYEKKLESRERKLKGKFLTMDQTVKK 666 (684) T ss_pred HHHHHHHHHHHHHHCCCCEEEHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 499999999998765686453066-67999998999999999999999999999999999999999 No 53 >COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms] Probab=33.65 E-value=27 Score=16.63 Aligned_cols=25 Identities=24% Similarity=0.458 Sum_probs=18.8 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 98569999999999999999999999999 Q gi|254780412|r 46 GVVRAEEIENVKRTTSHLREEITAIGKRL 74 (94) Q Consensus 46 dLVtREEFdv~~~~l~k~R~~~e~Le~rl 74 (94) ++|-|||||--.. .|.++.+|+.+. T Consensus 147 ~~i~~EefEeAA~----iRDqIr~Lk~k~ 171 (176) T COG3880 147 DLIEREEFEEAAV----IRDQIRALKAKN 171 (176) T ss_pred HHHHHHHHHHHHH----HHHHHHHHHHHC T ss_conf 9998888899999----999999988543 No 54 >pfam01920 Prefoldin_2 Prefoldin subunit. This family includes prefoldin subunits that are not detected by pfam02996. Probab=33.47 E-value=41 Score=15.47 Aligned_cols=38 Identities=29% Similarity=0.481 Sum_probs=25.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999999999999999999999999965002 Q gi|254780412|r 54 ENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQK 91 (94) Q Consensus 54 dv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k 91 (94) ..+.........++..|+.++..+++.+.+++..+.++ T Consensus 65 ~~L~~~~e~i~~~i~~le~q~~~~~~~~~~lk~~l~~~ 102 (104) T pfam01920 65 EELEERKETLEKEIKTLEKQLEKLEKELEELKEELYKL 102 (104) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999999999999887 No 55 >pfam00509 Hemagglutinin Hemagglutinin. Hemagglutinin from influenza virus causes membrane fusion of the viral membrane with the host membrane. Fusion occurs after the host cell internalises the virus by endocytosis. The drop of pH causes release of a hydrophobic fusion peptide and a large conformational change leading to membrane fusion. Probab=33.18 E-value=41 Score=15.44 Aligned_cols=49 Identities=16% Similarity=0.286 Sum_probs=33.5 Q ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999998739856999999999999999999999999999999999999965 Q gi|254780412|r 29 EAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 29 Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) .+=..+-..+.+.+.||+ +.|+++ ..+...||.||..|++++.+..+.+ T Consensus 371 ~AId~It~KlN~iiek~N----~qf~~i-------~~EF~evE~rI~~l~~~v~D~~~D~ 419 (550) T pfam00509 371 KAIDQITGKLNSLIEKMN----TQFEAI-------EKEFSELERRINNLNKKVDDGITDI 419 (550) T ss_pred HHHHHHHHHHHHHHHHHH----HHHHHH-------HHHHHHHHHHHHHHHHHHCCCCEEH T ss_conf 999988778888999877----678887-------7789999999999997630100010 No 56 >pfam01763 Herpes_UL6 Herpesvirus UL6 like. This family consists of various proteins from the herpesviridae that are similar to herpes simplex virus type I UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome. Probab=31.96 E-value=43 Score=15.31 Aligned_cols=57 Identities=21% Similarity=0.297 Sum_probs=46.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 68887799999999999999999987398569999999999999999999999999999999999999 Q gi|254780412|r 19 ASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLEL 86 (94) Q Consensus 19 a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~ 86 (94) ..++.+++|+-+-+++--.++..+|.+ || -++..++.++.++.|+..+|..|..... T Consensus 343 ~~~~~~~~r~~V~n~V~kcLe~qIn~q-------F~----tIe~Lk~~n~~~~~kl~~~e~~L~r~~~ 399 (551) T pfam01763 343 AETTRQAFRKSVSNSVNKCLEGQINEQ-------FD----TIEDLKEENEDLLKKLRELESELSRLRE 399 (551) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH-------HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 762778999999987999879999999-------99----9999999999999999999999999887 No 57 >PRK09039 hypothetical protein; Validated Probab=31.96 E-value=43 Score=15.31 Aligned_cols=43 Identities=16% Similarity=0.378 Sum_probs=32.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999999999999999999999999999999999999650023 Q gi|254780412|r 50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKE 92 (94) Q Consensus 50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k~ 92 (94) +++-+.+++....++.+++.|..+|.+|..+|+.+...++..+ T Consensus 122 ~~~L~~~~~~s~~a~~qi~~Ln~Qi~aLr~qL~~l~~~L~~~e 164 (343) T PRK09039 122 NQALDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASE 164 (343) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999988999999999999999999999999999999999 No 58 >TIGR02132 phaR_Bmeg polyhydroxyalkanoic acid synthase, PhaR subunit; InterPro: IPR011729 This entry describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit .. Probab=31.67 E-value=43 Score=15.28 Aligned_cols=62 Identities=18% Similarity=0.209 Sum_probs=50.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999986688877999999999999999999873985699999999999999999999999999 Q gi|254780412|r 10 QQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLE 75 (94) Q Consensus 10 ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~ 75 (94) .++|.++|+.+ ++-=--...+...-.++|...++-|+|+.=-+..+....-++++.||..++ T Consensus 35 EEyS~~MG~VL----~lNL~YQ~A~N~~T~~YL~QVNVPTKED~A~VA~LVIN~E~KV~~~EE~l~ 96 (189) T TIGR02132 35 EEYSALMGSVL----DLNLFYQKALNDVTKRYLEQVNVPTKEDVARVASLVINLEEKVDLLEEFLD 96 (189) T ss_pred HHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 48999978898----788999999999876676515898554687688887546888889988864 No 59 >smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association. Probab=31.54 E-value=44 Score=15.27 Aligned_cols=83 Identities=19% Similarity=0.268 Sum_probs=48.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999986688877999999999999999999873985699999999999999999999999999999999999996 Q gi|254780412|r 8 FFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 8 ~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) .+..-..++.+..+.+..-...+..-+.. ++.....++=...+|.+..+.-+...-.++......+..++.++.+++.. T Consensus 162 ~L~~~~~~l~~i~p~l~~~~~~L~~e~~~-L~~~~~e~~~~d~~eL~~lk~~L~~~~~ei~~~~~~l~e~~~~l~~l~~~ 240 (312) T smart00787 162 LLMKELELLNSIKPKLRDRKDALEEELRQ-LKQLEDELEDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESK 240 (312) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999988899999999999999999-99768888718999999999999999999999999999999999999999 Q ss_pred HHHC Q ss_conf 5002 Q gi|254780412|r 88 INQK 91 (94) Q Consensus 88 ~~~k 91 (94) |+.. T Consensus 241 I~~~ 244 (312) T smart00787 241 IEDL 244 (312) T ss_pred HHHH T ss_conf 9989 No 60 >COG3165 Uncharacterized protein conserved in bacteria [Function unknown] Probab=31.46 E-value=44 Score=15.26 Aligned_cols=59 Identities=15% Similarity=0.192 Sum_probs=30.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 7799999999999999999987-----3985699999999999999999999999999999999 Q gi|254780412|r 23 FKDISKEAESFAQIKIQRTLNS-----MGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQL 81 (94) Q Consensus 23 ~~~~~~Eie~~~r~~~e~~l~k-----ldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl 81 (94) +.+....+...+++.-+.+-.- --+|.+.|...-.+-+...|.-.+.|++|++.||.+. T Consensus 139 l~~~~~~l~~~~~~~q~~~Ae~iTEE~r~~v~~~ela~f~~evd~lr~~~~rL~~RL~rLe~k~ 202 (204) T COG3165 139 LRSGSRFLKHGLKQLQRNLAEAITEEWRMAVGPLELADFAEEVDALRDAVERLEARLERLERKA 202 (204) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9998999999999999999999868764368868999999999999999999999999999763 No 61 >COG3416 Uncharacterized protein conserved in bacteria [Function unknown] Probab=31.18 E-value=44 Score=15.23 Aligned_cols=76 Identities=13% Similarity=0.146 Sum_probs=29.0 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99750069999999998668887799999999999999999987398569999999999999999999999999999999 Q gi|254780412|r 1 MSFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ 80 (94) Q Consensus 1 m~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k 80 (94) |+.--.++++++-.....+--. +-+...-.++.+.+.+-- +--=+=||+.+++- .-+..+..+|.+||++ T Consensus 1 MtpeE~qlle~lf~rlk~a~~~------~rD~~Ae~lI~~~~~~qP--~a~Y~laQ~vliqE--~ALk~a~~~i~eLe~r 70 (233) T COG3416 1 MTPEEKQLLENLFHRLKKAEAN------ERDPQAEALIAEAVAKQP--DAAYYLAQRVLIQE--QALKKASTQIKELEKR 70 (233) T ss_pred CCHHHHHHHHHHHHHHHHCCCC------CCCHHHHHHHHHHHHCCC--CHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH T ss_conf 9878999999999998642467------777489999999985499--54899999999999--9999999999999999 Q ss_pred HHHHHH Q ss_conf 999999 Q gi|254780412|r 81 LADLEL 86 (94) Q Consensus 81 l~~le~ 86 (94) ++.++. T Consensus 71 i~~lq~ 76 (233) T COG3416 71 IAILQA 76 (233) T ss_pred HHHHHC T ss_conf 999841 No 62 >pfam11336 DUF3138 Protein of unknown function (DUF3138). This family of proteins with unknown function appear to be restricted to Proteobacteria. Probab=29.79 E-value=47 Score=15.08 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=21.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 9999999999999999999999999996500237 Q gi|254780412|r 60 TSHLREEITAIGKRLEKIEQQLADLELFINQKEK 93 (94) Q Consensus 60 l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k~~ 93 (94) +.-+-.++.+|.+++.+|.++..++.+-+.-|+. T Consensus 20 a~s~a~~ikalqaq~~~lq~q~~~l~a~laak~~ 53 (514) T pfam11336 20 AASDASQIKALQAQLTALQQQVNELRAALAAKPA 53 (514) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 2589999999999999999999999998614876 No 63 >pfam12269 zf-CpG_bind_C CpG binding protein zinc finger C terminal domain. This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA. Probab=29.75 E-value=47 Score=15.08 Aligned_cols=33 Identities=21% Similarity=0.451 Sum_probs=17.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999999996500 Q gi|254780412|r 58 RTTSHLREEITAIGKRLEKIEQQLADLELFINQ 90 (94) Q Consensus 58 ~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~ 90 (94) ..+.+.|.+......+|++|+.+-.+|++.|++ T Consensus 29 ~~Le~Ir~kq~~~~~~L~eLe~~~~eL~~iI~r 61 (236) T pfam12269 29 KALERIRKKQQVARTRLQELERRHQELETIISR 61 (236) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999999999999998 No 64 >pfam10393 Matrilin_ccoil Trimeric coiled-coil oligomerisation domain of matrilin. This short domain is a coiled coil structure and has a single cysteine residue at the start which is likely to form a di-sulfide bridge with a corresponding cysteine in an upstream EGF (pfam00008) domain thereby spanning a VWA (pfam00092) domain. All three domains can be associated together as in the cartilage matrix protein matrilin, where this domain is likely to be responsible for oligomerisation. Probab=29.01 E-value=48 Score=15.00 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=15.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999996 Q gi|254780412|r 60 TSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 60 l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) =.+..+.+.+|..||++.-++|..+|-. T Consensus 15 Q~kv~~~lq~Lt~KLe~vtkrl~~lEnr 42 (44) T pfam10393 15 QRKVEELLQKLTQKLEAVTKRLEALENR 42 (44) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999998751 No 65 >PRK05729 valS valyl-tRNA synthetase; Reviewed Probab=28.97 E-value=48 Score=14.99 Aligned_cols=43 Identities=26% Similarity=0.461 Sum_probs=25.0 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99998739856999999999999999999999999999999999999 Q gi|254780412|r 39 QRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLE 85 (94) Q Consensus 39 e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le 85 (94) +.-|+.-+.|.+ |=.++...-+++++.++.+++.+++.|+.|+ T Consensus 834 ~~kLsN~~Fi~k----AP~~VV~~ek~Kl~~~~~~i~~i~~~L~~Lk 876 (877) T PRK05729 834 EKKLSNEGFVAK----APEEVVEKEREKLAEYQEKLEKLKERLARLK 876 (877) T ss_pred HHHHCCHHHHHH----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 977678566673----8999999999999999999999999999725 No 66 >pfam08900 DUF1845 Domain of unknown function (DUF1845). This family of proteins are functionally uncharacterized. Probab=28.69 E-value=49 Score=14.96 Aligned_cols=46 Identities=7% Similarity=0.053 Sum_probs=26.9 Q ss_pred HHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999998-73985699999999999999999999999 Q gi|254780412|r 27 SKEAESFAQIKIQRTLN-SMGVVRAEEIENVKRTTSHLREEITAIGK 72 (94) Q Consensus 27 ~~Eie~~~r~~~e~~l~-kldLVtREEFdv~~~~l~k~R~~~e~Le~ 72 (94) -++....+|.....+.+ +.==|||++|..+.+...++.++.-.|.. T Consensus 153 l~~g~~~vR~vf~~~~~Yr~~gvtR~D~~~nn~~~~~A~e~~G~lp~ 199 (217) T pfam08900 153 LDEGGRLVRRVFGLVQRYRFSGVTRDDFAANNARAQAAIERMGELPQ 199 (217) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHCCCCCH T ss_conf 99988999999998877513797788788578999999998389998 No 67 >pfam04012 PspA_IM30 PspA/IM30 family. This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator. Probab=28.54 E-value=49 Score=14.94 Aligned_cols=36 Identities=11% Similarity=0.377 Sum_probs=20.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999999999999996 Q gi|254780412|r 52 EIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 52 EFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) .++.+...+.+.+..+..|+.+|..+..+...|.+. T Consensus 106 q~~~~~~~~~~L~~~l~~le~ki~e~k~k~~~L~Ar 141 (220) T pfam04012 106 QLTQQRSAVEQLRKQLAALETKIQQLKAKKTALKAR 141 (220) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999999999999999999 No 68 >COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms] Probab=28.53 E-value=49 Score=14.94 Aligned_cols=57 Identities=9% Similarity=0.270 Sum_probs=26.8 Q ss_pred HHHHHHHHHHHHHCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999998739856--999999999999999999999999999999999999965 Q gi|254780412|r 32 SFAQIKIQRTLNSMGVVR--AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 32 ~~~r~~~e~~l~kldLVt--REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) ...+..+++.-+--+.+. ..++..+...+.+.+..+..|+.+|..++++...+.+.. T Consensus 85 ~LAr~al~~~~~le~~~~~~~~~~~~~~~~~~~l~~~~~~Le~Ki~e~~~~~~~l~ar~ 143 (225) T COG1842 85 DLAREALEEKQSLEDLAKALEAELQQAEEQVEKLKKQLAALEQKIAELRAKKEALKARK 143 (225) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999899999999999999999999999999999999999999999999798 No 69 >pfam10046 BLOC1_2 Biogenesis of lysosome-related organelles complex-1 subunit 2. Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system. Probab=28.23 E-value=50 Score=14.91 Aligned_cols=49 Identities=29% Similarity=0.429 Sum_probs=33.4 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHH Q ss_conf 99987398569999999999999999999999999----------99999999999965 Q gi|254780412|r 40 RTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRL----------EKIEQQLADLELFI 88 (94) Q Consensus 40 ~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl----------~~LE~kl~~le~~~ 88 (94) +.|.+|+-++-.+|.-+..++...+..++.|..+- +.+|.+++.||... T Consensus 24 ~LLe~mN~~~~~kY~~~~~~a~~l~~~~~~L~~ky~~l~pyl~qId~Ie~~V~~LE~~a 82 (99) T pfam10046 24 KLLEKMNENTALKYKKMRQSAKGLRVEIEALNQKYEELKPYLQQIDAIEQQVTTLEEAV 82 (99) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999879999999999999998999999999988877899999999998999999999 No 70 >KOG4571 consensus Probab=27.69 E-value=51 Score=14.85 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=32.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 69999999999999999999999999999999999999650 Q gi|254780412|r 49 RAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 49 tREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) -|.|-+.+..-+.-.-.++++|..|+..||.-|.-++-+|- T Consensus 246 kRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~ 286 (294) T KOG4571 246 KRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLIL 286 (294) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89999888878777888779999999999999999999999 No 71 >pfam09766 FimP Fms-interacting protein. This entry carries part of the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C-terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes. Probab=27.61 E-value=51 Score=14.84 Aligned_cols=73 Identities=18% Similarity=0.194 Sum_probs=42.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH----------------HHHHHHHHHHHHHHH---HHHHHHHHHH Q ss_conf 668887799999999999999999987398569999----------------999999999999999---9999999999 Q gi|254780412|r 18 CASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEI----------------ENVKRTTSHLREEIT---AIGKRLEKIE 78 (94) Q Consensus 18 ~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEF----------------dv~~~~l~k~R~~~e---~Le~rl~~LE 78 (94) +.+--...+.+||.+-....- -=..++||+-||| |--..|+.|..-++. .|.++..+|+ T Consensus 37 NLlYE~~HL~KEI~~C~~FkS--~d~~i~Lv~~eEF~~~ap~~i~~~~~~~~d~H~~~L~RL~~EL~qRK~L~~~~~~L~ 114 (352) T pfam09766 37 NLLYEKSHLEKEIKRCLDFKS--KDEEIELVPEEEFYSDAPEDISRPEKTPLDEHNLMLARLEWELEQRKELCEKLKELE 114 (352) T ss_pred HHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCHHHHHHHCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 899999999999999870223--699835677799998571310564567888699999999999999999999999999 Q ss_pred HHHHHHHHHHHHCC Q ss_conf 99999999650023 Q gi|254780412|r 79 QQLADLELFINQKE 92 (94) Q Consensus 79 ~kl~~le~~~~~k~ 92 (94) ..-..+.-.|.+|. T Consensus 115 ~~K~~l~~~i~~k~ 128 (352) T pfam09766 115 SEKEKLLQDIEKKK 128 (352) T ss_pred HHHHHHHHHHHHHH T ss_conf 99999999999999 No 72 >pfam07407 Seadorna_VP6 Seadornavirus VP6 protein. This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown. Probab=27.36 E-value=51 Score=14.81 Aligned_cols=37 Identities=16% Similarity=0.402 Sum_probs=26.0 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 7398569999999999999999999999999999999 Q gi|254780412|r 44 SMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ 80 (94) Q Consensus 44 kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k 80 (94) .+.=|+-+|.-++++--+|...++++|..++..||.- T Consensus 25 elegvsfdelaalreenaklkkenealktkihrlesd 61 (420) T pfam07407 25 ELEGVSFDELAALREENAKLKKENEALKTKIHRLESD 61 (420) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 1457658998988876455654528887667544146 No 73 >COG2193 Bfr Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism] Probab=27.28 E-value=52 Score=14.80 Aligned_cols=48 Identities=19% Similarity=0.162 Sum_probs=30.0 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999987398569999999999999999999999999999 Q gi|254780412|r 27 SKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKI 77 (94) Q Consensus 27 ~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~L 77 (94) -.++....|..+.-.=+.-|.|||+.|+.+. .-+-+-++-||.++.-+ T Consensus 94 E~~a~~~lk~~i~~~e~~~Dyvsrdl~~~iL---~deEEHid~LetqL~li 141 (157) T COG2193 94 EYEARDALKEAIAYCEEVQDYVSRDLLEEIL---ADEEEHIDWLETQLDLI 141 (157) T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH---CCHHHHHHHHHHHHHHH T ss_conf 8999999999999998605633899999998---16077799999999999 No 74 >KOG0241 consensus Probab=27.03 E-value=52 Score=14.78 Aligned_cols=35 Identities=17% Similarity=0.399 Sum_probs=24.9 Q ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999-9999999999999999999999 Q gi|254780412|r 50 AEEIENVKRTTSH-LREEITAIGKRLEKIEQQLADL 84 (94) Q Consensus 50 REEFdv~~~~l~k-~R~~~e~Le~rl~~LE~kl~~l 84 (94) |||.|-++.+|.. .+++...|+.+++++|+-+.++ T Consensus 370 ReEve~lr~qL~~ae~~~~~el~e~l~esekli~ei 405 (1714) T KOG0241 370 REEVEKLREQLEQAEAMKLPELKEKLEESEKLIKEI 405 (1714) T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 999999999986543110467899999999999999 No 75 >pfam00846 Hanta_nucleocap Hantavirus nucleocapsid protein. Probab=26.98 E-value=52 Score=14.77 Aligned_cols=40 Identities=25% Similarity=0.292 Sum_probs=33.0 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5699999999999999999999999999999999999996 Q gi|254780412|r 48 VRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 48 VtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) |-++-=|+.+..+..-+..+.+|+.+|++|..+|+++-+. T Consensus 32 ~e~dPDdvnk~~l~~R~~~v~~l~~Kl~elkrqlAd~v~~ 71 (428) T pfam00846 32 VEVDPDDVNKSTLQSRRAAVSALEAKLAELKRQLADRIAT 71 (428) T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 5479636668999999999999999999999999999985 No 76 >PRK10014 DNA-binding transcriptional repressor MalI; Provisional Probab=26.76 E-value=53 Score=14.75 Aligned_cols=49 Identities=10% Similarity=0.196 Sum_probs=34.6 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 99750069999999998668887799---99999999999999998739856 Q gi|254780412|r 1 MSFRSNQFFQQASRLASCASDAFKDI---SKEAESFAQIKIQRTLNSMGVVR 49 (94) Q Consensus 1 m~~~~n~~~ddla~~~~~a~~~~~~~---~~Eie~~~r~~~e~~l~kldLVt 49 (94) |+.+.+.-+.|+|+.++-..+|++-+ +..+-.-.|.++..+..++|.+. T Consensus 1 m~~~kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~elgY~p 52 (342) T PRK10014 1 MATAKKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR 52 (342) T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC T ss_conf 9999988799999998969999999977989999999999999999948997 No 77 >COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning] Probab=26.04 E-value=54 Score=14.66 Aligned_cols=45 Identities=11% Similarity=0.129 Sum_probs=19.2 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 500699999999986688877999999999999999999873985 Q gi|254780412|r 4 RSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVV 48 (94) Q Consensus 4 ~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLV 48 (94) ..++.+.|++--+-+|...+.+..=++=---+..++++..+.+++ T Consensus 3 ~~dq~lg~la~~iP~A~~iFr~y~iDFCCGG~~~L~~Aa~~k~l~ 47 (221) T COG2846 3 YRDQPLGDLAISIPRAAEIFRSYDIDFCCGGKVTLERAAAEKGLD 47 (221) T ss_pred CCCCHHHHHHHHCCCHHHHHHHCCCCEECCCHHHHHHHHHHCCCC T ss_conf 311439999995743899999839862058719999999983898 No 78 >KOG4643 consensus Probab=26.01 E-value=54 Score=14.66 Aligned_cols=41 Identities=22% Similarity=0.311 Sum_probs=29.4 Q ss_pred CCCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH Q ss_conf 9856999999999999999999--9999999999999999999 Q gi|254780412|r 46 GVVRAEEIENVKRTTSHLREEI--TAIGKRLEKIEQQLADLEL 86 (94) Q Consensus 46 dLVtREEFdv~~~~l~k~R~~~--e~Le~rl~~LE~kl~~le~ 86 (94) +-|--|||+.+++-++++|.+. ..|+..|-.+.++|.++.. T Consensus 273 N~vLleekeMLeeQLq~lrarse~~tleseiiqlkqkl~dm~~ 315 (1195) T KOG4643 273 NRVLLEEKEMLEEQLQKLRARSEGATLESEIIQLKQKLDDMRS 315 (1195) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 6989999999999999988524568717889999887789998 No 79 >TIGR00081 purC phosphoribosylaminoimidazole-succinocarboxamide synthase; InterPro: IPR001636 Phosphoribosylaminoimidazole-succinocarboxamide synthase (6.3.2.6 from EC) (SAICAR synthetase) catalyzes the seventh step in the de novo purine biosynthetic pathway; the ATP-dependent conversion of 5'-phosphoribosyl-5-aminoimidazole-4-carboxylic acid and aspartic acid to SAICAR . In bacteria (purC), fungi (ADE1) and plants (Pur7), SAICAR synthetase is a monofunctional protein; in animals it is the N-terminal domain of a bifunctional enzyme that also catalyse phosphoribosylaminoimidazole carboxylase (AIRC) activity (see). ; GO: 0004639 phosphoribosylaminoimidazolesuccinocarboxamide synthase activity, 0006164 purine nucleotide biosynthetic process. Probab=25.67 E-value=55 Score=14.62 Aligned_cols=34 Identities=18% Similarity=0.336 Sum_probs=27.6 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999873985699999999999999999999999 Q gi|254780412|r 39 QRTLNSMGVVRAEEIENVKRTTSHLREEITAIGK 72 (94) Q Consensus 39 e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~ 72 (94) ++...-+++||+|+++.+++.+.+..+.+..+-. T Consensus 234 ~s~a~~~~~~~~e~~~~~Kela~~~n~~l~~~~~ 267 (374) T TIGR00081 234 ESYAEALGLATEEELERIKELALKVNEVLKRLFD 267 (374) T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7799882367888999999999999899999997 No 80 >KOG2802 consensus Probab=25.66 E-value=55 Score=14.62 Aligned_cols=77 Identities=12% Similarity=0.252 Sum_probs=46.8 Q ss_pred CCCCCHHHHHHHHHHHHHH-HHHHH----------------HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH-------- Q ss_conf 9750069999999998668-88779----------------9999999999999999987398569999999-------- Q gi|254780412|r 2 SFRSNQFFQQASRLASCAS-DAFKD----------------ISKEAESFAQIKIQRTLNSMGVVRAEEIENV-------- 56 (94) Q Consensus 2 ~~~~n~~~ddla~~~~~a~-~~~~~----------------~~~Eie~~~r~~~e~~l~kldLVtREEFdv~-------- 56 (94) |+..|||+|-+..+.-|++ |+.-. ++.|++=+-|-..+++|. |+||+-. T Consensus 384 s~tgnPIyD~~GSivvGaLLGmVe~diyDvK~~diG~g~vRfKAE~DFdGr~vtrsYL~------kqd~akml~e~~~~~ 457 (503) T KOG2802 384 SITGNPIYDSLGSIVVGALLGMVENDIYDVKATDIGLGKVRFKAEVDFDGRVVTRSYLE------KQDFAKMLQEIQEVK 457 (503) T ss_pred HHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEECCCEEEEEEEECCCCHHHHHHHHH------HHHHHHHHHHHHHCC T ss_conf 72189786542037898888777776541322340464168887852672216897872------889999999998209 Q ss_pred ------HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ------9999999999999999999999999999 Q gi|254780412|r 57 ------KRTTSHLREEITAIGKRLEKIEQQLADL 84 (94) Q Consensus 57 ------~~~l~k~R~~~e~Le~rl~~LE~kl~~l 84 (94) .-|+..-.+=++.|-+.++-||+.|.++ T Consensus 458 ~~e~le~fml~~GEnivd~lG~EvDRlEkel~~~ 491 (503) T KOG2802 458 TPEELETFMLKHGENIVDTLGAEVDRLEKELKKR 491 (503) T ss_pred CHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 9899999999734489987635778999999874 No 81 >pfam06962 rRNA_methylase Putative rRNA methylase. This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins. Probab=25.57 E-value=34 Score=15.94 Aligned_cols=17 Identities=6% Similarity=0.206 Sum_probs=13.9 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999 Q gi|254780412|r 53 IENVKRTTSHLREEITA 69 (94) Q Consensus 53 Fdv~~~~l~k~R~~~e~ 69 (94) ||+|.+-+..||.++.. T Consensus 5 FDIQ~~Ai~~T~~rL~~ 21 (140) T pfam06962 5 FDIQEEALENTKEKLEQ 21 (140) T ss_pred EECHHHHHHHHHHHHHH T ss_conf 96099999999999996 No 82 >pfam09340 NuA4 Histone acetyltransferase subunit NuA4. The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control. Probab=25.30 E-value=56 Score=14.58 Aligned_cols=29 Identities=24% Similarity=0.257 Sum_probs=20.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999965 Q gi|254780412|r 60 TSHLREEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 60 l~k~R~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) |..+-.+=..|+..++.||.+|-++|+-- T Consensus 4 L~~ll~kK~~Le~~L~~lE~qIY~~Et~Y 32 (80) T pfam09340 4 LKELLQKKKKLEKELAALERQIYDKETEY 32 (80) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999999 No 83 >TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent .. Probab=25.24 E-value=56 Score=14.57 Aligned_cols=38 Identities=39% Similarity=0.599 Sum_probs=18.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999999999999650 Q gi|254780412|r 52 EIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 52 EFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) +-...+..+.....++..++..++.++..|.++|...+ T Consensus 787 ~~~~~~~e~~~l~~~i~~~e~~~~~~~~~l~~le~~~~ 824 (1202) T TIGR02169 787 ELENVKSELKELEAEIEELEEKLAKLEEALEDLEASLS 824 (1202) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 88889999999999999999999999998852651101 No 84 >TIGR02231 TIGR02231 conserved hypothetical protein; InterPro: IPR011935 This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.. Probab=24.58 E-value=58 Score=14.49 Aligned_cols=76 Identities=21% Similarity=0.340 Sum_probs=50.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHCCCCCHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9866888779999999999999---999998739856999---------9999999999999999999999999999999 Q gi|254780412|r 16 ASCASDAFKDISKEAESFAQIK---IQRTLNSMGVVRAEE---------IENVKRTTSHLREEITAIGKRLEKIEQQLAD 83 (94) Q Consensus 16 ~~~a~~~~~~~~~Eie~~~r~~---~e~~l~kldLVtREE---------Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~ 83 (94) +.+..+.++..++.+++.+-.. +..-+.+-+.++|++ |+.+.....++..+.-..+.++.+|++|+++ T Consensus 90 ~~~~~~~l~~~~~~L~K~~~~~~~~~~~~~~~sg~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~r~~~~~~~el~~~~~~ 169 (558) T TIGR02231 90 LEDRGDALKALKSNLDKFLEDIREGLTEPIKDSGVLKRNEPDLKELKQLFDFVGSEIERLLTEDREVERRIRELEKQLSE 169 (558) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 77788899985301025677774201467321523561576568999999988999999988877899999999999999 Q ss_pred HHHHHHHC Q ss_conf 99965002 Q gi|254780412|r 84 LELFINQK 91 (94) Q Consensus 84 le~~~~~k 91 (94) |+.-++.. T Consensus 170 L~~el~~~ 177 (558) T TIGR02231 170 LENELRAL 177 (558) T ss_pred HHHHHHHH T ss_conf 99999874 No 85 >pfam10234 Cluap1 Clusterin-associated protein-1. This protein is conserved from worms to humans. The protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell. Probab=24.02 E-value=59 Score=14.42 Aligned_cols=69 Identities=19% Similarity=0.362 Sum_probs=39.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 888779999999999999999998-73985699999-999999999999999999999999999999996500237 Q gi|254780412|r 20 SDAFKDISKEAESFAQIKIQRTLN-SMGVVRAEEIE-NVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEK 93 (94) Q Consensus 20 ~~~~~~~~~Eie~~~r~~~e~~l~-kldLVtREEFd-v~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k~~ 93 (94) ++...-+++|++ +|..-+..++ .+++.+ +| +++..+.....+++.+.+.+..+..--+.|+.-|.+|.+ T Consensus 136 A~L~dlL~kE~~--lr~~R~~a~~r~~el~~---iEk~l~~~i~~~~~~~~~~~~~l~~~~~de~~Le~KIekkk~ 206 (269) T pfam10234 136 AALYDLLGKELD--LRESRQKALSRPLELAE---VEKALKEAIKNLAARLQQLQAELDNLKSDEANLEAKIERKKQ 206 (269) T ss_pred HHHHHHHHHHHH--HHHHHHHHHCCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999975898--99999999817667899---999999999999999999999999877378779989999888 No 86 >PRK11578 macrolide transporter subunit MacA; Provisional Probab=23.46 E-value=61 Score=14.36 Aligned_cols=51 Identities=12% Similarity=0.246 Sum_probs=38.3 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999987398569999999999999999999999999999999999999650 Q gi|254780412|r 39 QRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 39 e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) ...|.+.+.+++.+||--+.=+...+.+++.+++++...++.|...+..+. T Consensus 109 ~~~L~~~~~is~~~~d~a~~~~~~~~a~l~~~~a~~~~~~a~l~~a~~~l~ 159 (347) T PRK11578 109 QQRLAKTQAVSQQDLDTAATEMAVKQAQIGTIDAQIKRNQASLDTAKTNLD 159 (347) T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999987576247889887879998764588999999999999999987652 No 87 >pfam11488 Lge1 Transcriptional regulatory protein LGE1. This family of proteins is conserved in yeasts where it is involved in the ubiquitination of histones H2A and H2B. This ubiquitination step is a vital one in the regulation of the transcriptional activity of RNA polymerase II. In S. cerevisiae, Rad6 and Bre1 are present in a complex, also containing Lge1, that is required for H2B ubiquitination. Bre1 is the H2B ubiquitin ligase that interacts with acidic activators, such as Gal4, and recruits Rad6 and its binding partner Lge1 to target promoters. In S. pombe the equivalent protein to Lge1 appears to be Shf1. Probab=23.31 E-value=61 Score=14.34 Aligned_cols=57 Identities=19% Similarity=0.156 Sum_probs=30.8 Q ss_pred HHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999987398---569999999999999999999999999999999999999650 Q gi|254780412|r 33 FAQIKIQRTLNSMGV---VRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 33 ~~r~~~e~~l~kldL---VtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) .++....-||+=|++ -|.+.|+-...-+...-.+|+.|+.++..||--++.||+.+. T Consensus 156 ~i~~~~~P~I~Im~idd~~t~e~le~~~~e~~~~d~~L~~~~~~~~k~e~~~~~le~q~~ 215 (234) T pfam11488 156 KIKNFNNPWINIMDIDDEPTQEKLEERYKELEELDQKLEELQLKKLKLELELALLETQAA 215 (234) T ss_pred CCCCCCCCHHEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 675556641001105673148899998766888899999999999999999999988876 No 88 >cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=23.13 E-value=62 Score=14.32 Aligned_cols=31 Identities=16% Similarity=0.413 Sum_probs=21.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999999965 Q gi|254780412|r 58 RTTSHLREEITAIGKRLEKIEQQLADLELFI 88 (94) Q Consensus 58 ~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~ 88 (94) ++....+.++..++++++.|+.-.+.|+..+ T Consensus 81 ~~~~~l~~kl~ei~~~I~~L~~lr~~L~~~l 111 (112) T cd01282 81 DLLAVLRRELARIDRQIADLTRSRDRLDAYL 111 (112) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999999999975 No 89 >pfam05278 PEARLI-4 Arabidopsis phospholipase-like protein (PEARLI 4). This family contains several phospholipase-like proteins from Arabidopsis thaliana which are homologous to PEARLI 4. Probab=22.76 E-value=63 Score=14.27 Aligned_cols=40 Identities=18% Similarity=0.441 Sum_probs=25.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8569999999999999999999999999999999999999 Q gi|254780412|r 47 VVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLEL 86 (94) Q Consensus 47 LVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~ 86 (94) +-.|.|.+.+.+=+.+--.++..-.+|+.++-.+|.+||. T Consensus 168 ~~~k~EmE~~~~eL~~kEKevke~r~~v~e~~~~Lg~LEm 207 (234) T pfam05278 168 LLKKQEMEKQEAELVRKEKEVKEFREKVEEMAGRLGELEM 207 (234) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8778899999999999999999999999999988877777 No 90 >COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms] Probab=22.63 E-value=63 Score=14.25 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=21.8 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 9998739856999999999999999999 Q gi|254780412|r 40 RTLNSMGVVRAEEIENVKRTTSHLREEI 67 (94) Q Consensus 40 ~~l~kldLVtREEFdv~~~~l~k~R~~~ 67 (94) ..|.+-+.|||+|+|-.+.-+..++..+ T Consensus 140 ~~L~~~g~vs~~~~~~a~~a~~~A~A~~ 167 (352) T COG1566 140 AELAQRGVVSREELDRARAALQAAEAAL 167 (352) T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 9887567443999998888999998888 No 91 >pfam07195 FliD_C Flagellar hook-associated protein 2 C-terminus. The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria. This alignment covers the C-terminal region of this family of proteins. Probab=22.44 E-value=64 Score=14.23 Aligned_cols=61 Identities=15% Similarity=0.352 Sum_probs=32.1 Q ss_pred HHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHCC Q ss_conf 999999999999873-9856999999999999999999999999999999----9999999650023 Q gi|254780412|r 31 ESFAQIKIQRTLNSM-GVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ----QLADLELFINQKE 92 (94) Q Consensus 31 e~~~r~~~e~~l~kl-dLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~----kl~~le~~~~~k~ 92 (94) -..+...++.++..- +.++-.. +.+..-+.....+++.|+.|++..+. +-+.+|..+++=+ T Consensus 164 ~~~l~~~l~~~~~~~~G~l~~~~-~~l~~~~~~~~~~i~~l~~rl~~~~~~~~~qf~~me~~i~~mn 229 (230) T pfam07195 164 AKRLDDSLKPYTGSGNGILASRE-DSLNKQIKRLNKQIEDLDRRLDTLEARLKAQFTAMDDLMSKMN 229 (230) T ss_pred HHHHHHHHHHHHCCCCCEEHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999998478986405688-8899999999999999999999999999999999999999847 No 92 >PRK00591 prfA peptide chain release factor 1; Validated Probab=22.35 E-value=58 Score=14.50 Aligned_cols=27 Identities=30% Similarity=0.500 Sum_probs=18.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999999 Q gi|254780412|r 58 RTTSHLREEITAIGKRLEKIEQQLADL 84 (94) Q Consensus 58 ~~l~k~R~~~e~Le~rl~~LE~kl~~l 84 (94) ++..-+.+++..|++++..||.+|..+ T Consensus 76 el~e~a~~El~~l~~~l~~lE~eL~~l 102 (360) T PRK00591 76 EMREMAKEELKELEERLEELEEELKIL 102 (360) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 899999999999999999999999998 No 93 >PRK10697 DNA-binding transcriptional activator PspC; Provisional Probab=22.27 E-value=64 Score=14.21 Aligned_cols=27 Identities=22% Similarity=0.415 Sum_probs=14.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999650 Q gi|254780412|r 63 LREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 63 ~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) .+..+..+..+++.+|.+|.+.|..++ T Consensus 80 p~~~l~~i~~~~~~~E~RLr~ME~YVT 106 (119) T PRK10697 80 SSELLDEVDRELAAGEQRLREMERYVT 106 (119) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999999999999999999999988873 No 94 >PRK01885 greB transcription elongation factor GreB; Reviewed Probab=21.73 E-value=66 Score=14.14 Aligned_cols=58 Identities=10% Similarity=0.213 Sum_probs=39.6 Q ss_pred HHHHHHHHHHHH-------HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 779999999999-------99999999873985699999999999999999999999999999999999996 Q gi|254780412|r 23 FKDISKEAESFA-------QIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 23 ~~~~~~Eie~~~-------r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) ...++.|++... ...+..+-+.-||=--=||++ +++++..|++||..|+.+|+.-+-. T Consensus 14 ~~kL~~El~~L~~~~r~~~~~~i~~Ar~~GDlsENaeY~a-------Ake~q~~le~rI~~Le~~L~~A~ii 78 (159) T PRK01885 14 YERLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIY-------GKKRLREIDRRVRFLTKRLENLKVV 78 (159) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHH-------HHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 9999999999874530458999999998599430263899-------9999999999999999998733035 No 95 >pfam04508 Pox_A_type_inc Viral A-type inclusion protein repeat. The repeat is found in the A-type inclusion protein of the Poxvirus family. Probab=21.54 E-value=66 Score=14.12 Aligned_cols=18 Identities=28% Similarity=0.626 Sum_probs=9.0 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999 Q gi|254780412|r 67 ITAIGKRLEKIEQQLADL 84 (94) Q Consensus 67 ~e~Le~rl~~LE~kl~~l 84 (94) ++.+..+|..|+++|.+- T Consensus 3 ldr~r~~I~dLek~L~~c 20 (26) T pfam04508 3 LDRLRRRISDLEKQLSDC 20 (26) T ss_pred HHHHHHHHHHHHHHHHHH T ss_conf 889999988899999998 No 96 >pfam07426 Dynactin_p22 Dynactin subunit p22. This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localizes to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis. Family members are approximately 170 residues long and seem to be restricted to mammals. Probab=21.39 E-value=67 Score=14.10 Aligned_cols=43 Identities=9% Similarity=0.097 Sum_probs=19.7 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 975006999999999866888779999999999999999998739 Q gi|254780412|r 2 SFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMG 46 (94) Q Consensus 2 ~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kld 46 (94) +..++++.|.++++-....+++. ++|--+.+--+++....=+| T Consensus 27 ~~~~~~v~d~L~~vq~~l~~a~s--kRerik~l~kki~eL~kYLD 69 (172) T pfam07426 27 TGEPRKVAEGLVKIQVALGNIAN--KRERVKILYKKIEDLLKYLD 69 (172) T ss_pred CCCCCHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHHCC T ss_conf 78984177899999999999861--35999999997899998669 No 97 >PRK00226 greA transcription elongation factor GreA; Reviewed Probab=21.35 E-value=67 Score=14.09 Aligned_cols=58 Identities=19% Similarity=0.320 Sum_probs=40.2 Q ss_pred HHHHHHHHHHHHH-------HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 7799999999999-------9999999873985699999999999999999999999999999999999996 Q gi|254780412|r 23 FKDISKEAESFAQ-------IKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF 87 (94) Q Consensus 23 ~~~~~~Eie~~~r-------~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~ 87 (94) ..-+++|++.... ..+..+-+.-||=--=||++ +++++..+++||..|+..|+..+.. T Consensus 12 ~~~L~~El~~L~~~~r~~i~~~i~~Ar~~GDlsENaeY~a-------Ake~q~~~e~rI~~Le~~L~~A~ii 76 (157) T PRK00226 12 YEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHA-------AKEEQGFIEGRIRELEDKLSNAEVI 76 (157) T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 9999999999987236899999999998699640576999-------9999999999999999999850145 No 98 >cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth. Probab=21.15 E-value=68 Score=14.07 Aligned_cols=54 Identities=17% Similarity=0.283 Sum_probs=41.6 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999987398569999999999999--999999999999999999999999650 Q gi|254780412|r 35 QIKIQRTLNSMGVVRAEEIENVKRTTSH--LREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 35 r~~~e~~l~kldLVtREEFdv~~~~l~k--~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) +..+...+.++++ +.+.||.+..|=.. |+++++.|++.++.+++.++.++..++ T Consensus 374 k~~l~~~l~~~~~-~~~q~dyLL~M~L~~LT~~e~~kL~~e~~~l~~ei~~L~~~l~ 429 (445) T cd00187 374 KKALIEELEKLGF-SEIQADAILDMRLRRLTKLEREKLLKELKELEAEIEDLEKILA 429 (445) T ss_pred HHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999876799-9999999997669987589999999999999999999999867 No 99 >pfam06428 Sec2p GDP/GTP exchange factor Sec2p. In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion. Probab=20.91 E-value=68 Score=14.03 Aligned_cols=40 Identities=23% Similarity=0.362 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999999999999999650 Q gi|254780412|r 50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) |-|-.+...--.++++.+..-+.-|+.|..+|.+|+.++- T Consensus 43 r~e~~~~e~kn~qL~eqL~e~e~ll~slQ~QL~~LK~v~~ 82 (101) T pfam06428 43 RKEREAVEIKNEKLEEQLKEKETLLDSLQAQLKELKQVMQ 82 (101) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999998899999997699899999999999999999 No 100 >pfam04102 SlyX SlyX. The SlyX protein has no known function. It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure. Probab=20.86 E-value=69 Score=14.03 Aligned_cols=33 Identities=18% Similarity=0.441 Sum_probs=26.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999999999999 Q gi|254780412|r 53 IENVKRTTSHLREEITAIGKRLEKIEQQLADLE 85 (94) Q Consensus 53 Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le 85 (94) .|-+-.++.+-..+++.|+.++..|..++.+++ T Consensus 20 ie~Ln~vv~~Qq~~i~~L~~~l~~L~~rl~~~~ 52 (68) T pfam04102 20 IEELNQVVAEQQRQIDRLQRQLRLLVERLKEVE 52 (68) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999999999999999999999999999999742 No 101 >cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=20.45 E-value=70 Score=13.97 Aligned_cols=29 Identities=24% Similarity=0.401 Sum_probs=18.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999650 Q gi|254780412|r 61 SHLREEITAIGKRLEKIEQQLADLELFIN 89 (94) Q Consensus 61 ~k~R~~~e~Le~rl~~LE~kl~~le~~~~ 89 (94) .-...+.+.++++++.|+.....++.... T Consensus 82 ~~l~~~~~~i~~qI~~L~~~~~~L~~~~~ 110 (116) T cd04769 82 QALEDKKQEIRAQITELQQLLARLDAFEA 110 (116) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999999 Done!