Query gi|254780124|ref|YP_003064537.1| hypothetical protein CLIBASIA_00015 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 388 No_of_seqs 219 out of 911 Neff 7.5 Searched_HMMs 39220 Date Sun May 22 13:17:44 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780124.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam10926 DUF2800 Protein of u 100.0 0 0 780.8 33.7 354 4-375 1-363 (363) 2 TIGR03623 probable DNA repair 99.9 2E-23 5.1E-28 173.4 14.8 235 3-238 594-873 (874) 3 TIGR02773 addB_Gpos ATP-depend 99.6 3.2E-14 8.1E-19 112.9 16.2 176 6-182 801-1041(1192) 4 COG3857 AddB ATP-dependent nuc 99.6 6.7E-14 1.7E-18 110.8 14.7 171 6-178 751-973 (1108) 5 COG2887 RecB family exonucleas 99.6 1.4E-13 3.6E-18 108.7 14.6 225 7-242 1-255 (269) 6 TIGR02786 addB_alphas double-s 99.5 9E-13 2.3E-17 103.4 11.3 156 6-161 814-1005(1096) 7 TIGR02784 addA_alphas double-s 99.4 1.1E-11 2.7E-16 96.3 12.4 166 6-176 993-1183(1190) 8 TIGR00372 cas4 CRISPR-associat 99.3 1.6E-10 4.2E-15 88.5 13.6 186 7-238 1-205 (206) 9 TIGR02774 rexB_recomb ATP-depe 99.0 7.1E-08 1.8E-12 71.2 17.0 292 5-337 760-1108(1116) 10 PRK13909 putative recombinatio 99.0 8.5E-09 2.2E-13 77.3 11.8 134 34-178 766-904 (911) 11 KOG1805 consensus 99.0 9.1E-08 2.3E-12 70.5 15.5 228 5-240 183-451 (1100) 12 pfam01930 Cas_Cas4 Domain of u 98.9 3.8E-08 9.8E-13 73.0 12.4 158 9-238 2-161 (162) 13 pfam09810 Morph_protein1 Defec 98.7 9.6E-06 2.4E-10 57.2 17.4 138 7-157 14-176 (329) 14 TIGR03491 RecB family nuclease 98.6 4.6E-06 1.2E-10 59.3 15.2 193 7-243 1-205 (457) 15 PHA00619 CRISPR-associated Cas 98.4 1.9E-05 4.9E-10 55.3 13.9 162 14-238 36-207 (210) 16 COG1074 RecB ATP-dependent exo 98.4 1.5E-06 3.7E-11 62.6 7.2 47 112-158 1061-1118(1139) 17 PHA01622 CRISPR-associated Cas 98.3 1.1E-05 2.8E-10 56.9 11.0 131 96-238 68-200 (204) 18 COG1468 CRISPR-associated prot 98.3 4.3E-05 1.1E-09 52.9 13.2 169 5-239 14-188 (190) 19 pfam06023 DUF911 Archaeal prot 98.3 5.2E-05 1.3E-09 52.4 13.2 204 17-238 54-289 (290) 20 TIGR02785 addA_Gpos recombinat 98.1 1E-05 2.6E-10 57.0 7.4 52 109-160 1214-1277(1295) 21 TIGR00609 recB exodeoxyribonuc 97.9 5.7E-05 1.5E-09 52.1 7.8 55 112-166 1207-1279(1324) 22 COG2251 Predicted nuclease (Re 97.9 0.0013 3.3E-08 43.2 14.5 254 6-285 2-278 (474) 23 PRK10876 recB exonuclease V su 97.8 7.3E-05 1.9E-09 51.4 6.2 15 228-242 549-563 (1181) 24 pfam08696 Dna2 DNA replication 97.8 9.4E-05 2.4E-09 50.7 6.6 49 5-53 58-108 (209) 25 COG4343 CRISPR-associated prot 97.1 0.012 3.1E-07 36.8 10.9 207 15-238 51-280 (281) 26 TIGR01896 cas_AF1879 CRISPR-as 95.0 0.29 7.4E-06 27.8 9.8 122 99-238 164-295 (295) 27 PRK09709 exonuclease VIII; Rev 92.5 0.83 2.1E-05 24.8 10.9 16 145-160 791-806 (877) 28 TIGR00423 TIGR00423 conserved 86.1 0.66 1.7E-05 25.4 2.8 13 223-235 14-26 (331) 29 KOG4760 consensus 84.5 3 7.8E-05 21.1 8.1 40 99-138 156-196 (365) 30 pfam02477 Nairo_nucleo Nucleoc 80.8 1.1 2.9E-05 23.9 2.2 39 121-160 98-136 (442) 31 COG1023 Gnd Predicted 6-phosph 75.0 6.1 0.00016 19.1 5.0 60 250-312 195-254 (300) 32 pfam06250 DUF1016 Protein of u 68.3 8.4 0.00021 18.2 4.0 77 88-172 199-278 (320) 33 COG1060 ThiH Thiamine biosynth 65.3 6.4 0.00016 18.9 2.9 53 269-321 293-351 (370) 34 PRK06245 cofG FO synthase subu 64.7 9 0.00023 18.0 3.5 67 284-355 258-327 (336) 35 pfam05565 Sipho_Gp157 Siphovir 61.4 7.9 0.0002 18.4 2.7 29 258-286 61-89 (162) 36 TIGR03550 F420_cofG 7,8-dideme 59.2 13 0.00032 17.0 3.5 38 283-321 254-295 (322) 37 PRK08445 hypothetical protein; 58.6 8.6 0.00022 18.1 2.5 16 34-49 17-32 (348) 38 pfam00285 Citrate_synt Citrate 56.8 14 0.00035 16.7 4.1 51 257-318 218-268 (352) 39 PRK05904 coproporphyrinogen II 56.8 14 0.00035 16.7 3.6 13 10-22 5-17 (353) 40 PRK05927 hypothetical protein; 54.7 11 0.00029 17.3 2.6 13 351-363 305-317 (350) 41 PRK10880 adenine DNA glycosyla 50.7 16 0.00041 16.3 2.9 37 203-245 180-216 (350) 42 COG1194 MutY A/G-specific DNA 50.2 18 0.00045 16.1 4.2 52 189-246 164-222 (342) 43 PRK12349 citrate synthase 3; P 49.6 18 0.00046 16.0 4.3 41 257-308 224-265 (365) 44 cd06109 BsCS-I_like Bacillus s 47.1 20 0.0005 15.7 3.8 52 256-318 207-258 (349) 45 COG0792 Predicted endonuclease 46.7 20 0.00051 15.7 3.9 43 113-155 32-79 (114) 46 TIGR03551 F420_cofH 7,8-dideme 46.2 20 0.00051 15.7 2.8 13 35-47 16-28 (343) 47 PRK06582 coproporphyrinogen II 45.8 6.5 0.00017 18.9 0.2 12 305-316 313-324 (390) 48 PRK08444 hypothetical protein; 45.1 21 0.00054 15.5 3.9 13 351-363 307-319 (353) 49 PRK09736 5-methylcytosine-spec 44.3 22 0.00055 15.5 11.0 66 115-180 244-313 (350) 50 PRK06341 single-stranded DNA-b 43.6 13 0.00033 16.9 1.5 34 273-310 60-93 (165) 51 COG5175 MOT2 Transcriptional r 43.5 15 0.00039 16.4 1.9 11 112-122 143-153 (480) 52 cd06112 citrate_synt_like_1_1 42.2 23 0.00059 15.3 3.8 51 257-318 223-273 (373) 53 PRK07360 FO synthase subunit 2 42.2 18 0.00045 16.0 2.0 34 330-364 308-341 (375) 54 KOG1150 consensus 41.4 17 0.00043 16.2 1.8 14 358-371 139-152 (250) 55 TIGR00872 gnd_rel 6-phosphoglu 41.2 16 0.0004 16.4 1.6 57 253-312 239-295 (341) 56 KOG2672 consensus 40.7 8.6 0.00022 18.1 0.2 32 108-139 104-138 (360) 57 PRK03298 hypothetical protein; 40.5 25 0.00063 15.1 4.3 59 110-177 131-190 (224) 58 pfam07211 consensus 40.5 25 0.00063 15.1 6.6 54 272-326 55-114 (162) 59 COG4950 Uncharacterized protei 40.0 10 0.00026 17.6 0.5 62 226-287 75-145 (193) 60 PRK09058 coproporphyrinogen II 38.9 26 0.00067 14.9 3.5 11 125-135 209-219 (447) 61 TIGR01979 sufS cysteine desulf 37.2 26 0.00065 15.0 2.2 95 144-274 306-408 (409) 62 KOG0437 consensus 36.8 22 0.00056 15.4 1.8 59 226-284 841-914 (1080) 63 PRK05926 hypothetical protein; 36.5 28 0.00073 14.7 2.9 13 351-363 330-342 (371) 64 PRK08898 coproporphyrinogen II 36.2 21 0.00052 15.6 1.6 15 353-367 364-378 (393) 65 PRK12351 methylcitrate synthas 35.3 30 0.00076 14.6 3.6 51 257-318 228-278 (377) 66 pfam04577 DUF563 Protein of un 34.5 31 0.00078 14.5 2.5 31 291-322 210-240 (246) 67 PRK13347 coproporphyrinogen II 33.9 31 0.0008 14.4 5.2 14 354-367 412-425 (453) 68 pfam08011 DUF1703 Protein of u 33.3 32 0.00081 14.4 2.9 45 111-155 27-76 (101) 69 TIGR01823 PabB-fungal para-ami 32.9 31 0.00078 14.5 2.0 73 224-307 632-705 (851) 70 PRK06642 single-stranded DNA-b 32.7 21 0.00054 15.5 1.2 35 272-310 59-93 (152) 71 COG0372 GltA Citrate synthase 32.2 33 0.00085 14.2 4.0 51 257-317 235-285 (390) 72 cd06106 ScCit3_like Saccharomy 31.1 35 0.00088 14.1 3.4 56 256-318 273-331 (428) 73 PRK09234 fbiC FO synthase; Rev 30.9 35 0.00089 14.1 4.7 19 217-235 533-551 (846) 74 cd06110 BSuCS-II_like Bacillus 30.4 36 0.00091 14.0 4.0 51 257-318 219-269 (356) 75 TIGR01793 cit_synth_euk citrat 30.1 35 0.00088 14.1 1.9 50 275-326 299-348 (430) 76 COG1801 Uncharacterized conser 29.7 37 0.00093 14.0 6.7 32 4-35 47-79 (263) 77 KOG0649 consensus 29.0 27 0.00069 14.8 1.2 25 123-147 177-202 (325) 78 PRK08207 coproporphyrinogen II 28.6 38 0.00097 13.8 3.7 17 252-268 238-254 (497) 79 TIGR01084 mutY A/G-specific ad 27.7 35 0.0009 14.1 1.6 38 204-247 191-228 (297) 80 pfam09856 DUF2083 Predicted tr 27.0 34 0.00088 14.1 1.5 24 221-245 117-140 (156) 81 PRK13627 carnitine operon prot 26.8 28 0.00071 14.7 1.0 21 353-373 174-194 (196) 82 COG1637 Predicted nuclease of 26.0 42 0.0011 13.5 8.6 37 113-152 160-197 (253) 83 cd06115 AthCS_per_like Arabido 25.1 44 0.0011 13.4 3.9 52 257-319 258-309 (410) 84 PRK08173 DNA topoisomerase III 24.5 45 0.0012 13.4 2.4 32 327-363 766-797 (857) 85 cd06118 citrate_synt_like_1 Ci 24.4 45 0.0012 13.4 3.6 46 265-318 224-269 (358) 86 pfam01939 DUF91 Protein of unk 24.4 45 0.0012 13.4 5.0 59 111-177 133-192 (228) 87 KOG2457 consensus 23.5 27 0.00068 14.9 0.4 23 222-244 290-314 (555) 88 TIGR01311 glycerol_kin glycero 23.3 19 0.00047 15.9 -0.5 37 110-147 163-210 (518) 89 TIGR00770 Dcu transporter, ana 23.2 29 0.00074 14.6 0.5 11 45-55 72-82 (447) 90 COG2810 Predicted type IV rest 22.9 48 0.0012 13.2 3.6 73 85-163 32-105 (284) 91 KOG3300 consensus 22.4 50 0.0013 13.1 3.0 33 267-299 80-112 (146) 92 cd06111 DsCS_like Cold-active 22.2 50 0.0013 13.1 3.4 50 257-317 219-268 (362) 93 TIGR02187 GlrX_arch Glutaredox 22.0 32 0.00082 14.3 0.5 21 225-249 156-176 (237) 94 COG3894 Uncharacterized metal- 21.9 27 0.00069 14.8 0.1 24 125-148 177-200 (614) 95 PRK04247 hypothetical protein; 21.6 51 0.0013 13.0 5.0 56 112-176 158-214 (250) 96 cd06100 CCL_ACL-C Citryl-CoA l 21.5 52 0.0013 13.0 4.4 56 257-319 84-140 (227) 97 cd06103 ScCS-like Saccharomyce 21.2 52 0.0013 12.9 4.5 55 257-318 274-331 (426) 98 PRK12350 citrate synthase 2; P 21.1 53 0.0013 12.9 3.4 52 257-319 206-257 (352) 99 PRK04424 fatty acid biosynthes 20.4 54 0.0014 12.8 4.2 19 267-285 47-65 (185) 100 pfam05813 Orthopox_F7 Orthopox 20.0 33 0.00085 14.2 0.3 14 226-239 7-21 (82) No 1 >pfam10926 DUF2800 Protein of unknown function (DUF2800). This is a family of uncharacterized proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins. Probab=100.00 E-value=0 Score=780.78 Aligned_cols=354 Identities=36% Similarity=0.536 Sum_probs=329.0 Q ss_pred CCCCCCCCHHHHHCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 75618423677871832388621389998988999899999999997245765343220104564537757889999999 Q gi|254780124|r 4 HAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSM 83 (388) Q Consensus 4 HA~LSpSs~~rwl~CP~s~~Le~~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~ 83 (388) ||+|||||+||||+||+|++|+.++||++|+||.+||++|+++|.+|++.++.....+... ......++++|.++++. T Consensus 1 HA~LS~Ssa~RWl~Cp~S~~l~~~~pd~~S~~A~eGT~aH~l~E~~L~~~l~~~~~~~~~~--~~~~~~~~~eM~~~~~~ 78 (363) T pfam10926 1 HALLSASSAHRWLNCPPSARLEEGFPDKSSPAAAEGTAAHELAELKLRKGLDAITKLGRNS--EADGEYVDEEMAEYVQE 78 (363) T ss_pred CCCCCCCCCHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--CCCCEEECHHHHHHHHH T ss_conf 9867845124655698549987249998987899758999999999985169632256555--66880508899999999 Q ss_pred HHHHHHCCC---CCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 999985037---87368877553200044058999999998599799998113688767446687999999999984383 Q gi|254780124|r 84 VLAYVRTFS---GPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGD 160 (388) Q Consensus 84 ~~~~~r~~~---~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~ 160 (388) |++++++.- ....+.+|++++++.++|++|||+|+|++.+++|+|||||||+|++|+|++|+||++|||||++.|+. T Consensus 79 Yvd~v~e~~~~~~~~~~~iEqrvd~s~~~p~~fGTaD~vii~~~~L~IiDlKyG~GV~V~A~~N~QL~lYALGAl~~~~~ 158 (363) T pfam10926 79 YVDFVREQIELAKDGVLLIEQRVDFSQIVPEGFGTGDVVIIADGVLHIIDLKYGKGVLVSAEGNPQLMLYALGALDEFDV 158 (363) T ss_pred HHHHHHHHHHCCCCCEEEEEEEECHHHCCCCCCCCEEEEEEECCEEEEEECCCCCCCEECCCCCHHHHHHHHHHHHHHCC T ss_conf 99999999850679879999885223217887764128999388799998777877540246797899999999998166 Q ss_pred CCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 56765138999998304887754302589889999999999999999857765304776678886666725764456201 Q gi|254780124|r 161 IFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPAL 240 (388) Q Consensus 161 ~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~ 240 (388) +|+ +++|+|+|+|||+++ +|+|+++++||+.|++++ +++++..++.|++++.+|+|||||++|++|||| T Consensus 159 lyd-i~~V~mtI~QPR~~~---is~w~~s~~eL~~w~~~~-------~kp~A~~A~~g~gef~~G~~CrFCkak~~C~Ar 227 (363) T pfam10926 159 LYD-FDTVRMTIFQPRLDN---ISTWEISAEELLEWAEEV-------VKPAAELAYAGDGEFKPGEHCRFCKAKATCRAR 227 (363) T ss_pred CCC-CCEEEEEEECCCCCC---CCEEEEEHHHHHHHHHHH-------HHHHHHHHHCCCCCCCCCCCCCCCCCHHHCHHH T ss_conf 467-647999997457799---865887899999999999-------889999862799986789875306322228999 Q ss_pred HHHHHHHHHCC---CC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHH Q ss_conf 34678763022---00-599999999995438999999999999999997898478523205888786116989999999 Q gi|254780124|r 241 SRHVLLEATKD---PS-TNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELL 316 (388) Q Consensus 241 a~~~l~~~~~~---p~-~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l 316 (388) |++||.+++++ |+ .||++||++||.++++|++|++||++||++++++|++|||||||+|| |||+|+|+++|+++| T Consensus 228 a~~~l~la~~df~~~~~~Ls~~ei~~il~~~~~l~~W~~dv~~~a~~~~~~G~~~pG~KlV~GR-s~Rkw~de~~~~~~l 306 (363) T pfam10926 228 AQAVLNLAKYDFEDPTLDLTDEELAELLEKADLLEKWAKDVEAYALDEARNGKEVPGYKLVEGR-SNRKWTDEEAVAAAL 306 (363) T ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCC-CCCCCCCHHHHHHHH T ss_conf 9999988876215777689999999999714899999999999999999779987872661476-777647889999999 Q ss_pred HHCCC--CCCHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHEECCCCCCEECCCCCCCHHH Q ss_conf 86165--100000138988999974000242678987530015678982663078862000 Q gi|254780124|r 317 TSVLG--EEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQ 375 (388) Q Consensus 317 ~~~~~--~~~~~~~l~~~~~~ek~~~~~~~~~~~~~~l~~~i~k~~gkp~l~p~~d~~~~~ 375 (388) +.+|+ +++|+++|+|||+|||++|||+ |+++|++||+||+|||||||+||+||++ T Consensus 307 ~~~g~~~~~~y~~kli~pt~~ekllgkk~----f~ell~~li~k~~GkptLvp~sDkRpa~ 363 (363) T pfam10926 307 KAAGLKDEDIYKKKLISPTQAEKLLGKKK----FKELLGALIVKPPGKPTLVPESDKRPAL 363 (363) T ss_pred HHCCCCHHHCCCCCCCCHHHHHHHHCHHH----HHHHHHHHEECCCCCCEEEECCCCCCCC T ss_conf 98699655421013689899998878788----9999761263689961782478888999 No 2 >TIGR03623 probable DNA repair protein. Members of this protein family are bacterial proteins of about 900 amino acids in length. Members show extended homology to proteins in TIGR02786, the AddB protein of double-strand break repair via homologous recombination. Members of this family, therefore, may be DNA repair proteins. Probab=99.91 E-value=2e-23 Score=173.43 Aligned_cols=235 Identities=14% Similarity=0.073 Sum_probs=130.7 Q ss_pred CCCCCCCCCHHHHHCCCHHHHHHC----CCCCCC---CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC----------- Q ss_conf 775618423677871832388621----389998---98899989999999999724576534322010----------- Q gi|254780124|r 3 HHAFLSASSSHRWLKCPIAPTLES----KIPQTT---SIYASEGTFAHNLLAHCLEQGVDAETVSHQKL----------- 64 (388) Q Consensus 3 ~HA~LSpSs~~rwl~CP~s~~Le~----~~pd~~---S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~----------- 64 (388) .+...|+|-.+.++.||+.++++. .-+++. -.++.+||++|.++|.+++...+...+..... T Consensus 594 ~~~~gg~s~L~~qa~CPf~~f~~~rL~~~~~~~~~~gl~~~~rG~i~H~~Le~~~~~l~~~~~L~~l~~~~l~~~i~~a~ 673 (874) T TIGR03623 594 ERISGGTGLLKAQAACPFRAFAQHRLGARALEEPVDGLDALERGTLVHRVLELFWERLKNQAALNALDEAELEQLIAEAI 673 (874) T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHH T ss_conf 43567289999887092999999984998889866677977765999999999999825736454189999999999999 Q ss_pred -----CC-CC----CC----HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEE-ECCEEEEE Q ss_conf -----45-64----53----775788999999999998503787368877553200044058999999998-59979999 Q gi|254780124|r 65 -----TF-EN----DT----RIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIF-NSTQWIIV 129 (388) Q Consensus 65 -----~~-~~----~~----~~~~~e~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~-~dg~l~Ii 129 (388) .. .. .. ..-.+.+..++..+++.-+...+..++..|..++..+++..+.|+|||||. .||...|| T Consensus 674 ~~~l~~~~~~~~~~~~~~~~~le~~rl~~~l~~~L~~e~~r~pF~v~~~E~~~~~~~~~l~l~~riDRiD~~~dG~~~Ii 753 (874) T TIGR03623 674 GEALAEEEARHSQTFPERFLELEQERLLQLLLEWLELERQRPPFEVVATEQNHSIEIGGLELKVRIDRIDRLADGRRLII 753 (874) T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEEECCEEEEEEEECCCCCCCCCEEEE T ss_conf 99999987643434548999999999999999999975567991388721564156757899768744301699988999 Q ss_pred EEECCCCCCCCC----CCCHHHHHHHHHHHHH-CCCCCCCCCEEEEEEEEEECCCC--CCCCCCC--CCHHHHHHHHHHH Q ss_conf 811368876744----6687999999999984-38356765138999998304887--7543025--8988999999999 Q gi|254780124|r 130 DFKYGAGVPVKA----ENNTQLMLYACGALHQ-YGDIFGRPEALTLTIIQPRVRTG--SPINEWV--ISADDLLEKAKEF 200 (388) Q Consensus 130 DyKtGk~~~v~a----~~n~QL~lYALgA~~~-~~~~~~~~~~v~~~I~qpr~~~~--~~vs~~~--~s~eeL~~~~~~v 200 (388) |||||+...... -.+|||+|||+..-.. -+..|..++.-...+...-.+.. +.+.... -.......|.+-+ T Consensus 754 DYKTG~~~~~~~~~~r~~~pQLplYa~~~~~~v~~i~~a~v~~~~~~~~gl~~~~~~~~~~~~~~~~~~~~~~~~w~~~~ 833 (874) T TIGR03623 754 DYKTGAPSVRDWLGERPVEPQLPLYALLAEDEVAGVAFAQVRAGKMKFSGLAEDKELIPGVKAFAKLKAEDEPDSWEEVL 833 (874) T ss_pred EECCCCCCCCHHHCCCCCCCCHHHHHHHCCCCCCHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHCCCCCCCCHHHHH T ss_conf 82799998502221784445489999871587551021643157764100002443365554233421333446899999 Q ss_pred HHHHHHHHHHHHHHHCCCCCCC-C--CCCCCCCCCCCCCCC Q ss_conf 9999999857765304776678-8--866667257644562 Q gi|254780124|r 201 KERGTLALSLKSKRAVSLEHYG-V--NDDSCRFCRAKVRCP 238 (388) Q Consensus 201 ~~~a~~~~~~~a~~~~~~~~~~-~--~g~~CrfC~~k~~Cr 238 (388) ..|-+ .+...+..-.+|.... | +.+.|+||+|+.+|| T Consensus 834 ~~w~~-~L~~la~e~~~G~a~v~p~~~~~~C~yCd~~~lCR 873 (874) T TIGR03623 834 ARWRQ-ELTALAEEFSAGYAAVDPKNSETDCRYCDLQPLCR 873 (874) T ss_pred HHHHH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHCCC T ss_conf 99999-99999999968988878999877688798441037 No 3 >TIGR02773 addB_Gpos ATP-dependent nuclease subunit B; InterPro: IPR014140 DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in others. AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. This entry describes the ATP-dependent nuclease subunit B (AddB/RexB) protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous and functionally equivalent, merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.. Probab=99.64 E-value=3.2e-14 Score=112.93 Aligned_cols=176 Identities=17% Similarity=0.110 Sum_probs=98.6 Q ss_pred CCCCCCHHHHHCCCHHHHHHCCC--CCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHH------- Q ss_conf 61842367787183238862138--99989---8899989999999999724576534322010456453775------- Q gi|254780124|r 6 FLSASSSHRWLKCPIAPTLESKI--PQTTS---IYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIV------- 73 (388) Q Consensus 6 ~LSpSs~~rwl~CP~s~~Le~~~--pd~~S---~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~------- 73 (388) -+|-|..++|-.||++++...+. .+... +|-+.|.++|++++.. ...++.+.+.......+.-.... T Consensus 801 ~~SVSRlE~Y~~CpF~hfa~yGLkl~ER~~Y~L~apDlG~~fH~~L~~I-s~~l~~e~Ldw~~L~k~~c~~~~~~ave~l 879 (1192) T TIGR02773 801 QASVSRLEKYNACPFAHFAQYGLKLKERKIYKLEAPDLGQLFHEALKEI-SDELKEEELDWSDLTKEQCRALANEAVEEL 879 (1192) T ss_pred EEEEECCHHHCCCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHH-HHHHHHCCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 2344010000178325565025320025525679963678999999999-999962378701147689999999999876 Q ss_pred ----H------HHHHHHHHHHHHHH-----------HCCCCCCEEEEEEEEEEECC----C------------EEEEEEE Q ss_conf ----7------88999999999998-----------50378736887755320004----4------------0589999 Q gi|254780124|r 74 ----D------TEMASSVSMVLAYV-----------RTFSGPFLSETEVPLEPFTT----E------------PGATGTA 116 (388) Q Consensus 74 ----~------~e~~~~v~~~~~~~-----------r~~~~~~~ve~E~~~~~~~~----~------------~~~~Gti 116 (388) + ...-.|++.-+..+ .......-+..|+.|-.... . ..+.|+| T Consensus 880 ~p~~q~~IL~SS~Ry~Y~~~rl~~i~~ra~~vl~Eq~K~S~F~P~g~E~~FG~~~~~se~~ppl~~~L~~G~~~~L~GRI 959 (1192) T TIGR02773 880 VPKIQHEILLSSKRYRYVQKRLKRIVTRAVKVLSEQAKRSKFVPVGLELGFGFGGDNSEELPPLKLILKNGEELKLRGRI 959 (1192) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCE T ss_conf 34534776223467899999999999999999998753278721224541367989875678732232688767873210 Q ss_pred EEEEEE---CCE-EEEEEEECCCCCC------CCCCCCHHHHHHHHHHHHH----C--CCCCCCCCEEEEEEEEEECCCC Q ss_conf 999985---997-9999811368876------7446687999999999984----3--8356765138999998304887 Q gi|254780124|r 117 DILIFN---STQ-WIIVDFKYGAGVP------VKAENNTQLMLYACGALHQ----Y--GDIFGRPEALTLTIIQPRVRTG 180 (388) Q Consensus 117 D~I~~~---dg~-l~IiDyKtGk~~~------v~a~~n~QL~lYALgA~~~----~--~~~~~~~~~v~~~I~qpr~~~~ 180 (388) ||||.. +++ |+|||||+|...+ |..--..||+.|--.++.. . |.-..+.-...+.|+-|+.... T Consensus 960 DRvD~~e~e~~~ylRIIDYKSsnPsk~LDL~~VYYGl~LQmLtYLD~~l~~s~~~~~lg~~a~PaGvLYFhihdp~~~a~ 1039 (1192) T TIGR02773 960 DRVDKAEKEDETYLRIIDYKSSNPSKKLDLTEVYYGLALQMLTYLDIVLTNSEKWLKLGNQAKPAGVLYFHIHDPIVSAK 1039 (1192) T ss_pred EEEEHCCCCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEC T ss_conf 00211015898148888703788873543577666899999999999998589999710654776045566437233007 Q ss_pred CC Q ss_conf 75 Q gi|254780124|r 181 SP 182 (388) Q Consensus 181 ~~ 182 (388) .. T Consensus 1040 ~~ 1041 (1192) T TIGR02773 1040 KD 1041 (1192) T ss_pred CC T ss_conf 88 No 4 >COG3857 AddB ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair] Probab=99.60 E-value=6.7e-14 Score=110.80 Aligned_cols=171 Identities=20% Similarity=0.145 Sum_probs=94.3 Q ss_pred CCCCCCHHHHHCCCHHHHHHCCC--CCCCC---HHHHHHHHHHHHHHHHHHCCCCC----CCCC----CCCC--CCCCCC Q ss_conf 61842367787183238862138--99989---88999899999999997245765----3432----2010--456453 Q gi|254780124|r 6 FLSASSSHRWLKCPIAPTLESKI--PQTTS---IYASEGTFAHNLLAHCLEQGVDA----ETVS----HQKL--TFENDT 70 (388) Q Consensus 6 ~LSpSs~~rwl~CP~s~~Le~~~--pd~~S---~aA~~GT~~H~llE~~l~~~l~~----~~~~----~~~~--~~~~~~ 70 (388) -+|.|+..+|-+||.|++++.++ .+... .+-..|.++|.+.|+.....-.. .... .... ..+... T Consensus 751 ~~SVSrlE~f~~Cpf~yf~~ygL~Lker~~~~l~~~dlG~~fH~v~e~i~e~~~~~~~d~~~l~~~~~~~l~~~i~~~~~ 830 (1108) T COG3857 751 YLSVSRLEKFYRCPFSYFLEYGLGLKERKDIHLDARDLGNFFHRVFERISEEENLENQDWNFLNEEDCERLTQKIVEVLL 830 (1108) T ss_pred EEEHHHHHHHHCCCHHHHHHHHHCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 76518778887396799999862645000157786147899999999999864210688421358899999999999862 Q ss_pred HHHH------HHHHHHHHHHHHH-HH----------CCCCCCEEEEEEEEEEEC-----------CCEEEEEEEEEEEEE Q ss_conf 7757------8899999999999-85----------037873688775532000-----------440589999999985 Q gi|254780124|r 71 RIVD------TEMASSVSMVLAY-VR----------TFSGPFLSETEVPLEPFT-----------TEPGATGTADILIFN 122 (388) Q Consensus 71 ~~~~------~e~~~~v~~~~~~-~r----------~~~~~~~ve~E~~~~~~~-----------~~~~~~GtiD~I~~~ 122 (388) +... .-...|...-+.. ++ ...+...+..|..|.... ....+.|+||||+.. T Consensus 831 ~~~~~~il~ss~r~~y~~~kL~~Ivr~t~~iL~e~~~~~~f~pi~~E~~Fglk~~~~~~i~l~~g~~i~l~GrIDRID~~ 910 (1108) T COG3857 831 EKEQEQILLSSARYEYTLEKLEDIVRRTATILAEQAKFSDFEPIGEEASFGLKGLPPLTIGLPSGSEILLRGRIDRIDQL 910 (1108) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEECHHHHCCCCCCCCCCEECCCCCCEEEEEEEEEHHHHH T ss_conf 78899998500777999999999999879999743455453020033314789987610117999869997433123332 Q ss_pred --CCEEEEEEEECCCCCC----CCCCCCHHHHHHHHHHHHHCCCC---CCCCCEEEEEEEEEECC Q ss_conf --9979999811368876----74466879999999999843835---67651389999983048 Q gi|254780124|r 123 --STQWIIVDFKYGAGVP----VKAENNTQLMLYACGALHQYGDI---FGRPEALTLTIIQPRVR 178 (388) Q Consensus 123 --dg~l~IiDyKtGk~~~----v~a~~n~QL~lYALgA~~~~~~~---~~~~~~v~~~I~qpr~~ 178 (388) ||-+.|||||+|...- |..--++||+.|--++.+..... +. -...+.+.-|+.. T Consensus 911 ~~~~~l~IvDYKSsa~~f~l~~vYyGL~lQlmTYLdai~q~~~~~~~~p~--GalYfhm~eP~i~ 973 (1108) T COG3857 911 EKDGYLGIVDYKSSAHQFDLTDVYYGLSLQLMTYLDAIKQNAPEDDVKPG--GALYFHMHEPEIK 973 (1108) T ss_pred CCCCCEEEEEECCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCC--CEEEEEECCHHHH T ss_conf 25881588872365211452432144128799999999874043115644--1478884385653 No 5 >COG2887 RecB family exonuclease [DNA replication, recombination, and repair] Probab=99.58 E-value=1.4e-13 Score=108.67 Aligned_cols=225 Identities=19% Similarity=0.156 Sum_probs=115.2 Q ss_pred CCCCCHHHHHCCCHHHHHHC--CCCCC-----CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--------CCCCCCCH Q ss_conf 18423677871832388621--38999-----89889998999999999972457653432201--------04564537 Q gi|254780124|r 7 LSASSSHRWLKCPIAPTLES--KIPQT-----TSIYASEGTFAHNLLAHCLEQGVDAETVSHQK--------LTFENDTR 71 (388) Q Consensus 7 LSpSs~~rwl~CP~s~~Le~--~~pd~-----~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~--------~~~~~~~~ 71 (388) ||+|.+.+...||.+++... .++.. ....+.+||+.|.+++.+... .......... ...+.... T Consensus 1 ls~s~~~~l~r~p~~~~a~~i~~l~~~~~~~e~~~~~~~g~~~h~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~ 79 (269) T COG2887 1 LSVSRAEALRRCPYLFYARRILALPPLGTRAEEPEAAVRGTLLHAILEALVGE-RYHAAAAALAKLAWLLRKELAEAELP 79 (269) T ss_pred CCHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHCCCC T ss_conf 96535756255851699998635377875100244243354799999988631-24432031677765555544310233 Q ss_pred H-----HHHHHHHHHHHHH--HHHHCCCCCCE-EEEEEE-EEEECCC-EEEEEEEEEEEEE-CCEEEEEEEECCCCCC-- Q ss_conf 7-----5788999999999--99850378736-887755-3200044-0589999999985-9979999811368876-- Q gi|254780124|r 72 I-----VDTEMASSVSMVL--AYVRTFSGPFL-SETEVP-LEPFTTE-PGATGTADILIFN-STQWIIVDFKYGAGVP-- 138 (388) Q Consensus 72 ~-----~~~e~~~~v~~~~--~~~r~~~~~~~-ve~E~~-~~~~~~~-~~~~GtiD~I~~~-dg~l~IiDyKtGk~~~-- 138 (388) . +...........+ .+-++..+... ...+.. ++..+.+ ..+.|+||||+++ +|++.|+|||||+.+. T Consensus 80 ~~~~~~~~~r~~~~~~~~~~~~~e~~r~~~~~~~~~e~~~~~~~i~~~i~l~G~aDRid~~~~g~i~ilDYKTG~~p~~a 159 (269) T COG2887 80 GYTDAEWLDRLRARARAFLVYDWERERGTAFHAWLEEERGAELLIDGGIRLRGRADRIDKDADGELEILDYKTGKSPSAA 159 (269) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCEEEEECCCCEECCEEEECCCCCCCCEEEEEEECCCCCCHH T ss_conf 34662034889986654534568761677333665552230467303402211430002478884689986348886243 Q ss_pred -CCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf -7446687999999999984383567651389999983048877543025898899999999999999998577653047 Q gi|254780124|r 139 -VKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVS 217 (388) Q Consensus 139 -v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~ 217 (388) ..+...+|+.+|+++.....-... ..-.++....+ ..+.+.......+... +.......|........+ T Consensus 160 ~~~~~~~~ql~~~~~~l~~~~~~~~---~p~~l~~v~~~--~~~~~~~~~~~~~~~~-----~~~~~~e~~~~l~~~~~~ 229 (269) T COG2887 160 RAPAAVSPQLALEALALIEGRFRGV---EPGQLRLVYLR--KSGRVGEAPDNREQLP-----QLALAREALAELAELLAG 229 (269) T ss_pred HCHHCCCHHHHHHHHHHHHCCCCCC---CCCCEEEEEEC--CCCCCCCCCHHHHHHH-----HHHHHHHHHHHHHHHCCC T ss_conf 3211105346888998871455666---78872488865--7776677850666540-----057799999999875345 Q ss_pred CCC-CCCCCCCCCCCCCCCCCCHHHH Q ss_conf 766-7888666672576445620134 Q gi|254780124|r 218 LEH-YGVNDDSCRFCRAKVRCPALSR 242 (388) Q Consensus 218 ~~~-~~~~g~~CrfC~~k~~Cra~a~ 242 (388) .+. ......-|+||+....||.+.. T Consensus 230 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 255 (269) T COG2887 230 LEVRPRGYSSRCDLCPHQDLCPAYGG 255 (269) T ss_pred CCCCCCCCCHHCCCCCCCCCCCCCCC T ss_conf 54344562100244444455776444 No 6 >TIGR02786 addB_alphas double-strand break repair protein AddB; InterPro: IPR014153 AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage . More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This family consists of AddB proteins of alphaproteobacterial types.. Probab=99.47 E-value=9e-13 Score=103.39 Aligned_cols=156 Identities=21% Similarity=0.149 Sum_probs=96.8 Q ss_pred CCCCCCHHHHHCCCHHHHHHC-------CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC---------CCCC Q ss_conf 618423677871832388621-------389998988999899999999997245765343220104---------5645 Q gi|254780124|r 6 FLSASSSHRWLKCPIAPTLES-------KIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLT---------FEND 69 (388) Q Consensus 6 ~LSpSs~~rwl~CP~s~~Le~-------~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~---------~~~~ 69 (388) .+|-|-+++|+.=|++++-.. +=.+..-.||.+||++|.++|.+.+...+.-........ .... T Consensus 814 ~~SVTeie~L~rDPYAiYAk~ILkL~pLdPl~~~p~AA~RG~liH~ile~f~~~~~~~~~~~a~~~L~~~~~~~l~~~~~ 893 (1096) T TIGR02786 814 KLSVTEIETLRRDPYAIYAKHILKLRPLDPLDRDPEAADRGTLIHDILERFVEEVADPLPADAADVLRKIGRKELASLNL 893 (1096) T ss_pred CEEEEEECCCCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 13553200356882177875521677677767883246632299999999987511467321799999999998674247 Q ss_pred C----HHHHHHHHHHHHHHHHHHHCCCC---CCEEEEE--EEEEE------ECCCEEEEEEEEEEEE-ECCEEEEEEEEC Q ss_conf 3----77578899999999999850378---7368877--55320------0044058999999998-599799998113 Q gi|254780124|r 70 T----RIVDTEMASSVSMVLAYVRTFSG---PFLSETE--VPLEP------FTTEPGATGTADILIF-NSTQWIIVDFKY 133 (388) Q Consensus 70 ~----~~~~~e~~~~v~~~~~~~r~~~~---~~~ve~E--~~~~~------~~~~~~~~GtiD~I~~-~dg~l~IiDyKt 133 (388) . ..|-..+.....++.++.+++.. ....|.+ +.+.. -+.+++++|++|||++ .||++.|+|||| T Consensus 894 p~~~~a~W~pRf~~~A~~~~~wE~~Rr~~~~~~~~E~~~~~~~~~~~e~~~~~~g~tL~GrADRID~~~~G~~~I~DYKT 973 (1096) T TIGR02786 894 PPEAEALWWPRFARIADWFADWERARRLDVRRIFAEARGRKELVGERELRAAIRGFTLSGRADRIDRTADGSAAILDYKT 973 (1096) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCEECCEEEEEEEEEEEECCCCCEEEEEECC T ss_conf 87588863889999999999999874434321246300402576413440001452787787677636988479886246 Q ss_pred CCCCC---CCCCCCHHHHHHHHHHHH-HCCCC Q ss_conf 68876---744668799999999998-43835 Q gi|254780124|r 134 GAGVP---VKAENNTQLMLYACGALH-QYGDI 161 (388) Q Consensus 134 Gk~~~---v~a~~n~QL~lYALgA~~-~~~~~ 161 (388) |..+. |...-.+||.|=|..+.+ .|..+ T Consensus 974 G~pPS~kQv~~gl~pQLaLEaAll~~GaF~D~ 1005 (1096) T TIGR02786 974 GAPPSGKQVRAGLSPQLALEAALLMRGAFKDI 1005 (1096) T ss_pred CCCCHHHHHHCCCCHHHHHHHHHHHHCCCCCC T ss_conf 88952898850362779999999981888577 No 7 >TIGR02784 addA_alphas double-strand break repair helicase AddA; InterPro: IPR014151 AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the alphaproteobacteria and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.. Probab=99.39 E-value=1.1e-11 Score=96.31 Aligned_cols=166 Identities=21% Similarity=0.232 Sum_probs=92.2 Q ss_pred CCCCCCHHHHHCCC--HHHH----HHCCCCCC--C-CHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCCC-CCC-HHH Q ss_conf 61842367787183--2388----62138999--8-98899989999999999724576534-322010456-453-775 Q gi|254780124|r 6 FLSASSSHRWLKCP--IAPT----LESKIPQT--T-SIYASEGTFAHNLLAHCLEQGVDAET-VSHQKLTFE-NDT-RIV 73 (388) Q Consensus 6 ~LSpSs~~rwl~CP--~s~~----Le~~~pd~--~-S~aA~~GT~~H~llE~~l~~~l~~~~-~~~~~~~~~-~~~-~~~ 73 (388) .||||++..-..-+ +..- |+.-+-++ . .-+..+||++|.++|++=.-.-..+. ......... ..+ +-- T Consensus 993 pl~PS~~~~~i~~~~~~~~~~~~llSPvl~e~~~~~~~A~~RG~~lH~LLQ~LP~~~~~~R~~aA~ryL~~~~~~w~~a~ 1072 (1190) T TIGR02784 993 PLAPSGLSAAIDSAEPGEAVRSTLLSPVLGEKTAARAFALLRGTLLHRLLQHLPDLPPEEREDAARRYLARSAADWPEAE 1072 (1190) T ss_pred CCCCCCCCCCCCCCCCCCCCHHHEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCHHH T ss_conf 42676665334467874101001010113787657689999999999999626798867779999998741024578688 Q ss_pred HHHHHHHHHHHHHHHHC---CCCCCEEEEEE--EEEEECCC-EEEEEEEEEEEEECC--EEEEEEEECCCCCCCCCCC-- Q ss_conf 78899999999999850---37873688775--53200044-058999999998599--7999981136887674466-- Q gi|254780124|r 74 DTEMASSVSMVLAYVRT---FSGPFLSETEV--PLEPFTTE-PGATGTADILIFNST--QWIIVDFKYGAGVPVKAEN-- 143 (388) Q Consensus 74 ~~e~~~~v~~~~~~~r~---~~~~~~ve~E~--~~~~~~~~-~~~~GtiD~I~~~dg--~l~IiDyKtGk~~~v~a~~-- 143 (388) .+.+...|...++..+- +.....-|+.+ .+...... ..+.|+|||+.|+++ ++.|+|||||+.+|..++. T Consensus 1073 R~~l~~~v~~vL~~p~~~~~F~~~SRAEV~i~G~l~~~g~~P~avSG~IDRL~v~~~kk~V~iVDyKTNr~~P~~~~e~p 1152 (1190) T TIGR02784 1073 REKLLAAVLAVLDDPRLAPVFAEGSRAEVAIMGTLKEGGKQPLAVSGQIDRLAVDEDKKRVLIVDYKTNRPVPKTAEEVP 1152 (1190) T ss_pred HHHHHHHHHHHHCCCHHHHCCCCCCCEEEEEEEEECCCCCCCEEECCEEEEEEECCCCCEEEEEEECCCCCCCCCHHHHH T ss_conf 99999999998416013200477773213454652358898516601688877737887899986216889888976521 Q ss_pred ---CHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEE Q ss_conf ---879999999999843835676513899999830 Q gi|254780124|r 144 ---NTQLMLYACGALHQYGDIFGRPEALTLTIIQPR 176 (388) Q Consensus 144 ---n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr 176 (388) -.||.+|.-.....|+. +.|+-.+.... T Consensus 1153 ~~Y~~QlA~Yr~~L~~lYPg-----~~v~a~Ll~Te 1183 (1190) T TIGR02784 1153 PAYLRQLALYRALLRPLYPG-----RAVEAALLWTE 1183 (1190) T ss_pred HHHHHHHHHHHHHHHHHCCC-----CEEEEEEEECC T ss_conf 89999999999998865889-----75999888627 No 8 >TIGR00372 cas4 CRISPR-associated protein Cas4; InterPro: IPR013343 This entry consists of conserved proteins found in many prokaryotic genomes whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats). The function of these proteins has not been experimentally determined, but computational analysis suggests that they be nucleases like RecB (IPR004586 from INTERPRO), functioning as part of a hypothetical DNA repair system , . . Probab=99.29 E-value=1.6e-10 Score=88.54 Aligned_cols=186 Identities=19% Similarity=0.227 Sum_probs=116.4 Q ss_pred CCCCCHHHHHCCCHHHHHHC--CCCCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 18423677871832388621--3899989---889998999999999972457653432201045645377578899999 Q gi|254780124|r 7 LSASSSHRWLKCPIAPTLES--KIPQTTS---IYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSV 81 (388) Q Consensus 7 LSpSs~~rwl~CP~s~~Le~--~~pd~~S---~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v 81 (388) +++|-+..|+-||..+++.. +.+..+. +...+|+.+|+-++...+..+ T Consensus 1 ~~~s~v~~Y~yCPr~~~~~~~~~~~~~~~~~~~~m~~G~~~~~~~~~~~r~~~--------------------------- 53 (206) T TIGR00372 1 ITVSDVKEYLYCPRKLWLMKKGGSEEESEERKVSMEEGRLIHEEAERAVRKFL--------------------------- 53 (206) T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--------------------------- T ss_conf 95667888875126999997525546754465012321466678765678887--------------------------- Q ss_pred HHHHHHHHCCC-CCCEEEEEEEEEEECCCEEEEEEEEEEEEECC------EEEEEEEECCCCC---CCC--CCCCHHHHH Q ss_conf 99999985037-87368877553200044058999999998599------7999981136887---674--466879999 Q gi|254780124|r 82 SMVLAYVRTFS-GPFLSETEVPLEPFTTEPGATGTADILIFNST------QWIIVDFKYGAGV---PVK--AENNTQLML 149 (388) Q Consensus 82 ~~~~~~~r~~~-~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg------~l~IiDyKtGk~~---~v~--a~~n~QL~l 149 (388) +... .....+.++.+.....+-.+.|.+|.+...++ ...++++|+|+.. ..+ ..+..||.. T Consensus 54 -------~~~~~~~~~~~~~v~l~~~~~g~~l~G~~D~~~~~~~~~~~g~~~~pvE~K~~~~~~~~~~~~~~~~~~Ql~a 126 (206) T TIGR00372 54 -------KSLGFEEVKEEKEVELKSKKYGKGLKGVIDVVLEEDGEIGKGAEPVPVEVKSGKAKKRLLRERGLAHKLQLLA 126 (206) T ss_pred -------HHCCCCEEEEECCEEECCCCCCCEEECCEEEEEEECCCCCCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHH T ss_conf -------6403300222101453278546415401478986156444652012676762446677643565235789999 Q ss_pred HHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC Q ss_conf 999999843835676513899999830488775430258988999999999999999985776530477667--888666 Q gi|254780124|r 150 YACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHY--GVNDDS 227 (388) Q Consensus 150 YALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~--~~~g~~ 227 (388) ||+.+...++.-... .++..|+.+..+... -.-.++.++ ...+..+...++.+++. +..+ ...+.. T Consensus 127 Ya~~~~~~~~~~~~~--i~~~~~~y~~~~~~~--y~v~~~~~~-~k~~~~~~~~i~~~~~~-------~~~P~~~~~~~k 194 (206) T TIGR00372 127 YALLLEERYGVEVSD--IVKGYLLYLEEGKKV--YEVEISEEL-RKKAVKLIEKIEKLLEG-------EKLPPPPKKSRK 194 (206) T ss_pred HHHHHHHHCCCCHHH--HHEEEEEEECCCEEE--EEEEECHHH-HHHHHHHHHHHHHHHHC-------CCCCCCCCCCCC T ss_conf 999985521843006--002202563077389--998628248-99999999999999848-------815576888775 Q ss_pred CCCCCCCCCCC Q ss_conf 67257644562 Q gi|254780124|r 228 CRFCRAKVRCP 238 (388) Q Consensus 228 CrfC~~k~~Cr 238 (388) |.+|+|+.+|. T Consensus 195 C~~C~y~~~C~ 205 (206) T TIGR00372 195 CKFCPYREICL 205 (206) T ss_pred CCCCCCCCCCC T ss_conf 77755521258 No 9 >TIGR02774 rexB_recomb ATP-dependent nuclease subunit B; InterPro: IPR014141 DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RecAB) in other. The AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. The partner may be designated AddB, as in Bacillus and in alphaproteobacteria, or RexB as in Streptococcus and Lactococcus. Note, however, that RexB proteins lack an N-terminal GxxGxGK[ST] ATP-binding motif found in Bacillus subtilis and related species, and this difference may be important. This entry represents RexB proteins as found in Streptococcus and Lactococcus.. Probab=99.03 E-value=7.1e-08 Score=71.21 Aligned_cols=292 Identities=15% Similarity=0.104 Sum_probs=164.8 Q ss_pred CCCCCCCHHHHHCCCHHHHHHC--CCCCCCCHH--H-HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC----C---CHH Q ss_conf 5618423677871832388621--389998988--9-99899999999997245765343220104564----5---377 Q gi|254780124|r 5 AFLSASSSHRWLKCPIAPTLES--KIPQTTSIY--A-SEGTFAHNLLAHCLEQGVDAETVSHQKLTFEN----D---TRI 72 (388) Q Consensus 5 A~LSpSs~~rwl~CP~s~~Le~--~~pd~~S~a--A-~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~----~---~~~ 72 (388) =+||+||.-.+=+=-.+|+|.. +..+..|.. + .-|+..|.+-|++|+..-..+.....+...-. + ... T Consensus 760 L~LSaSaLT~FYnNqY~YFL~YVL~L~e~~siHPD~R~HG~YLHrvFEr~m~~~e~~e~Fd~~L~qaI~~t~QE~~F~~~ 839 (1116) T TIGR02774 760 LKLSASALTTFYNNQYKYFLKYVLGLEEEESIHPDARHHGNYLHRVFERLMKDQEGEESFDEKLNQAINETSQEEVFKAL 839 (1116) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHH T ss_conf 42201132135535578999874064422357888441343367999998416788961788999985202658899986 Q ss_pred HHHHH-HHHHHH-HHHHHHCCC-----------------------------CCCE--EEE----EEEEEEECCCEEEEEE Q ss_conf 57889-999999-999985037-----------------------------8736--887----7553200044058999 Q gi|254780124|r 73 VDTEM-ASSVSM-VLAYVRTFS-----------------------------GPFL--SET----EVPLEPFTTEPGATGT 115 (388) Q Consensus 73 ~~~e~-~~~v~~-~~~~~r~~~-----------------------------~~~~--ve~----E~~~~~~~~~~~~~Gt 115 (388) +.+.. ..+... ..|.+|+-. +... .+. ++.++-....+.++|. T Consensus 840 Y~~~~Ea~yt~~iL~Diar~TA~ILr~n~~i~v~~~e~~qhylGdkdWqktPqalka~~~~~~~~L~~~nh~R~~~v~G~ 919 (1116) T TIGR02774 840 YQEDAEARYTLEILLDIARSTAPILRDNSAIQVIKEEEAQHYLGDKDWQKTPQALKALEGKDNFQLQIDNHGREIKVRGI 919 (1116) T ss_pred HCCCHHHHHHHHHHHHHHHHCCHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEE T ss_conf 04364478869999998861222202585220477876421025401100057888606762056520565447898116 Q ss_pred EEEEEE-EC-CEEEEEEEECCCCC---CCC-CCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCC Q ss_conf 999998-59-97999981136887---674-4668799999999998438356765138999998304887754302589 Q gi|254780124|r 116 ADILIF-NS-TQWIIVDFKYGAGV---PVK-AENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVIS 189 (388) Q Consensus 116 iD~I~~-~d-g~l~IiDyKtGk~~---~v~-a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s 189 (388) |||||+ .+ |.|-|||||.|... +.. --=||||+-|-.|.-+..+.-+...=-.-|+.+ ..++.++ T Consensus 920 iDRiDrLs~~~sLGvVDYKSS~~~F~~~~FYNGL~pQL~TYl~ALk~~~p~e~~~~~FGAmYLh---------mqeP~~~ 990 (1116) T TIGR02774 920 IDRIDRLSDGDSLGVVDYKSSAKKFDIAKFYNGLSPQLLTYLAALKRDKPSEIEAPIFGAMYLH---------MQEPKQD 990 (1116) T ss_pred EECEEECCCCCCEEEEECCCCCCCCCCHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHH---------HCCCCCH T ss_conf 6000220578821456604676523641104787624799999984304444678755202123---------1485400 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC--CCCCCHHHHHHHHHHH Q ss_conf 88999999999999999985776530477667888666672576445620134678763022--0059999999999543 Q gi|254780124|r 190 ADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKD--PSTNTTVELSKAYSSI 267 (388) Q Consensus 190 ~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l~~~~~~--p~~l~~~e~~~~l~~~ 267 (388) ...+......+ .. ..-+--+||++=-+.-..-|...... ....|++|+.=+| T Consensus 991 L~~~K~Ldn~~----v~-------------------~~~kal~Y~GLF~e~e~~~La~~~y~~K~~~ys~~El~~Ll--- 1044 (1116) T TIGR02774 991 LVKLKNLDNDL----VE-------------------ELSKALKYKGLFSEKEKEHLAEGYYKSKANLYSDEELELLL--- 1044 (1116) T ss_pred HHHHHHHHHHH----HH-------------------HHHHHHCCCCCHHHHHHHHHHHHHHHCHHHCCCHHHHHHHH--- T ss_conf 88861023789----99-------------------99987304663147777775510011113206578999999--- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHCCCCHHHHHH Q ss_conf 8999999999999999997898478523205888786116989999999861651000001389889999 Q gi|254780124|r 268 SLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQ 337 (388) Q Consensus 268 ~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~~~~~~~~~~l~~~~~~ek 337 (388) .+-+.+..-|.+.+++|+=.-.==--.|| |.--|.|+-+++.-..+ .++=.+-|.|+++...|| T Consensus 1045 ----~Yn~~LYkKAA~~I~~G~F~INPYT~dGr-sv~PygdQ~kaITGFEA-d~hm~~AR~L~kLpak~k 1108 (1116) T TIGR02774 1045 ----DYNKYLYKKAAETILSGRFLINPYTEDGR-SVQPYGDQLKAITGFEA-DRHMGQARRLVKLPAKEK 1108 (1116) T ss_pred ----HHHHHHHHHHHHHHHCCCCCCCCCCCCCC-EECCHHHHHHHHHHHHH-HHHHHHHHHHCCCCHHHH T ss_conf ----99899999999886538740157478883-55742424343213245-457888403036870210 No 10 >PRK13909 putative recombination protein RecB; Provisional Probab=99.01 E-value=8.5e-09 Score=77.27 Aligned_cols=134 Identities=12% Similarity=0.067 Sum_probs=71.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC--C-CCCCHHHHHHHHHHHHHHHHH--HHCCCCCCEEEEEEEEEEECC Q ss_conf 88999899999999997245765343220104--5-645377578899999999999--850378736887755320004 Q gi|254780124|r 34 IYASEGTFAHNLLAHCLEQGVDAETVSHQKLT--F-ENDTRIVDTEMASSVSMVLAY--VRTFSGPFLSETEVPLEPFTT 108 (388) Q Consensus 34 ~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~--~-~~~~~~~~~e~~~~v~~~~~~--~r~~~~~~~ve~E~~~~~~~~ 108 (388) .+...||++|.++|.................. + ..-...-..++...+..++.. .+...+...+..|+.|.. . T Consensus 766 ~~~~~G~~iH~~lE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~--~ 843 (911) T PRK13909 766 EAIYFGEALHYCLEMLYAFKEENLKVLKNLLKNKYGHFLSESDFEDLEKRLELLINNKEFQELIKDGKLLKEQALLF--N 843 (911) T ss_pred HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHHCCCCEEEEEEEEE--C T ss_conf 88989999999996586579867899999998743057998999999999999975966898717885568777865--8 Q ss_pred CEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECC Q ss_conf 4058999999998599799998113688767446687999999999984383567651389999983048 Q gi|254780124|r 109 EPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVR 178 (388) Q Consensus 109 ~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~ 178 (388) +..|+|||+...++.+.|||||||+.. ...+.+||..|+-+....++. +.|+.+++....+ T Consensus 844 --g~~~~ID~l~~~~~~~~IiDYKT~~~~--~~~y~~QL~~Y~~al~~i~~~-----k~v~~~l~yl~~~ 904 (911) T PRK13909 844 --GELKQIDLLLEKDEEYFVIDYKSSKKY--QDKHKAQVREYKEAISEIIPK-----KKVRAFIIYLLED 904 (911) T ss_pred --CEECCCEEEEEECCEEEEEECCCCCCC--CHHHHHHHHHHHHHHHHHCCC-----CEEEEEEEEECCC T ss_conf --806680489998999999973889998--568999999999999987799-----9468999995698 No 11 >KOG1805 consensus Probab=98.96 E-value=9.1e-08 Score=70.50 Aligned_cols=228 Identities=14% Similarity=0.164 Sum_probs=130.8 Q ss_pred CCCCCCCHHHHHCCCHHHHHHCCCC--CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC------------CCCCCCC Q ss_conf 5618423677871832388621389--9989889998999999999972457653432201------------0456453 Q gi|254780124|r 5 AFLSASSSHRWLKCPIAPTLESKIP--QTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQK------------LTFENDT 70 (388) Q Consensus 5 A~LSpSs~~rwl~CP~s~~Le~~~p--d~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~------------~~~~~~~ 70 (388) .+.|..+...=+-|+.+..|...|. ++++.++..||++|++.+..+.+...+....... ....... T Consensus 183 ~Lis~TtVasS~~C~Rr~VL~erfr~~n~~t~~mllGtIvHevfQ~al~qk~~~~~~~~~~~~~q~~~~~s~l~~~~~~~ 262 (1100) T KOG1805 183 DLISGTTVASSLFCLRRTVLNERFRSGNSHTKAMLLGTIVHEVFQKALIQKSFAVDELILQASLQISKYISELYALGVSE 262 (1100) T ss_pred CCCCCCCHHHCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCH T ss_conf 52021000101455228888777415897225678889999999999870465055677778777788999999734677 Q ss_pred HHHHHHHHHHHHHHHHHHHCC----------------CCCC-EEEEEEEEEEECCCE--EEEEEEEEEEE---ECC--EE Q ss_conf 775788999999999998503----------------7873-688775532000440--58999999998---599--79 Q gi|254780124|r 71 RIVDTEMASSVSMVLAYVRTF----------------SGPF-LSETEVPLEPFTTEP--GATGTADILIF---NST--QW 126 (388) Q Consensus 71 ~~~~~e~~~~v~~~~~~~r~~----------------~~~~-~ve~E~~~~~~~~~~--~~~GtiD~I~~---~dg--~l 126 (388) ...+.+|.++...++.++-.+ .... .+---.+++-.+|.| ++.|.||.... ..+ ++ T Consensus 263 ~~i~~el~~~l~~i~~~i~~f~~~~~s~~~~s~~~~~~~~~i~i~ev~DIEEniWsp~fGLKG~iDatv~v~v~~~~eti 342 (1100) T KOG1805 263 DVIRNELEKYLPNICLWIEHFVHKPLSGSFPSKRGPLPSKSIQISEVIDIEENIWSPKFGLKGKIDATVRVKVEEGKETI 342 (1100) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCEEEEEEEEHHHHHCCCCCCCCCEEEEEEEEEECCCCCCC T ss_conf 89999999999999999987511455577602027878876055321225655356213776400358999970475433 Q ss_pred EEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 99981136887674466879999999999843835676513899999830488775430258988999999999999999 Q gi|254780124|r 127 IIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTL 206 (388) Q Consensus 127 ~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~ 206 (388) .=..+|||+..- +-++.-|..||+|.....++.... ...+++.+-+....+..-.....+|+...+++..+... T Consensus 343 ~PLElKTGk~~~-sieh~~QvlLYtLl~seRy~~~~~-----~glL~YLk~~~~~~v~~~~~dlr~LL~~RN~lA~~~~h 416 (1100) T KOG1805 343 MPLELKTGKSSS-SIEHVGQVLLYTLLLSERYEIPIL-----PGLLYYLKDGQLVEVPSKHSDLRGLLMLRNRLANDLVH 416 (1100) T ss_pred CCEEEECCCCCC-CHHHHHHHHHHHHHHHHHCCCCCC-----CCEEEEECCCCEEECCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 532430577666-367789999999998764067766-----65589961797754362147799999988887766655 Q ss_pred HHHHHHHHHCCCCCCC---CCCCCCCCCCCCCCCCHH Q ss_conf 9857765304776678---886666725764456201 Q gi|254780124|r 207 ALSLKSKRAVSLEHYG---VNDDSCRFCRAKVRCPAL 240 (388) Q Consensus 207 ~~~~~a~~~~~~~~~~---~~g~~CrfC~~k~~Cra~ 240 (388) .....+. ..+.+.+ ....-|..|.++..|-.. T Consensus 417 ~~~~~~s--~~~~~lpe~~~~d~~C~~cs~~~~c~~~ 451 (1100) T KOG1805 417 QEDVSAS--AQGGNLPEPILEDSSCDHCSHKTACSFF 451 (1100) T ss_pred HCCCCCC--CCCCCCCCCCCCCCCCCHHHHHHHHHHH T ss_conf 3022322--3458998741246424267777788999 No 12 >pfam01930 Cas_Cas4 Domain of unknown function DUF83. This domain has no known function. The domain contains three conserved cysteines at its C terminus. Probab=98.93 E-value=3.8e-08 Score=72.98 Aligned_cols=158 Identities=17% Similarity=0.151 Sum_probs=98.4 Q ss_pred CCCHHHHHCCCHHHHHHC--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 423677871832388621--389998988999899999999997245765343220104564537757889999999999 Q gi|254780124|r 9 ASSSHRWLKCPIAPTLES--KIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLA 86 (388) Q Consensus 9 pSs~~rwl~CP~s~~Le~--~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~ 86 (388) .|-.+-|..||..++|.. ..++..+..+..|.++|+-. .. T Consensus 2 g~~i~~y~~CpR~~wl~~~~~~~e~~~~~v~~Gr~lhE~~---y~----------------------------------- 43 (162) T pfam01930 2 GTLINYYFICKRKLWLFSHGITMEENSETVEIGKLLHEES---YE----------------------------------- 43 (162) T ss_pred CCEEEEEEECHHHHHHHHCCCCCCCCHHHHHHHHHHHHHC---CC----------------------------------- T ss_conf 7588688566679999973776013767887545751301---02----------------------------------- Q ss_pred HHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 98503787368877553200044058999999998599799998113688767446687999999999984383567651 Q gi|254780124|r 87 YVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPE 166 (388) Q Consensus 87 ~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~ 166 (388) +.. .++.+ ...|.+|.|...+|.+.++.||.|+.. ..+ +..||..|++.+. ..+. . T Consensus 44 --r~~-------k~v~l-------~~~g~iD~v~~~~~~~~~vE~K~s~~~-~~a-~~~QL~~ya~~Le-~~g~-----~ 99 (162) T pfam01930 44 --REK-------KEVEI-------DGSIKIDFVTRRKGGLVVHEVKKSSKM-EEA-HRMQLLYYLYLLK-KRGI-----E 99 (162) T ss_pred --CCC-------CEEEE-------CCCEEEEEEEEECCEEEEEEEECCCCC-CHH-HHHHHHHHHHHHH-HCCC-----C T ss_conf --365-------16980-------574899999986995999998558999-808-9999999999999-8298-----6 Q ss_pred EEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 389999983048877543025898899999999999999998577653047766788866667257644562 Q gi|254780124|r 167 ALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP 238 (388) Q Consensus 167 ~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr 238 (388) .....|+.+.......| +++. ++.....++...+..++.. ... +.+...+.|+.|.++..|- T Consensus 100 v~~G~l~y~~~rrr~~V---~lt~-e~r~~~~~~i~~i~~i~~~----~~p--P~~~~~~~C~~Csy~~~C~ 161 (162) T pfam01930 100 AKEGVLHYPKERKREEV---ELTE-EDREELEEAIKEIEEIISS----EKP--PPPEKKKYCKKCAYREFCW 161 (162) T ss_pred CCCEEEEECCCCEEEEE---ECCH-HHHHHHHHHHHHHHHHHHC----CCC--CCCCCCCCCCCCCCHHHCC T ss_conf 66179998568879999---8699-9999999999999999847----999--7999899798999741038 No 13 >pfam09810 Morph_protein1 Defects in morphology protein 1, mitochondrial precursor. Members of this family of proteins are thought to be involved in cellular morphology, though little else is known about them. Probab=98.65 E-value=9.6e-06 Score=57.21 Aligned_cols=138 Identities=19% Similarity=0.135 Sum_probs=73.8 Q ss_pred CCCCCHHHHHCCCHHHH--HHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 18423677871832388--6213899989889998999999999972457653432201045645377578899999999 Q gi|254780124|r 7 LSASSSHRWLKCPIAPT--LESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMV 84 (388) Q Consensus 7 LSpSs~~rwl~CP~s~~--Le~~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~ 84 (388) ||-+-+-.=.=|=.++. |....+-..++|+..||.+|..+|.-+.....-+. ....+.+.-.+-+.++. T Consensus 14 LSVTdL~s~~WCElQ~~Y~L~~~g~~~~T~aMk~G~~~H~~LE~Evh~~V~vev--------~t~ED~~al~~~N~I~~- 84 (329) T pfam09810 14 LSVTDLSSPAWCELQYEYTLTKFGRKERTPAMKRGIKIHEKLELEVHTTVPVEV--------TTKEDAWALRLLNIILG- 84 (329) T ss_pred EEECCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEC--------CCCHHHHHHHHHHHHHH- T ss_conf 403102771024423330012478765568889879999998874367658754--------88207899999999999- Q ss_pred HHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEE-C-----------------CEEEEEEEECCCCCCCCCC---- Q ss_conf 99985037873688775532000440589999999985-9-----------------9799998113688767446---- Q gi|254780124|r 85 LAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFN-S-----------------TQWIIVDFKYGAGVPVKAE---- 142 (388) Q Consensus 85 ~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~-d-----------------g~l~IiDyKtGk~~~v~a~---- 142 (388) +...+..+ . --|+.+-..+.+.-+.|.||-+-.. + ..+.|.|.||-....+..+ T Consensus 85 L~tL~~~G--~--tREl~V~G~v~g~lv~GIIDeL~~~~~~~~~~~~~~~~~~~~~~~~l~i~DvKTR~~~~~Ps~~q~~ 160 (329) T pfam09810 85 LRTLREEG--I--TRELPVWGVVKGELLNGIIDELSYENPDPSLEETAASNYSSNAISELIISDTKTRRSKSLPSEAQKR 160 (329) T ss_pred HHHHHHCC--C--EEEEEEEEEECCEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHH T ss_conf 99998548--4--4799999998899999996798974898430000013333467780699853057898898867762 Q ss_pred -CCHHHHHHHHHHHHH Q ss_conf -687999999999984 Q gi|254780124|r 143 -NNTQLMLYACGALHQ 157 (388) Q Consensus 143 -~n~QL~lYALgA~~~ 157 (388) ...|+++|-.....+ T Consensus 161 ~s~lQlmlY~~~l~~l 176 (329) T pfam09810 161 PTLLQLMLYKYLLDDM 176 (329) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 4577999999999998 No 14 >TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats. Probab=98.63 E-value=4.6e-06 Score=59.32 Aligned_cols=193 Identities=15% Similarity=0.112 Sum_probs=98.2 Q ss_pred CCCCCHHHHHCCCHHHHHHCC----CCCCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 184236778718323886213----8999898899-98999999999972457653432201045645377578899999 Q gi|254780124|r 7 LSASSSHRWLKCPIAPTLESK----IPQTTSIYAS-EGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSV 81 (388) Q Consensus 7 LSpSs~~rwl~CP~s~~Le~~----~pd~~S~aA~-~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v 81 (388) ||+|-+..|+.|+.++.|... .++.+...+. .-...++..+..+... .. .+ T Consensus 1 is~~~L~~~~rC~rra~LD~~gd~~~~~~~~~~~~~l~~~~~~~~~~~l~~~--------------------~~----~~ 56 (457) T TIGR03491 1 ITDSDLLSFLRCRRRAWLDLYGDKQQKEAPPDFLLQLRQDKQAFVQLILEDP--------------------AA----RA 56 (457) T ss_pred CCHHHHHHHHCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCH--------------------HH----HH T ss_conf 9878989885687088870258965589996778999999999999840473--------------------56----69 Q ss_pred HHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECC-------EEEEEEEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 9999998503787368877553200044058999999998599-------799998113688767446687999999999 Q gi|254780124|r 82 SMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNST-------QWIIVDFKYGAGVPVKAENNTQLMLYACGA 154 (388) Q Consensus 82 ~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg-------~l~IiDyKtGk~~~v~a~~n~QL~lYALgA 154 (388) +.-++ +....-+.+...-+..+.. .+....|..|+++..+| ...++|.|-|+.+ ..+.-.||.+|+..+ T Consensus 57 ~aT~~-am~~G~~~I~~~~L~~~~~-~~~~~~g~pdlLvk~~g~S~~G~~~Yepvd~Kl~r~~--k~~~~lqla~ys~lL 132 (457) T TIGR03491 57 EAGLD-ACAAGADGIYGGRLKHDLP-QNLPHVSHPDLLVKDPGRSAWGDWAYEPVLIKLGKRP--KDEYRLVLAFHALLL 132 (457) T ss_pred HHHHH-HHHCCCCEEEEEEEECCCC-CCCCEEEECCEEEECCCCCCCCCCEEEEEEEEECCCC--CHHHHHHHHHHHHHH T ss_conf 99999-9973886599999804667-7884047779899628988878832578776506779--899999999999999 Q ss_pred HHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC Q ss_conf 98438356765138999998304887754302589889999999999999999857765304776678886666725764 Q gi|254780124|r 155 LHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAK 234 (388) Q Consensus 155 ~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k 234 (388) ....+..+. .+.++. ++.. ...+...++.....+ .....+..... ...++ .+++.++|.+|+++ T Consensus 133 ~~~Qg~~p~-----~~~lil---g~~~---~~~~~~~~~~~~~~~---~l~~~~~~l~~-~~~P~-~~~~r~~C~~C~w~ 196 (457) T TIGR03491 133 ESFQGVAPK-----KGLIIL---RDGN---SLKVELIKLLPQLRQ---DLADFLLTLNA-DLEPE-VFISRKKCTLCSWR 196 (457) T ss_pred HHHHCCCCC-----EEEEEE---CCCC---EEEEEHHHHHHHHHH---HHHHHHHHHCC-CCCCC-CCCCCCCCCCCCHH T ss_conf 986378887-----599997---8996---799788998999999---99999998526-78998-89985548869638 Q ss_pred CCCCHHHHH Q ss_conf 456201346 Q gi|254780124|r 235 VRCPALSRH 243 (388) Q Consensus 235 ~~Cra~a~~ 243 (388) ..|-+.++. T Consensus 197 ~~C~~~~~~ 205 (457) T TIGR03491 197 KDCEAVAKE 205 (457) T ss_pred HHHHHHHHH T ss_conf 898899884 No 15 >PHA00619 CRISPR-associated Cas4-like protein Probab=98.42 E-value=1.9e-05 Score=55.25 Aligned_cols=162 Identities=17% Similarity=0.075 Sum_probs=83.0 Q ss_pred HHHCCCHHHHHHC-CCCCCCC-HHH---HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 7871832388621-3899989-889---9989999999999724576534322010456453775788999999999998 Q gi|254780124|r 14 RWLKCPIAPTLES-KIPQTTS-IYA---SEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYV 88 (388) Q Consensus 14 rwl~CP~s~~Le~-~~pd~~S-~aA---~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~~~ 88 (388) .-+.||.+.+|+. ..+.+.+ .++ ..|+..|..++..|+.. +-+. T Consensus 36 els~ClRrs~l~~k~g~~k~~~~~~~rm~iG~~lH~~L~~iL~~~-gfE~------------------------------ 84 (210) T PHA00619 36 ELSRCLRRSWLMRKKGGVKLALEEAMKMHIGSGLHMRLQDILKKH-GFET------------------------------ 84 (210) T ss_pred HHHHCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC-CCEE------------------------------ T ss_conf 644466799999865884741667766556388999999999857-9625------------------------------ Q ss_pred HCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCC---CCC-CCCCHHHHHHHHHHHHHCCCCCCC Q ss_conf 5037873688775532000440589999999985997999981136887---674-466879999999999843835676 Q gi|254780124|r 89 RTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGV---PVK-AENNTQLMLYACGALHQYGDIFGR 164 (388) Q Consensus 89 r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~---~v~-a~~n~QL~lYALgA~~~~~~~~~~ 164 (388) .+.+|.... .+..+.|++|.+.. +.-.|+.+||.... .+. ..+-.||-.|--.|-...+.+| T Consensus 85 -------E~~Ver~~~---lGf~I~GRiDay~~--e~~~v~eiK~t~~~~l~~~~~~~hl~QLN~Yl~m~~a~~GyLy-- 150 (210) T PHA00619 85 -------ECRVERKTA---LGFEIVGRIDVYDK--EENTIYELKYTHMQDLDKGRLNNYLRQLNYYIEMANAMAGYLI-- 150 (210) T ss_pred -------EEEEEEEEC---CCEEEEEEEEEECC--CCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEE-- T ss_conf -------788998603---56599978874237--7775999985366667778707499999999999874257699-- Q ss_pred CCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 5138999998304887754302589889999999-9999999998577653047766788866667257644562 Q gi|254780124|r 165 PEALTLTIIQPRVRTGSPINEWVISADDLLEKAK-EFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP 238 (388) Q Consensus 165 ~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~-~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr 238 (388) ++. +.+....|. ..|.+ ++..++...-.+..+..+++ ....|+..|.||||..+|= T Consensus 151 -------~V~-~dgr~eeik---------~~~~~t~l~~r~~af~i~~~E~~lpp-~K~~p~~~C~~CP~~~~Cw 207 (210) T PHA00619 151 -------IVH-ADGRVEEIK---------RDWKETDLENRANAFGISVEENILPP-KKSKPDRECIECPFYNVCW 207 (210) T ss_pred -------EEE-CCCCHHHHH---------HHHHHHHHHHHHHHHCCCCHHCCCCC-CCCCCCCCEEECCCEEEEE T ss_conf -------998-489847776---------66443026665444002320202799-9899996102477101664 No 16 >COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair] Probab=98.37 E-value=1.5e-06 Score=62.58 Aligned_cols=47 Identities=26% Similarity=0.277 Sum_probs=22.0 Q ss_pred EEEEEEEEEEECCEEEEEEEECCCCCCCCCC-----------CCHHHHHHHHHHHHHC Q ss_conf 8999999998599799998113688767446-----------6879999999999843 Q gi|254780124|r 112 ATGTADILIFNSTQWIIVDFKYGAGVPVKAE-----------NNTQLMLYACGALHQY 158 (388) Q Consensus 112 ~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~-----------~n~QL~lYALgA~~~~ 158 (388) +.|.||++.+.+|.+.|+||||.+-....+. ...|+.+|+.++...+ T Consensus 1061 ~~G~IDl~f~~~~~~yivDYKTn~l~~~~~~y~~~~~~~~~~Y~~Q~~lY~~al~~~l 1118 (1139) T COG1074 1061 LQGIIDLLFRHEGRYYILDYKTNRLGDDSAAYSPAEAMLKQRYDLQLQLYAEALHRIL 1118 (1139) T ss_pred EEEEEEEEEEECCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 6778789999899999997048888985133114566666559999999999999983 No 17 >PHA01622 CRISPR-associated Cas4-like protein Probab=98.34 E-value=1.1e-05 Score=56.86 Aligned_cols=131 Identities=18% Similarity=0.137 Sum_probs=81.2 Q ss_pred EEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCC--CCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEE Q ss_conf 688775532000440589999999985997999981136887--674466879999999999843835676513899999 Q gi|254780124|r 96 LSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGV--PVKAENNTQLMLYACGALHQYGDIFGRPEALTLTII 173 (388) Q Consensus 96 ~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~--~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~ 173 (388) -.+.|++++....+..+.|++|.|-.++ ++.+||.+-. .+...+-.|+.+|-++. +....++..+.+ +| T Consensus 68 nCetEv~Is~ei~GI~IsGRiD~iC~Nd----lIEiKTt~~~~~~p~~~Hl~Qv~vY~~l~----~~q~~~~~~iYi-VY 138 (204) T PHA01622 68 NCQTEVEIKDEIEGIKISGRIDIVCNND----LLEIKTISYNYFQVKEYHLYQVALYYHIL----KKQNYQINNVYI-VY 138 (204) T ss_pred CCEEECCCCCCEEEEEEEEEEEEECCCC----EEEEEEEECCCCCCHHHHHHHHHHHHHHH----CCCCCCCCCEEE-EE T ss_conf 7457323355401599972550102574----49999630203770588999999999997----347863342799-99 Q ss_pred EEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 83048877543025898899999999999999998577653047766788866667257644562 Q gi|254780124|r 174 QPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP 238 (388) Q Consensus 174 qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr 238 (388) .-|. ...|.++.++..-|...-.++.+++...-+...+....-- +....--|+.|.|+..|= T Consensus 139 i~R~--~~eVkef~idesvLet~~~~~~~~i~~yk~~~~e~dyk~v-p~~d~~fCk~CeF~~kCi 200 (204) T PHA01622 139 LNRN--TREVKQFKIDEKVLETYYQKVIEWIKKFKEYLKETDYKKV-PGVNNYICKSCEFKQKCI 200 (204) T ss_pred EECC--CCHHHHEEECHHHHHHHHHHHHHHHHHHHHHHHCCCHHCC-CCCCCEEECCCEEEEEEE T ss_conf 9547--3255721204999999999999999999998520452017-787605751434421377 No 18 >COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms] Probab=98.30 E-value=4.3e-05 Score=52.94 Aligned_cols=169 Identities=17% Similarity=0.168 Sum_probs=91.1 Q ss_pred CCCCCCCHHHHHCCCHHHHH-HCCCCCCCCHHHH----HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 56184236778718323886-2138999898899----989999999999724576534322010456453775788999 Q gi|254780124|r 5 AFLSASSSHRWLKCPIAPTL-ESKIPQTTSIYAS----EGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMAS 79 (388) Q Consensus 5 A~LSpSs~~rwl~CP~s~~L-e~~~pd~~S~aA~----~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~ 79 (388) ..++.|-.+.++.||...++ ...+|..+++++. .|..+|...+.+++... T Consensus 14 ~~i~~~~v~~y~~Cprk~w~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~------------------------- 68 (190) T COG1468 14 MRITGSDVNEYLYCPRKLWLFSRGGPEESPEVYSEGVELGKLIHEKLEKFLRDEK------------------------- 68 (190) T ss_pred EEECHHHHHHHHHCCHHHHHHHHCCCCCCCHHCCHHHHHHHHHHHHHHHHHCCCC------------------------- T ss_conf 2412888788885679899998448656500025135555788888998851244------------------------- Q ss_pred HHHHHHHHHHCCCCCCEEEEE-EEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHC Q ss_conf 999999998503787368877-5532000440589999999985997999981136887674466879999999999843 Q gi|254780124|r 80 SVSMVLAYVRTFSGPFLSETE-VPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQY 158 (388) Q Consensus 80 ~v~~~~~~~r~~~~~~~ve~E-~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~ 158 (388) . +..+ .++ ..-.+.|..|... ...++++|.|+...... +-.||.-|+. ....+ T Consensus 69 --------------~--v~l~~~~i----~~d~lk~~~~~~~----~~~~vEiK~~~~~~~~~-~~~Ql~~yly-l~e~~ 122 (190) T COG1468 69 --------------E--VELEGEWI----KIDFLKGRMDLEV----KDVVVEIKKSKKMEKAP-HKLQLAYYLY-LEEKL 122 (190) T ss_pred --------------C--CEECCEEE----EEEEECCCCEEEC----CCEEEEEECCCCCCCCH-HHHHHHHHHH-HHHHH T ss_conf --------------6--32312056----5542235300441----42138986576765354-7999999999-99860 Q ss_pred CCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 83567651389999983048877543025898899999999999999998577653047766788866667257644562 Q gi|254780124|r 159 GDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP 238 (388) Q Consensus 159 ~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr 238 (388) +. ..-...|+.|.... +-.-+++.+.... ...+...+...+... .-+.+..+..|++|.|+.+|. T Consensus 123 g~-----~v~~g~i~Y~~~~k---~~~Vei~~~~~e~-v~~~~~ei~~ile~~------~~p~~~~~~~C~~C~y~~iC~ 187 (190) T COG1468 123 GI-----AVAKGYIYYPKLKK---RVEVELTEELREE-VERVLKEIEEILEGG------KPPPPKKKKKCKKCAYREICF 187 (190) T ss_pred CC-----EEEEEEEEECCCCC---EEEEEECHHHHHH-HHHHHHHHHHHHHCC------CCCCCCCCCCCCCCCCCEECC T ss_conf 92-----00368998525673---7999808999999-999999999998289------999999988699998633426 Q ss_pred H Q ss_conf 0 Q gi|254780124|r 239 A 239 (388) Q Consensus 239 a 239 (388) . T Consensus 188 ~ 188 (190) T COG1468 188 P 188 (190) T ss_pred C T ss_conf 7 No 19 >pfam06023 DUF911 Archaeal protein of unknown function (DUF911). This family consists of several archaeal proteins of unknown function. Probab=98.27 E-value=5.2e-05 Score=52.40 Aligned_cols=204 Identities=16% Similarity=0.120 Sum_probs=100.5 Q ss_pred CCCHH--HHHH--CCCCCCCCHHHHHHHHHHHHHHHHHHCCC----CCCCCCCCCCCCCCCCHHH-HHHHHHHHHH---- Q ss_conf 18323--8862--13899989889998999999999972457----6534322010456453775-7889999999---- Q gi|254780124|r 17 KCPIA--PTLE--SKIPQTTSIYASEGTFAHNLLAHCLEQGV----DAETVSHQKLTFENDTRIV-DTEMASSVSM---- 83 (388) Q Consensus 17 ~CP~s--~~Le--~~~pd~~S~aA~~GT~~H~llE~~l~~~l----~~~~~~~~~~~~~~~~~~~-~~e~~~~v~~---- 83 (388) .||-+ .+|. .+..-+++....+|.++|++.-..++... ................... .++....+.. T Consensus 54 yCpT~RDvYLrrVlg~r~~~~~~~~~G~~iH~v~~~~~~~~kr~iysg~~~~~~~e~~~~~~~~~~~~e~~~~~~~l~~~ 133 (290) T pfam06023 54 YCPTGRDVYLKRVLGVRGEEGGPLVLGQAIHEAFAKAIEEVKSLIYSGEPPDSSLERSFMADEFGCPEDVREYAKALWKY 133 (290) T ss_pred CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 68985076888862645796354565189999999999999888744777755789987420225767888999999999 Q ss_pred -------HHHHHHCC----CCC------CEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHH Q ss_conf -------99998503----787------3688775532000440589999999985997999981136887674466879 Q gi|254780124|r 84 -------VLAYVRTF----SGP------FLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQ 146 (388) Q Consensus 84 -------~~~~~r~~----~~~------~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~Q 146 (388) -++.+++. ..+ .-+..|..++...-|.-..=++|..+..-+ .|+|.|+|.. +..+..| T Consensus 134 ~a~r~~a~~~ev~a~~~~~~~dsl~~~aiPv~~E~~VDGs~LGLS~~l~~Da~i~~~~--~Vve~K~G~~---~~~H~La 208 (290) T pfam06023 134 LASRVSAELSEVRSKFPKATEDSAAFRVIPVAVEVRVDGSPLGLSSYLRVDAFIPILP--LVVEMKVGSY---QERHELA 208 (290) T ss_pred HHHHHHHHHHHHHHCCCCCCCCHHHHEECCEEEEECCCCCCCCCCCCCCCCHHHCCCC--EEEEEECCCH---HHHHHHH T ss_conf 9999987788887404457730233210445788235884136764404442320466--4899961754---5678988 Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 999999999843835676513899999830488775430-2589889999999999999999857765304776678886 Q gi|254780124|r 147 LMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINE-WVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVND 225 (388) Q Consensus 147 L~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~-~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g 225 (388) |.-|||+....++...|.-- .++- ..+....+.- ...=.++|..|-=+.+..++.++. ++..+..+ T Consensus 209 lAGYALAiEs~~e~PVD~G~----lVyv-~~~~~v~~~~~~~~I~d~LR~~FLE~RDe~~~~v~-------~~~DPG~a- 275 (290) T pfam06023 209 LAGYALAIESDLEIPVDYGL----LVYV-TFNGGVKIKARLVYISDSLRTEFLEERDRAIEIVD-------NGSDPGLA- 275 (290) T ss_pred HHHHHHHHHHHHCCCCEEEE----EEEE-EECCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHH-------CCCCCCCC- T ss_conf 88899999887548714405----9999-97797589889998387899999998789999986-------27899998- Q ss_pred CCC-CCCCCCCCCC Q ss_conf 666-7257644562 Q gi|254780124|r 226 DSC-RFCRAKVRCP 238 (388) Q Consensus 226 ~~C-rfC~~k~~Cr 238 (388) +.| .+|+|...|- T Consensus 276 ~~C~~~CpF~~~Ch 289 (290) T pfam06023 276 KKCPPTCPFYEVCH 289 (290) T ss_pred CCCCCCCCHHHHHC T ss_conf 78998886477636 No 20 >TIGR02785 addA_Gpos recombination helicase AddA; InterPro: IPR014152 AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the Firmicutes and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.. Probab=98.14 E-value=1e-05 Score=56.99 Aligned_cols=52 Identities=17% Similarity=0.095 Sum_probs=38.5 Q ss_pred CEEEEEEEEEEEEECCEEEEEEEECCCCC---CCCCC---------CCHHHHHHHHHHHHHCCC Q ss_conf 40589999999985997999981136887---67446---------687999999999984383 Q gi|254780124|r 109 EPGATGTADILIFNSTQWIIVDFKYGAGV---PVKAE---------NNTQLMLYACGALHQYGD 160 (388) Q Consensus 109 ~~~~~GtiD~I~~~dg~l~IiDyKtGk~~---~v~a~---------~n~QL~lYALgA~~~~~~ 160 (388) ..-+.|+|||.+..+|.+..+||||=.-- +.+.+ ..-||.||+-+....+.. T Consensus 1214 ~~lv~GiIDgy~e~ed~~~L~DYKTD~v~gkf~~~~~~~~~~lk~rY~~Q~~LY~~AL~~~~~~ 1277 (1295) T TIGR02785 1214 KILVQGIIDGYLESEDGLVLFDYKTDHVEGKFGSSFEGAINELKERYRGQLKLYEKALEEILKK 1277 (1295) T ss_pred EEEEEEEEEEEEEECCCEEEEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 0788741222233368578987213334266788743312478888899999999999998389 No 21 >TIGR00609 recB exodeoxyribonuclease V, beta subunit; InterPro: IPR004586 Exodeoxyribonuclease V, or RecBCD holoenzyme, (3.1.11.5 from EC) is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. The complex catalyses exonucleolytic cleavage in either the 5' to 3' or 3' to 5' direction to yield 5-phosphooligonucleotides in the presence of ATP. This is the beta subunit .; GO: 0005524 ATP binding, 0008854 exodeoxyribonuclease V activity, 0006281 DNA repair. Probab=97.93 E-value=5.7e-05 Score=52.12 Aligned_cols=55 Identities=16% Similarity=0.257 Sum_probs=38.0 Q ss_pred EEEEEEEEEEECC-EEEEEEEECCC-CCCCCC-------------CCCHHHHHHHHHHHH---HCCCCCCCCC Q ss_conf 8999999998599-79999811368-876744-------------668799999999998---4383567651 Q gi|254780124|r 112 ATGTADILIFNST-QWIIVDFKYGA-GVPVKA-------------ENNTQLMLYACGALH---QYGDIFGRPE 166 (388) Q Consensus 112 ~~GtiD~I~~~dg-~l~IiDyKtGk-~~~v~a-------------~~n~QL~lYALgA~~---~~~~~~~~~~ 166 (388) +.|.||+|...+| ...||||||.. |.-.++ ..+.|=.||++|+.. ....-|+... T Consensus 1207 L~GfiDLvF~~~g~~yyi~DYKsN~LG~~~s~Y~~~~l~~~i~~~~YdlQy~lY~~A~hryL~~r~~~y~~~~ 1279 (1324) T TIGR00609 1207 LKGFIDLVFRHEGQRYYILDYKSNWLGKDASDYSPEALTEAILKERYDLQYLLYTLALHRYLKKRLKDYDYER 1279 (1324) T ss_pred HCCEEEEEEEECCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCHHH T ss_conf 1551689997089837998621064468821014799999999735817899999999999973588853554 No 22 >COG2251 Predicted nuclease (RecB family) [General function prediction only] Probab=97.91 E-value=0.0013 Score=43.22 Aligned_cols=254 Identities=15% Similarity=0.092 Sum_probs=116.3 Q ss_pred CCCCCCHHHHHCCCHHHHHHC----CCCCCCCHHH---HHHHHHH--HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHH Q ss_conf 618423677871832388621----3899989889---9989999--999999724576534322010456453775788 Q gi|254780124|r 6 FLSASSSHRWLKCPIAPTLES----KIPQTTSIYA---SEGTFAH--NLLAHCLEQGVDAETVSHQKLTFENDTRIVDTE 76 (388) Q Consensus 6 ~LSpSs~~rwl~CP~s~~Le~----~~pd~~S~aA---~~GT~~H--~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e 76 (388) +.|+|-.--+-.|+..+.|.. -.+++.+..- ..-+.+| ...+.-+ .+..+ ...+.....-....... T Consensus 2 ~~~~s~l~~~~Rc~rr~~l~~~~~~~~r~~~~~~l~kl~~~~~~~~~~~~~~~f--~~~e~--~~~~~~i~~r~~~t~~~ 77 (474) T COG2251 2 LYSASDLLAYQRCQRRALLRTFDARLGRGPPVAVLLKLPQERAALINDHELKEF--QLREE--ETAKRLIIGRAAYTGTL 77 (474) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHCCC--CCCCCEEECCCCCCHHH T ss_conf 553889999874115678888777644585277887776789887668987663--11352--34531231443321788 Q ss_pred HHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHH Q ss_conf 99999999999850378736887755320004405899999999859979999811368876744668799999999998 Q gi|254780124|r 77 MASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALH 156 (388) Q Consensus 77 ~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~ 156 (388) |...+.....-+--....+. ..... ++..++.|..|.++.++++.+|+|-|.++..++. ...|+..||+.... T Consensus 78 ~~~~a~~~~r~~L~~n~~~~-~~~~~----~~~~~~vg~pD~likdG~~yriv~~kl~k~pK~~--~~lq~a~ya~~La~ 150 (474) T COG2251 78 MAAGADEIFREVLIANRAPL-YQPVL----VGKIELVGFPDFLIKDGDVYRIVDAKLAKRPKLP--YRLQAAFYALLLAK 150 (474) T ss_pred HHHHHHHHHHHHHHHCCCCC-CCCCC----CCCCEEECCCCCEECCCCEEEEEECCCCCCCCCH--HHHHHHHHHHHHHH T ss_conf 87557899999997277621-26410----0361460478524416867888522001376507--89999999999985 Q ss_pred HCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCCCCCCCCC Q ss_conf 4383567651389999983048877543025898899999999999999998577653047766-788866667257644 Q gi|254780124|r 157 QYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEH-YGVNDDSCRFCRAKV 235 (388) Q Consensus 157 ~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~-~~~~g~~CrfC~~k~ 235 (388) ........+ .+.+.--+ .+ ..+ .+++.|...+..-........ ...... ..-....|+.|.|-. T Consensus 151 ~g~~v~~~a---el~l~~~~-----~~---~y~-~~~l~~~~~v~~~l~~~~~~L---~~~~~~avr~~r~rC~~C~f~p 215 (474) T COG2251 151 SGVPVAGNA---ELSLIGKV-----AV---PYS-VEDLIWLNDVQRFLDTIEEDL---HYEAKTAVRWIRARCTTCQFEP 215 (474) T ss_pred CCCCCCCCC---EEEECCCC-----CC---CCC-HHHHCCCHHHHHHHHHHHHHH---CCCCCCCCHHHHHHHHHHHCCH T ss_conf 178667876---14402454-----56---662-233224157799999999972---3678875414664411854143 Q ss_pred CCCHH--HHHHHHHH-HC---------CCCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 56201--34678763-02---------2005999999999-9543899999999999999999 Q gi|254780124|r 236 RCPAL--SRHVLLEA-TK---------DPSTNTTVELSKA-YSSISLIKSYVKACEDEMFKRL 285 (388) Q Consensus 236 ~Cra~--a~~~l~~~-~~---------~p~~l~~~e~~~~-l~~~~~l~~w~~~v~~~a~~~~ 285 (388) .|-+. ++..|.+. -. +-...|.+++++. ++..+.+....+.+-..+-.|+ T Consensus 216 ~C~~~a~e~~~L~Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa 278 (474) T COG2251 216 QCESEALEEDDLSLVPGITPSRYDVLEEVGITTIEDLADASLPILELVAGALTALAAQLVLQA 278 (474) T ss_pred HHHHHHHHCCCEECCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 356888513551013799878899999738223999975255402566546777789999999 No 23 >PRK10876 recB exonuclease V subunit beta; Provisional Probab=97.78 E-value=7.3e-05 Score=51.41 Aligned_cols=15 Identities=13% Similarity=0.031 Sum_probs=7.5 Q ss_pred CCCCCCCCCCCHHHH Q ss_conf 672576445620134 Q gi|254780124|r 228 CRFCRAKVRCPALSR 242 (388) Q Consensus 228 CrfC~~k~~Cra~a~ 242 (388) ++|=+..-.||.+.+ T Consensus 549 l~~~DIaILvRs~~~ 563 (1181) T PRK10876 549 VRASDISVLVRSRQE 563 (1181) T ss_pred CCCCCEEEEECCCHH T ss_conf 772116888446146 No 24 >pfam08696 Dna2 DNA replication factor Dna2. Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways. Probab=97.76 E-value=9.4e-05 Score=50.71 Aligned_cols=49 Identities=20% Similarity=0.350 Sum_probs=43.4 Q ss_pred CCCCCCCHHHHHCCCHHHHHHCCC--CCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 561842367787183238862138--9998988999899999999997245 Q gi|254780124|r 5 AFLSASSSHRWLKCPIAPTLESKI--PQTTSIYASEGTFAHNLLAHCLEQG 53 (388) Q Consensus 5 A~LSpSs~~rwl~CP~s~~Le~~~--pd~~S~aA~~GT~~H~llE~~l~~~ 53 (388) -++|+++...++.||+++.|...+ +++.|.++..||.+|++.+..|+.. T Consensus 58 ~LIS~T~Va~s~~C~RraVL~~r~k~~~~~s~~ml~GtivHelfQ~~l~~~ 108 (209) T pfam08696 58 ILVSGTSVASSIQCPRRAVLQERFKGSGEPSKPMLIGTILHEIFQEALRAN 108 (209) T ss_pred CCEEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 425400440424366199999984468987534502343999999999739 No 25 >COG4343 CRISPR-associated protein, RecB family exonuclease [Defense mechanisms] Probab=97.13 E-value=0.012 Score=36.83 Aligned_cols=207 Identities=18% Similarity=0.174 Sum_probs=95.6 Q ss_pred HHCCCHH--HHHH--CCCCCCCCHHHHHHHHHHHHHHHHHHCC----CCCCCCCCCCCC--CCCCC---HHHHHHHHHHH Q ss_conf 8718323--8862--1389998988999899999999997245----765343220104--56453---77578899999 Q gi|254780124|r 15 WLKCPIA--PTLE--SKIPQTTSIYASEGTFAHNLLAHCLEQG----VDAETVSHQKLT--FENDT---RIVDTEMASSV 81 (388) Q Consensus 15 wl~CP~s--~~Le--~~~pd~~S~aA~~GT~~H~llE~~l~~~----l~~~~~~~~~~~--~~~~~---~~~~~e~~~~v 81 (388) +-.||-+ .+|. .++.-+.+....+|.++|++.-..++.. ...+.+...... .+... ..+-.+..++. T Consensus 51 y~yCpt~RdvYLk~Vlg~Rge~~~~l~lG~aIHea~~~~~~e~k~~~~sg~sp~~sv~~d~~~~~~~~~k~v~~~~~~~~ 130 (281) T COG4343 51 YGYCPTGRDVYLKRVLGVRGEGGFPLLLGAAIHEAFAKAIEEHKSLIYSGESPRESVLEDAREMANILAKRVWARLNEYC 130 (281) T ss_pred CCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 26788740668999862034677430367899999999999999875045683312067899987789888889887788 Q ss_pred HH-HHHHH-----HCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEE--CCEEEEEEEECCCCCCCCCCCCHHHHHHHHH Q ss_conf 99-99998-----5037873688775532000440589999999985--9979999811368876744668799999999 Q gi|254780124|r 82 SM-VLAYV-----RTFSGPFLSETEVPLEPFTTEPGATGTADILIFN--STQWIIVDFKYGAGVPVKAENNTQLMLYACG 153 (388) Q Consensus 82 ~~-~~~~~-----r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~--dg~l~IiDyKtGk~~~v~a~~n~QL~lYALg 153 (388) +. |.... ++.+....+..++-.++.+++-. -|-.|++..+ .+.-.|+++|+|.- +..+..-|.-|||+ T Consensus 131 ~~~y~~~~~e~~~~tsds~~~~~~Pv~vE~~vDGsp-LGlS~lv~~D~~~~l~vv~elKvG~~---~e~hrLalAGYAlA 206 (281) T COG4343 131 EISYMAVRSEKASRTSDSALSIGAPVLVEFNVDGSP-LGLSDLVRVDALVGLPVVVELKVGSY---REVHRLALAGYALA 206 (281) T ss_pred HHHHHHHHHHHHHHCCCCCEEECCCEEEEECCCCCC-CCCCCEECCHHHCCCCEEEEEECCCH---HHHHHHHHHHHHHH T ss_conf 999999998765422441013125358981478974-55533223001036765999941652---68999887446765 Q ss_pred HHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCC Q ss_conf 99843835676513899999830488775430258-9889999999999999999857765304776678886666-725 Q gi|254780124|r 154 ALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVI-SADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSC-RFC 231 (388) Q Consensus 154 A~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~-s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~C-rfC 231 (388) ....++...|.- .+.+.+.+....++-.-+ -.+.|..|.=+.+.+++.++. .+.++..+ +.| .-| T Consensus 207 iEa~~eiPVD~G-----~li~vtvN~~vk~~~~l~~i~d~lRseFLe~RD~~~div~-------~g~DPG~a-~~C~~~C 273 (281) T COG4343 207 IEADTEIPVDYG-----VLISVTVNSGVKIKARLVYIDDSLRSEFLEERDRVADIVE-------YGSDPGLA-KSCPSGC 273 (281) T ss_pred HHHHHCCCCCEE-----EEEEEEECCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHH-------CCCCCCCC-CCCCCCC T ss_conf 324105873235-----7999997686068889997383788999987788999997-------38898999-8899998 Q ss_pred CCCCCCC Q ss_conf 7644562 Q gi|254780124|r 232 RAKVRCP 238 (388) Q Consensus 232 ~~k~~Cr 238 (388) +|...|- T Consensus 274 ~F~~~Ch 280 (281) T COG4343 274 PFYEVCH 280 (281) T ss_pred CHHHHCC T ss_conf 4587518 No 26 >TIGR01896 cas_AF1879 CRISPR-associated protein, Csa1 family; InterPro: IPR009260 This family consists of several archaeal strongly conserved proteins whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats). The function of these proteins has not been experimentally determined, but computational analysis has suggested that they may function as nucleases in DNA repair, similar to RecB (IPR004586 from INTERPRO) . . Probab=95.03 E-value=0.29 Score=27.76 Aligned_cols=122 Identities=21% Similarity=0.224 Sum_probs=63.7 Q ss_pred EEEEEEEECCCEEEEEEEEEEEEECC--EEE---EEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEE Q ss_conf 77553200044058999999998599--799---9981136887674466879999999999843835676513899999 Q gi|254780124|r 99 TEVPLEPFTTEPGATGTADILIFNST--QWI---IVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTII 173 (388) Q Consensus 99 ~E~~~~~~~~~~~~~GtiD~I~~~dg--~l~---IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~ 173 (388) +++-.++.++|-. -|=.|++.++.. .+- |+..|+|+. +..+.+=|+-||||....++...|. ...+ T Consensus 164 iP~~~E~~VDGsp-lGLs~~l~Vda~~~~l~~dlVvE~K~G~~---~~~h~LALAGYALAiEa~~e~PvDy-----G~lv 234 (295) T TIGR01896 164 IPVAVEYKVDGSP-LGLSDRLRVDALVLILPVDLVVEMKVGSY---QERHELALAGYALAIEADLEVPVDY-----GLLV 234 (295) T ss_pred CCEEEEECCCCCC-CCCCCCHHHHHHHHHCCCEEEEEEECCCH---HHHHHHHHHHHHHHHHHHHCCCEEE-----EEEE T ss_conf 6557751268855-46420000654320178317998525873---5677777654588777630783213-----4789 Q ss_pred EEECCCC--CCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCCCCCCC Q ss_conf 8304887--754302--589889999999999999999857765304776678886666-7257644562 Q gi|254780124|r 174 QPRVRTG--SPINEW--VISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSC-RFCRAKVRCP 238 (388) Q Consensus 174 qpr~~~~--~~vs~~--~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~C-rfC~~k~~Cr 238 (388) +-+..+. .++... .++ ++|+. ++.+.=.+++..+.. +.++.-+ ..| .-|||..+|. T Consensus 235 ~v~v~~gs~v~~~~~~~~i~-d~lR~---eFLe~RD~~~~~v~~----~~DPGlp-~~C~~~CPF~~~C~ 295 (295) T TIGR01896 235 YVNVNEGSKVEIKARLVYIS-DDLRR---EFLEERDEVIEIVES----GSDPGLP-PKCPPTCPFYEVCH 295 (295) T ss_pred EEEEECCCCEEEEEEEEEEC-HHHHH---HHHHHHHHHHHHHHC----CCCCCCC-CCCCCCCCCCCCCC T ss_conf 99862787436899999847-47779---999988999999864----7742338-88834678435789 No 27 >PRK09709 exonuclease VIII; Reviewed Probab=92.54 E-value=0.83 Score=24.77 Aligned_cols=16 Identities=31% Similarity=0.376 Sum_probs=6.3 Q ss_pred HHHHHHHHHHHHHCCC Q ss_conf 7999999999984383 Q gi|254780124|r 145 TQLMLYACGALHQYGD 160 (388) Q Consensus 145 ~QL~lYALgA~~~~~~ 160 (388) .|-.+|.-|...++|. T Consensus 791 vQaA~Y~dG~~~~tG~ 806 (877) T PRK09709 791 VQDAFYSDGYEAQFGV 806 (877) T ss_pred HHHHHHHCCHHHHCCC T ss_conf 1456653320231277 No 28 >TIGR00423 TIGR00423 conserved hypothetical protein TIGR00423; InterPro: IPR005244 This entry describes a family of conserved hypothetical proteins with no known function. . Probab=86.15 E-value=0.66 Score=25.42 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=6.0 Q ss_pred CCCCCCCCCCCCC Q ss_conf 8866667257644 Q gi|254780124|r 223 VNDDSCRFCRAKV 235 (388) Q Consensus 223 ~~g~~CrfC~~k~ 235 (388) .+-.+|+||.|++ T Consensus 14 IC~~~C~FCAF~~ 26 (331) T TIGR00423 14 ICVGKCKFCAFRR 26 (331) T ss_pred HHHHCCCCCCCCC T ss_conf 0232479633113 No 29 >KOG4760 consensus Probab=84.53 E-value=3 Score=21.06 Aligned_cols=40 Identities=15% Similarity=0.051 Sum_probs=26.4 Q ss_pred EEEEEEEECCCEEEEEEEEEEEEE-CCEEEEEEEECCCCCC Q ss_conf 775532000440589999999985-9979999811368876 Q gi|254780124|r 99 TEVPLEPFTTEPGATGTADILIFN-STQWIIVDFKYGAGVP 138 (388) Q Consensus 99 ~E~~~~~~~~~~~~~GtiD~I~~~-dg~l~IiDyKtGk~~~ 138 (388) .|..+-....++-++|.||-+-.+ =+++..+|+||-++.. T Consensus 156 refpv~ge~e~v~~vgVidE~~~~~f~~lel~~lktr~~~~ 196 (365) T KOG4760 156 REFPVFGEGEGVLLVGVIDELHYTAFGELELAELKTRRRPM 196 (365) T ss_pred CEEEECCCCCEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCC T ss_conf 02121024520489988754013555235776501224666 No 30 >pfam02477 Nairo_nucleo Nucleocapsid N protein. The nucleoprotein of the ssRNA negative-strand Nairovirus is an internal part of the virus particle. Probab=80.85 E-value=1.1 Score=23.86 Aligned_cols=39 Identities=26% Similarity=0.152 Sum_probs=26.4 Q ss_pred EECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 8599799998113688767446687999999999984383 Q gi|254780124|r 121 FNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGD 160 (388) Q Consensus 121 ~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~ 160 (388) -+.+++-+.|-||+.- .++.-.-.||.-|+.+|+..... T Consensus 98 kN~~~iK~WD~~Y~~L-~~evP~~EqL~~YQ~AAlkWRkD 136 (442) T pfam02477 98 KNKDTIKLWDAKYMDL-KKEIPEPEQLVSYQQAALKWRKD 136 (442) T ss_pred CCCCCEEECHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHH T ss_conf 5986203201058887-40599989999999999987774 No 31 >COG1023 Gnd Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism] Probab=75.01 E-value=6.1 Score=19.06 Aligned_cols=60 Identities=20% Similarity=0.276 Sum_probs=44.9 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHH Q ss_conf 220059999999999543899999999999999999789847852320588878611698999 Q gi|254780124|r 250 KDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRA 312 (388) Q Consensus 250 ~~p~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~ 312 (388) .-|..++-+++++++.+-+.|.+|+=++-+.|+..--+=.++.|+ |.+ +|--+||=+++. T Consensus 195 ~s~fD~D~~~VA~vW~hGSVIrSWLldLt~~Af~~d~~L~q~~g~--v~d-SGEGrWTv~~al 254 (300) T COG1023 195 NSPFDYDLEAVAEVWNHGSVIRSWLLDLTAEAFKKDPDLDQISGR--VSD-SGEGRWTVEEAL 254 (300) T ss_pred HCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCHHHHCCE--ECC-CCCCEEEHHHHH T ss_conf 188887779999998276459999999999998548887776176--345-887506668777 No 32 >pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria. Probab=68.35 E-value=8.4 Score=18.17 Aligned_cols=77 Identities=17% Similarity=0.210 Sum_probs=44.3 Q ss_pred HHCCC-CCCEEEEEEEEEEECCCEEEEEEEEEEEEE--CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC Q ss_conf 85037-873688775532000440589999999985--997999981136887674466879999999999843835676 Q gi|254780124|r 88 VRTFS-GPFLSETEVPLEPFTTEPGATGTADILIFN--STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGR 164 (388) Q Consensus 88 ~r~~~-~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~--dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~ 164 (388) ..+.+ +..+|....++.... -+. .+|.|..+ =.-++|||+|+|+-.+ ++--||-+|-- ++...-..++. T Consensus 199 LLELG~GFaFvgrQ~ri~v~~--~df--yiDLlFYh~~L~c~V~IELK~g~f~p---e~~GQl~~Yl~-~~d~~~k~~~d 270 (320) T pfam06250 199 LLELGAGFAFVGRQKRIQVDD--EDF--YIDLLFYHRKLRCLVAVDLKIGKFKP---EYAGQMNFYLR-YLDKHEKQPGE 270 (320) T ss_pred HHHHCCCCEEEEEEEEEEECC--CEE--EHHHHHHHHHCCCEEEEEECCCCCCH---HHHHHHHHHHH-HHHHHHCCCCC T ss_conf 998189816754557888779--323--40476663411413677641587677---88888999999-99888568889 Q ss_pred CCEEEEEE Q ss_conf 51389999 Q gi|254780124|r 165 PEALTLTI 172 (388) Q Consensus 165 ~~~v~~~I 172 (388) -.+|-+.+ T Consensus 271 NPtIGilL 278 (320) T pfam06250 271 NPPIGIIL 278 (320) T ss_pred CCCEEEEE T ss_conf 99800798 No 33 >COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only] Probab=65.27 E-value=6.4 Score=18.92 Aligned_cols=53 Identities=9% Similarity=0.123 Sum_probs=26.7 Q ss_pred HHHHHHHHHHHHHHHHHHCCC-CCCC----CEECCCCC-CCCCCCCHHHHHHHHHHCCC Q ss_conf 999999999999999997898-4785----23205888-78611698999999986165 Q gi|254780124|r 269 LIKSYVKACEDEMFKRLNAGD-EIQG----YQLVEGRK-GNRSFKDINRAQELLTSVLG 321 (388) Q Consensus 269 ~l~~w~~~v~~~a~~~~~~G~-~~~g----~Klv~gr~-~~r~~~d~~~~~~~l~~~~~ 321 (388) ....|+.+=..-+...+..|- .|-| =++..... ....|...+.....++.+|. T Consensus 293 ~~a~w~~~g~~~~~~~l~~GanD~ggt~~~E~v~~~a~~~~~~~~~~eel~~~i~~aG~ 351 (370) T COG1060 293 IQASWLRDGVILAQAALLSGANDLGGTGYEEKVNPAAGAFSGDWRSVEELAALIKEAGR 351 (370) T ss_pred CCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCC T ss_conf 41744103669999999828616767775534365555556789999999999998499 No 34 >PRK06245 cofG FO synthase subunit 1; Reviewed Probab=64.73 E-value=9 Score=17.98 Aligned_cols=67 Identities=25% Similarity=0.316 Sum_probs=32.5 Q ss_pred HHHCCC-CCCCCEECCC--CCCCCCCCCHHHHHHHHHHCCCCCCHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 997898-4785232058--88786116989999999861651000001389889999740002426789875300 Q gi|254780124|r 284 RLNAGD-EIQGYQLVEG--RKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQEL 355 (388) Q Consensus 284 ~~~~G~-~~~g~Klv~g--r~~~r~~~d~~~~~~~l~~~~~~~~~~~~l~~~~~~ek~~~~~~~~~~~~~~l~~~ 355 (388) .+..|- .|-|--=|+- -...+-|.+-+...+.+...|. .+-+|-.+-|.=. .++=++++..+.+..+ T Consensus 258 ~L~~GanDlGGisp~t~d~vnpe~~wp~~~~l~~~~~~~g~-~l~~Rl~vyp~~~----~~~w~~~~~~~~~~~~ 327 (336) T PRK06245 258 FLEAGADDLGGISPVTKDEVNPEYPWPDIDELKEILEEAGW-QLKERLPVYPKYV----KEGWLSPRLQEKIERL 327 (336) T ss_pred HHHCCCCCCCCCCCCCCCEECCCCCCCCHHHHHHHHHHCCC-CCCCCCCCCHHHH----CCCCCCHHHHHHHHHH T ss_conf 98678766788775766601889999899999999997599-6564368886675----1576698999999986 No 35 >pfam05565 Sipho_Gp157 Siphovirus Gp157. This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage. Probab=61.39 E-value=7.9 Score=18.35 Aligned_cols=29 Identities=17% Similarity=0.194 Sum_probs=16.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999995438999999999999999997 Q gi|254780124|r 258 VELSKAYSSISLIKSYVKACEDEMFKRLN 286 (388) Q Consensus 258 ~e~~~~l~~~~~l~~w~~~v~~~a~~~~~ 286 (388) +|+-.+-.+..-+++-++.+++|....+. T Consensus 61 ~e~krl~erkk~~enk~~~LK~yl~~~m~ 89 (162) T pfam05565 61 AEIKRLAERKKSIENKVKRLKDYLEEAME 89 (162) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999899999999999999 No 36 >TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit. This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria. Probab=59.20 E-value=13 Score=16.99 Aligned_cols=38 Identities=13% Similarity=0.098 Sum_probs=19.1 Q ss_pred HHHHCCC-CCCCCE-EC--CCCCCCCCCCCHHHHHHHHHHCCC Q ss_conf 9997898-478523-20--588878611698999999986165 Q gi|254780124|r 283 KRLNAGD-EIQGYQ-LV--EGRKGNRSFKDINRAQELLTSVLG 321 (388) Q Consensus 283 ~~~~~G~-~~~g~K-lv--~gr~~~r~~~d~~~~~~~l~~~~~ 321 (388) ..+..|- .+-|-- +. .+ ++.+.|...+.......++|+ T Consensus 254 ~aL~~GanDlGG~~~~~~~~v-~~~~~~~~~~el~~~i~~aG~ 295 (322) T TIGR03550 254 LLLDAGIDDWGGVSPVTPDHV-NPEAPWPEIDELARATEEAGF 295 (322) T ss_pred HHHHCCCCCCCCCCCCCHHHC-CCCCCCCCHHHHHHHHHHCCC T ss_conf 999679977888771427544-888999999999999998499 No 37 >PRK08445 hypothetical protein; Provisional Probab=58.55 E-value=8.6 Score=18.10 Aligned_cols=16 Identities=13% Similarity=-0.056 Sum_probs=8.5 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 8899989999999999 Q gi|254780124|r 34 IYASEGTFAHNLLAHC 49 (388) Q Consensus 34 ~aA~~GT~~H~llE~~ 49 (388) +-...|.+|+.+-+.. T Consensus 17 dl~~L~~~A~~~R~~~ 32 (348) T PRK08445 17 PLKELGQMALARKQEL 32 (348) T ss_pred CHHHHHHHHHHHHHHH T ss_conf 9999999999999997 No 38 >pfam00285 Citrate_synt Citrate synthase. Probab=56.84 E-value=14 Score=16.74 Aligned_cols=51 Identities=22% Similarity=0.421 Sum_probs=33.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 99999999543899999999999999999789847852320588878611698999999986 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) ++++.+.|..+ .+ .++++.|+.+.+.+|+.+||| |.|.|++.|-=+..|+. T Consensus 218 n~~v~~ml~~i---~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~l~~ 268 (352) T pfam00285 218 NEAVLEMLEEI---GS-PENVEEYIEKALDKGERLMGF-------GHRVYKTYDPRARILKK 268 (352) T ss_pred HHHHHHHHHHH---CC-CHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH T ss_conf 89999999995---58-166899999998468977678-------97668889956999999 No 39 >PRK05904 coproporphyrinogen III oxidase; Provisional Probab=56.76 E-value=14 Score=16.73 Aligned_cols=13 Identities=15% Similarity=0.534 Sum_probs=5.2 Q ss_pred CCHHHHHCCCHHH Q ss_conf 2367787183238 Q gi|254780124|r 10 SSSHRWLKCPIAP 22 (388) Q Consensus 10 Ss~~rwl~CP~s~ 22 (388) ...+-|++=|... T Consensus 5 k~~~LYIHIPFC~ 17 (353) T PRK05904 5 KTKHLYIHIPFCQ 17 (353) T ss_pred CCCEEEEEECCCC T ss_conf 8666999808998 No 40 >PRK05927 hypothetical protein; Provisional Probab=54.66 E-value=11 Score=17.34 Aligned_cols=13 Identities=23% Similarity=0.248 Sum_probs=6.3 Q ss_pred HHHHHEECCCCCC Q ss_conf 7530015678982 Q gi|254780124|r 351 ELQELITRGDGKP 363 (388) Q Consensus 351 ~l~~~i~k~~gkp 363 (388) ++.+-|.+..|.. T Consensus 305 ~~eE~I~~aaG~~ 317 (350) T PRK05927 305 ILDESVHKCTGWD 317 (350) T ss_pred CEEEEEECCCCCC T ss_conf 3000464322899 No 41 >PRK10880 adenine DNA glycosylase; Provisional Probab=50.67 E-value=16 Score=16.31 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=23.9 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH Q ss_conf 9999985776530477667888666672576445620134678 Q gi|254780124|r 203 RGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVL 245 (388) Q Consensus 203 ~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l 245 (388) ..+.+++..+..+ .+....|.-||.+..|.|.....- T Consensus 180 ~nQAlMDLGA~vC------tp~~P~C~~CPl~~~C~A~~~~~~ 216 (350) T PRK10880 180 FNQAMMDLGAMVC------TRSKPKCELCPLQNGCIAAANHSW 216 (350) T ss_pred HHHHHHHHHHHHC------CCCCCCCCCCCCCCCCHHHHCCCH T ss_conf 9999999734102------799998788988220646427985 No 42 >COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair] Probab=50.19 E-value=18 Score=16.05 Aligned_cols=52 Identities=15% Similarity=0.286 Sum_probs=32.8 Q ss_pred CHHHHHHHHHH-------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH Q ss_conf 98899999999-------99999999857765304776678886666725764456201346787 Q gi|254780124|r 189 SADDLLEKAKE-------FKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLL 246 (388) Q Consensus 189 s~eeL~~~~~~-------v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l~ 246 (388) +..++...++. .....+.++...|..+. +....|.-||++..|.|..+.+.. T Consensus 164 ~~~~~~~~~~~ll~p~~~~~~fnqammdlGA~ICt------~~~P~C~~CPl~~~c~a~~~g~~~ 222 (342) T COG1194 164 TKKELWELAEQLLTPDRRPGDFNQAMMDLGATICT------AKKPKCSLCPLRDNCAAYRNGTPE 222 (342) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHC------CCCCCCCCCCCHHHHHHHHCCCCC T ss_conf 05899999997448988767999999986367615------899987739466889999819964 No 43 >PRK12349 citrate synthase 3; Provisional Probab=49.60 E-value=18 Score=15.99 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=27.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCC-CC Q ss_conf 99999999543899999999999999999789847852320588878611-69 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSF-KD 308 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~-~d 308 (388) ++.+.+.| +.+.+ .+++++|+.+.+.+|+.++|| |.|.| +. T Consensus 224 ne~v~~ml---~ei~~-~~~~~~~i~~~l~~~~~i~GF-------GHrVY~k~ 265 (365) T PRK12349 224 NEAVMYML---LEAGT-VEKFEELLQKKLYNKEKIMGF-------GHRVYMKK 265 (365) T ss_pred HHHHHHHH---HHHCC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCC T ss_conf 89999999---98288-877999999987179961157-------87555788 No 44 >cd06109 BsCS-I_like Bacillus subtilis (Bs) citrate synthase CS-I_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-I, one of two CS isozymes in the gram-positive B. subtilis. The majority of CS activity in B. subtilis is provided by the other isozyme, BsCS-II (not included in this group). BsCS- Probab=47.11 E-value=20 Score=15.74 Aligned_cols=52 Identities=15% Similarity=0.342 Sum_probs=35.4 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 999999999543899999999999999999789847852320588878611698999999986 Q gi|254780124|r 256 TTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 256 ~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) -++++.+.+..+. . .+++++|..+.+.+|+.+||| |.|.|++.|-=+..|++ T Consensus 207 A~~~v~~~l~ei~---~-~~~~~~~i~~~l~~~~~i~Gf-------GHrvY~~~DPRa~~l~~ 258 (349) T cd06109 207 APGPVLDMLDAIG---T-PENAEAWLREALARGERLMGF-------GHRVYRVRDPRADVLKA 258 (349) T ss_pred HHHHHHHHHHHHC---C-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH T ss_conf 6799999999958---8-346999999998357875378-------98878999944999999 No 45 >COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair] Probab=46.68 E-value=20 Score=15.70 Aligned_cols=43 Identities=19% Similarity=0.241 Sum_probs=31.8 Q ss_pred EEEEEEEEEECCEEEEEEEECCCCCC----CC-CCCCHHHHHHHHHHH Q ss_conf 99999999859979999811368876----74-466879999999999 Q gi|254780124|r 113 TGTADILIFNSTQWIIVDFKYGAGVP----VK-AENNTQLMLYACGAL 155 (388) Q Consensus 113 ~GtiD~I~~~dg~l~IiDyKtGk~~~----v~-a~~n~QL~lYALgA~ 155 (388) +|-||.|-.++++++.|.-||.++.. .. .....|.++...+-+ T Consensus 32 ~GEIDlIa~~~~~ivFVEVK~R~~~~~g~a~~aV~~~K~~ki~~aA~~ 79 (114) T COG0792 32 YGEIDLIARDGDTVVFVEVKYRRNDLYGGAAEAVTPRKQRKLRRAARL 79 (114) T ss_pred CCCEEEEEECCCEEEEEEEEEECCCCCCCHHHHCCHHHHHHHHHHHHH T ss_conf 874689996599899999974126776666774899999999999999 No 46 >TIGR03551 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit. This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases. Probab=46.21 E-value=20 Score=15.67 Aligned_cols=13 Identities=15% Similarity=-0.084 Sum_probs=5.8 Q ss_pred HHHHHHHHHHHHH Q ss_conf 8999899999999 Q gi|254780124|r 35 YASEGTFAHNLLA 47 (388) Q Consensus 35 aA~~GT~~H~llE 47 (388) -...|.+|+.+=+ T Consensus 16 l~~L~~~A~~vR~ 28 (343) T TIGR03551 16 LFELFRLADELRR 28 (343) T ss_pred HHHHHHHHHHHHH T ss_conf 9999999999999 No 47 >PRK06582 coproporphyrinogen III oxidase; Provisional Probab=45.79 E-value=6.5 Score=18.91 Aligned_cols=12 Identities=17% Similarity=0.293 Sum_probs=6.1 Q ss_pred CCCCHHHHHHHH Q ss_conf 116989999999 Q gi|254780124|r 305 SFKDINRAQELL 316 (388) Q Consensus 305 ~~~d~~~~~~~l 316 (388) +.++++...+.+ T Consensus 313 ~Ls~~d~~~e~i 324 (390) T PRK06582 313 KLTHQEIIEEIL 324 (390) T ss_pred CCCHHHHHHHHH T ss_conf 189889999999 No 48 >PRK08444 hypothetical protein; Provisional Probab=45.12 E-value=21 Score=15.55 Aligned_cols=13 Identities=23% Similarity=0.184 Sum_probs=5.8 Q ss_pred HHHHHEECCCCCC Q ss_conf 7530015678982 Q gi|254780124|r 351 ELQELITRGDGKP 363 (388) Q Consensus 351 ~l~~~i~k~~gkp 363 (388) ++.+-|.+..|.+ T Consensus 307 ~~eE~i~~~aGa~ 319 (353) T PRK08444 307 IEKESIQSAAGAK 319 (353) T ss_pred CCCCCEECCCCCC T ss_conf 5545244212589 No 49 >PRK09736 5-methylcytosine-specific restriction enzyme subunit McrC; Provisional Probab=44.27 E-value=22 Score=15.46 Aligned_cols=66 Identities=17% Similarity=0.170 Sum_probs=34.5 Q ss_pred EEEEEEEECCEEEEEEEECCCCCCCCC---CCCHHHHHHHHHHHHHC-CCCCCCCCEEEEEEEEEECCCC Q ss_conf 999999859979999811368876744---66879999999999843-8356765138999998304887 Q gi|254780124|r 115 TADILIFNSTQWIIVDFKYGAGVPVKA---ENNTQLMLYACGALHQY-GDIFGRPEALTLTIIQPRVRTG 180 (388) Q Consensus 115 tiD~I~~~dg~l~IiDyKtGk~~~v~a---~~n~QL~lYALgA~~~~-~~~~~~~~~v~~~I~qpr~~~~ 180 (388) ..|.++...|...|||-||-+.....- ..-.|--+|++.|+-.- ........++.+....|..+.. T Consensus 244 ktDIvL~~~~~~lIIDTKy~~~~~~~~~~~~~i~s~dLYQm~AYlkn~~~~~~~~~~~~G~LLYp~~~~~ 313 (350) T PRK09736 244 RTDIVLDSKGRRLIIDTKFYSSLTSGRYGTEKLHSNNLYQIYAYLKSQAGGDELADTASGLLLYPKVDED 313 (350) T ss_pred CCCEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCC T ss_conf 7627982498189997765344331225778846556799999986031367667745689982688888 No 50 >PRK06341 single-stranded DNA-binding protein; Provisional Probab=43.65 E-value=13 Score=16.92 Aligned_cols=34 Identities=18% Similarity=0.327 Sum_probs=18.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHH Q ss_conf 99999999999997898478523205888786116989 Q gi|254780124|r 273 YVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDIN 310 (388) Q Consensus 273 w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~ 310 (388) |-+.+.+.+.+-+.+|..+ +|+||-..|+|+|.+ T Consensus 60 ~~~~lae~~~~yl~KG~~V----~VeGrL~~r~w~dk~ 93 (165) T PRK06341 60 FNEGLCKVAEQYLKKGAKV----YIEGQLQTRKWTDQS 93 (165) T ss_pred HHHHHHHHHHHHHCCCCEE----EEECCEEEEEEECCC T ss_conf 5289999999973789879----883226873118799 No 51 >COG5175 MOT2 Transcriptional repressor [Transcription] Probab=43.50 E-value=15 Score=16.45 Aligned_cols=11 Identities=18% Similarity=0.365 Sum_probs=6.2 Q ss_pred EEEEEEEEEEE Q ss_conf 89999999985 Q gi|254780124|r 112 ATGTADILIFN 122 (388) Q Consensus 112 ~~GtiD~I~~~ 122 (388) .+|.|--|.++ T Consensus 143 QyGkI~KIvvN 153 (480) T COG5175 143 QYGKIKKIVVN 153 (480) T ss_pred HCCCEEEEEEC T ss_conf 12543578862 No 52 >cd06112 citrate_synt_like_1_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, an Probab=42.20 E-value=23 Score=15.26 Aligned_cols=51 Identities=20% Similarity=0.334 Sum_probs=34.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 99999999543899999999999999999789847852320588878611698999999986 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) ++++.+.|..+ .+ .+++++|..+.+.+|+.+||| |.|.|++.|-=+..|++ T Consensus 223 n~~v~~ml~ei---~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~L~~ 273 (373) T cd06112 223 NEDVLEMLEEI---GS-PENVKAYLDKKLANKQKIWGF-------GHRVYKTKDPRATILQK 273 (373) T ss_pred HHHHHHHHHHH---CC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH T ss_conf 99999999984---99-888999999987268877888-------87657889942899999 No 53 >PRK07360 FO synthase subunit 2; Reviewed Probab=42.15 E-value=18 Score=16.03 Aligned_cols=34 Identities=18% Similarity=-0.018 Sum_probs=14.8 Q ss_pred CCHHHHHHHHHHCCCCHHHHHHHHHHEECCCCCCE Q ss_conf 89889999740002426789875300156789826 Q gi|254780124|r 330 KTPKELEQLYKEQKVSDEFWEELQELITRGDGKPV 364 (388) Q Consensus 330 ~~~~~~ek~~~~~~~~~~~~~~l~~~i~k~~gkp~ 364 (388) +++..++..|--.. ++--..++.+-|.+..|.+. T Consensus 308 ~g~~~~q~aL~~Ga-nD~ggt~~ee~i~~~aG~~~ 341 (375) T PRK07360 308 LGLKLAQEALNCGA-NDLGGTLMEEHITKMAGASG 341 (375) T ss_pred CCHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCCCC T ss_conf 48999999996699-76766566675001226899 No 54 >KOG1150 consensus Probab=41.41 E-value=17 Score=16.19 Aligned_cols=14 Identities=43% Similarity=0.793 Sum_probs=9.3 Q ss_pred CCCCCCEECCCCCC Q ss_conf 67898266307886 Q gi|254780124|r 358 RGDGKPVIAPRDIP 371 (388) Q Consensus 358 k~~gkp~l~p~~d~ 371 (388) |..||||.+++||| T Consensus 139 kKegkpt~ieedDp 152 (250) T KOG1150 139 KKEGKPTIIEEDDP 152 (250) T ss_pred HHCCCCCCCCCCCH T ss_conf 73389987655688 No 55 >TIGR00872 gnd_rel 6-phosphogluconate dehydrogenase (decarboxylating); InterPro: IPR004849 This family resembles a larger family of bacterial and eukaryotic 6-phosphogluconate dehydrogenases (Gnd) but differs from it by a deep split in a UPGMA similarity clustering tree and the lack of a central region of about 140 residues. Among complete genomes, it is found is found in Bacillus subtilis and Mycobacterium tuberculosis, both of which also contain Gnd, and in Aquifex aeolicus. . Probab=41.16 E-value=16 Score=16.35 Aligned_cols=57 Identities=14% Similarity=0.185 Sum_probs=44.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHH Q ss_conf 059999999999543899999999999999999789847852320588878611698999 Q gi|254780124|r 253 STNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRA 312 (388) Q Consensus 253 ~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~ 312 (388) ..-+-+|+|+++.+-+.|.+|+=|+-..|++.--+=.++.|+=---| -=+||=++++ T Consensus 239 fDfD~~eVArVw~~GSVIrSwL~dLt~~Af~~~~dL~~~~G~v~dSG---EGrWtv~~a~ 295 (341) T TIGR00872 239 FDFDLEEVARVWRRGSVIRSWLLDLTAKAFEESADLEEVEGIVEDSG---EGRWTVKEAV 295 (341) T ss_pred CCCCHHHHHHHHCCCCEEEHHHHHHHHHHHHCCCCCCCEEEEECCCC---CCHHHHHHHH T ss_conf 76874889998708986412688899999750788213223670278---7278999988 No 56 >KOG2672 consensus Probab=40.70 E-value=8.6 Score=18.10 Aligned_cols=32 Identities=19% Similarity=0.209 Sum_probs=16.4 Q ss_pred CCEEEEEEEEEEEEEC---CEEEEEEEECCCCCCC Q ss_conf 4405899999999859---9799998113688767 Q gi|254780124|r 108 TEPGATGTADILIFNS---TQWIIVDFKYGAGVPV 139 (388) Q Consensus 108 ~~~~~~GtiD~I~~~d---g~l~IiDyKtGk~~~v 139 (388) ++-....|+-.....| -.-+..--||.+.++. T Consensus 104 G~d~~~ATATIMlmGDTCTRGCRFCsVKTsR~PpP 138 (360) T KOG2672 104 GGDKSTATATIMLMGDTCTRGCRFCSVKTSRNPPP 138 (360) T ss_pred CCCCCCEEEEEEEECCCCCCCCCEEEEECCCCCCC T ss_conf 89875236898863474346752012103788967 No 57 >PRK03298 hypothetical protein; Provisional Probab=40.53 E-value=25 Score=15.09 Aligned_cols=59 Identities=17% Similarity=0.107 Sum_probs=37.9 Q ss_pred EEEEEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEC Q ss_conf 0589999999985-9979999811368876744668799999999998438356765138999998304 Q gi|254780124|r 110 PGATGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRV 177 (388) Q Consensus 110 ~~~~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~ 177 (388) +.-.|.+|.+-++ +|.+.||..|- ++ +.+.-.||.=|--.. + ..+. ...|+..+.-|.. T Consensus 131 ~T~~G~VDll~~D~~G~~V~VEiKR-ra---~idaV~QL~RYve~l-~---rd~~-~~~VRGIlvAp~I 190 (224) T PRK03298 131 MTAIGPVDLLCRDADGATVAVEIKR-RG---EIDGVEQLTRYLELL-N---RDPL-LAPVRGVFAAQQI 190 (224) T ss_pred CCCCCCEEEEEECCCCCEEEEEEEE-CC---CHHHHHHHHHHHHHH-H---HCCC-CCCEEEEEECCCC T ss_conf 1798835389987999999999983-06---810899999999998-5---5758-8851499998747 No 58 >pfam07211 consensus Probab=40.50 E-value=25 Score=15.09 Aligned_cols=54 Identities=15% Similarity=0.102 Sum_probs=37.8 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCC------CCCHHHHHHHHHHCCCCCCHH Q ss_conf 9999999999999978984785232058887861------169899999998616510000 Q gi|254780124|r 272 SYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRS------FKDINRAQELLTSVLGEEAFK 326 (388) Q Consensus 272 ~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~------~~d~~~~~~~l~~~~~~~~~~ 326 (388) -.-.-|.+|+..+...--.+. ++-.-|+.+.|+ +.|+++..+-|+.+|.++..+ T Consensus 55 ffegli~~Y~~~~~~~DpK~K-~~tpyGkv~srK~k~~~~~~De~~Ll~~lk~n~~~~~Ik 114 (162) T pfam07211 55 YFEGLVTQYYLKQLTKDPKAK-LSTPYGKVKSRKRKKAPNASDKDQLLNHLKEAGFTEFIK 114 (162) T ss_pred HHHHHHHHHHHHHHHCCCCCC-CCCCCCCEEEECCCCCCCCCCHHHHHHHHHHCCCHHHEE T ss_conf 999999999999873187520-056676411103578856479999999998658333300 No 59 >COG4950 Uncharacterized protein conserved in bacteria [Function unknown] Probab=39.96 E-value=10 Score=17.56 Aligned_cols=62 Identities=15% Similarity=0.170 Sum_probs=45.8 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHH---------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 666725764456201346787630---------22005999999999954389999999999999999978 Q gi|254780124|r 226 DSCRFCRAKVRCPALSRHVLLEAT---------KDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNA 287 (388) Q Consensus 226 ~~CrfC~~k~~Cra~a~~~l~~~~---------~~p~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~ 287 (388) -.|+-|++...|...+.....+-. -++...+|+.++.|+..+..|..-=+++.-.++.++.. T Consensus 75 ~va~~~~~~~L~~hY~arLap~p~~~~~~~~~~pd~~~es~~RLaai~~yar~L~~~P~~~~r~~l~~L~~ 145 (193) T COG4950 75 TVAQVTGAQRLCAHYAARLAPLPGSESEPSGADPDAARESNERLAAITQYARLLASSPSDIDREALERLYD 145 (193) T ss_pred HHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH T ss_conf 99986070466678998855588862223567886034550799999999999853965378899998761 No 60 >PRK09058 coproporphyrinogen III oxidase; Provisional Probab=38.90 E-value=26 Score=14.93 Aligned_cols=11 Identities=18% Similarity=0.531 Sum_probs=6.7 Q ss_pred EEEEEEEECCC Q ss_conf 79999811368 Q gi|254780124|r 125 QWIIVDFKYGA 135 (388) Q Consensus 125 ~l~IiDyKtGk 135 (388) .-..+|+=||- T Consensus 209 ~~iniDLIyGl 219 (447) T PRK09058 209 AAVVCDLIFGL 219 (447) T ss_pred CCEEEHHHCCC T ss_conf 63764764279 No 61 >TIGR01979 sufS cysteine desulfurases, SufS subfamily; InterPro: IPR010970 Cysteine desulphurases are pyridoxal-phosphate enzymes which catalyse the removal of sulphur from L-cysteine to form L-alanine and elemental sulphur. These enzymes have been shown to play an important role in the biosynthesis of iron-sulphur clusters, thionucleosides in tRNA, thiamine, biotin, lipoate and molydopterin This entry represents a subfamily of NifS-related cysteine desulphurases that are often involved in iron-sulphur cluster formation, which is needed for nitrogen fixation and other vital functions . Many of these enzymes, in addition to cysteine desulphurase activity, also show selenocysteine lyase activity where L-selenocysteine is converted to L-alanine and selenide . Some of these enzymes are much more specific for selenocysteine than cysteine and are thus believed to function in selenium metabolism rather than sulphur metabolism. Structural studies of the E. coli and Synechocystis enzymes indicate that they are homodimers which show a similar fold to other members of the alpha family of pyridoxal-phosphate enzymes .; GO: 0030170 pyridoxal phosphate binding, 0031071 cysteine desulfurase activity, 0006534 cysteine metabolic process. Probab=37.17 E-value=26 Score=14.99 Aligned_cols=95 Identities=19% Similarity=0.326 Sum_probs=53.3 Q ss_pred CHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEC--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 8799999999998438356765138999998304--88775430258988999999999999999985776530477667 Q gi|254780124|r 144 NTQLMLYACGALHQYGDIFGRPEALTLTIIQPRV--RTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHY 221 (388) Q Consensus 144 n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~--~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~ 221 (388) -.+|.-||+ +++..++ .+.||.|+- +..+.|| +.+++.-.- ++ ..+++..+-.. T Consensus 306 E~~L~~yal---~~L~~ip------g~~iyGP~~~~~R~g~is---Fn~~g~HpH--DV----g~~LD~~GiAv------ 361 (409) T TIGR01979 306 EKELTAYAL---ERLGEIP------GLRIYGPRDAEDRGGIIS---FNVEGVHPH--DV----GTILDEEGIAV------ 361 (409) T ss_pred HHHHHHHHH---HHHHCCC------CEEEECCCCCCCCCCEEE---ECCCCCCCC--HH----HHHCCCCCCEE------ T ss_conf 999999999---9960189------858746877432643333---025888700--22----30122677568------ Q ss_pred CCCCCCC-----CCCCCCCCCCH-HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 8886666-----72576445620-13467876302200599999999995438999999 Q gi|254780124|r 222 GVNDDSC-----RFCRAKVRCPA-LSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYV 274 (388) Q Consensus 222 ~~~g~~C-----rfC~~k~~Cra-~a~~~l~~~~~~p~~l~~~e~~~~l~~~~~l~~w~ 274 (388) ++|.|| +|=...++||| .+=| .|.+||-.+...+.-+.+|. T Consensus 362 -R~GHHCAqPlm~~~~v~atcRASf~~Y-----------NT~ediD~Lv~aL~~v~~~F 408 (409) T TIGR01979 362 -RSGHHCAQPLMRRFGVPATCRASFYLY-----------NTEEDIDALVEALKKVRKFF 408 (409) T ss_pred -EECCHHHHHHHHHCCCCEEEEEEEEEC-----------CCHHHHHHHHHHHHHHHHHH T ss_conf -617053248986559963678874103-----------89899999999999999860 No 62 >KOG0437 consensus Probab=36.75 E-value=22 Score=15.42 Aligned_cols=59 Identities=20% Similarity=0.228 Sum_probs=35.0 Q ss_pred CCCCCCCCC-----CCCCHHHHHHHHHHHCC--------CCCCCHHHHHHHH--HHHHHHHHHHHHHHHHHHHH Q ss_conf 666725764-----45620134678763022--------0059999999999--54389999999999999999 Q gi|254780124|r 226 DSCRFCRAK-----VRCPALSRHVLLEATKD--------PSTNTTVELSKAY--SSISLIKSYVKACEDEMFKR 284 (388) Q Consensus 226 ~~CrfC~~k-----~~Cra~a~~~l~~~~~~--------p~~l~~~e~~~~l--~~~~~l~~w~~~v~~~a~~~ 284 (388) =.||||... .+||..|++.-.+..+. |..-.+.++..+- -...-|..-....+.+++.. T Consensus 841 Lv~r~ietqtlLLaPi~Ph~aeyiw~~~~~~~~~v~~~wP~~s~~~e~~~~~~~yl~~~l~r~~~~l~~~~~~k 914 (1080) T KOG0437 841 LVFRFIETQTLLLAPICPHLAEYIWRTVLKKNFSVNVGWPFVSPPDEKLGSSALYLKRTLKRLRAELEKQMLKK 914 (1080) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH T ss_conf 99999999999874125279999999961688554268997897788754657999999999999988652311 No 63 >PRK05926 hypothetical protein; Provisional Probab=36.48 E-value=28 Score=14.68 Aligned_cols=13 Identities=8% Similarity=0.059 Sum_probs=6.0 Q ss_pred HHHHHEECCCCCC Q ss_conf 7530015678982 Q gi|254780124|r 351 ELQELITRGDGKP 363 (388) Q Consensus 351 ~l~~~i~k~~gkp 363 (388) ++++-|.+..|.. T Consensus 330 ~~eE~I~~aAGa~ 342 (371) T PRK05926 330 HMGEKVFQMASSK 342 (371) T ss_pred CCCCEEEHHHCCC T ss_conf 3133464310279 No 64 >PRK08898 coproporphyrinogen III oxidase; Provisional Probab=36.19 E-value=21 Score=15.61 Aligned_cols=15 Identities=20% Similarity=0.315 Sum_probs=8.5 Q ss_pred HHHEECCCCCCEECC Q ss_conf 300156789826630 Q gi|254780124|r 353 QELITRGDGKPVIAP 367 (388) Q Consensus 353 ~~~i~k~~gkp~l~p 367 (388) .+|++.-.+.-.|-+ T Consensus 364 ~GLl~~~~~~i~lT~ 378 (393) T PRK08898 364 RGLLERDPTRIRPTP 378 (393) T ss_pred CCCEEEECCEEEECH T ss_conf 898998099999997 No 65 >PRK12351 methylcitrate synthase; Provisional Probab=35.30 E-value=30 Score=14.56 Aligned_cols=51 Identities=24% Similarity=0.360 Sum_probs=32.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 99999999543899999999999999999789847852320588878611698999999986 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) ++++.+.| ++|.+ .++|++|..+.+.+|+.++|| |.|.|++.|-=+.+|+. T Consensus 228 n~~v~~ml---~eI~~-~~~v~~~i~~~l~~~~rl~GF-------GHrvYk~~DPRa~~l~~ 278 (377) T PRK12351 228 NEAVMEML---EEIGS-PEEAEAYLRKRLANKEKIMGF-------GHRVYKVSDPRAKILKE 278 (377) T ss_pred HHHHHHHH---HHHCC-CHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH T ss_conf 79999999---99589-257799999998558976577-------87657899936899999 No 66 >pfam04577 DUF563 Protein of unknown function (DUF563). Family of uncharacterized proteins. Probab=34.49 E-value=31 Score=14.48 Aligned_cols=31 Identities=16% Similarity=0.134 Sum_probs=23.8 Q ss_pred CCCCEECCCCCCCCCCCCHHHHHHHHHHCCCC Q ss_conf 78523205888786116989999999861651 Q gi|254780124|r 291 IQGYQLVEGRKGNRSFKDINRAQELLTSVLGE 322 (388) Q Consensus 291 ~~g~Klv~gr~~~r~~~d~~~~~~~l~~~~~~ 322 (388) =|-.=|+.=+ +.|++.|+++++.++..+|++ T Consensus 210 rPRL~iisR~-~~R~ilN~~evv~~ae~vGFe 240 (246) T pfam04577 210 KPRLLIISRR-GSRKILNEDEVVRAAEEVGFE 240 (246) T ss_pred CCEEEEEECC-CCCEECCHHHHHHHHHHCCCE T ss_conf 9869999878-962552899999999984987 No 67 >PRK13347 coproporphyrinogen III oxidase; Provisional Probab=33.91 E-value=31 Score=14.42 Aligned_cols=14 Identities=29% Similarity=0.449 Sum_probs=5.9 Q ss_pred HHEECCCCCCEECC Q ss_conf 00156789826630 Q gi|254780124|r 354 ELITRGDGKPVIAP 367 (388) Q Consensus 354 ~~i~k~~gkp~l~p 367 (388) +||+...+.-.|-| T Consensus 412 GLl~~~~~~l~lT~ 425 (453) T PRK13347 412 GLVTIDGGGIRVTP 425 (453) T ss_pred CCEEEECCEEEECH T ss_conf 98899899999997 No 68 >pfam08011 DUF1703 Protein of unknown function (DUF1703). This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus. Probab=33.34 E-value=32 Score=14.36 Aligned_cols=45 Identities=24% Similarity=0.229 Sum_probs=28.1 Q ss_pred EEEEEEEEEEE-ECCEEEEEEEECCCCCCCC---C-CCCHHHHHHHHHHH Q ss_conf 58999999998-5997999981136887674---4-66879999999999 Q gi|254780124|r 111 GATGTADILIF-NSTQWIIVDFKYGAGVPVK---A-ENNTQLMLYACGAL 155 (388) Q Consensus 111 ~~~GtiD~I~~-~dg~l~IiDyKtGk~~~v~---a-~~n~QL~lYALgA~ 155 (388) .+.|++|.++. .++...|+.+|+-+..... + +.-.|+.-|..... T Consensus 27 s~~GR~Di~l~p~~~~~~IiE~K~~~~~~~~~~~~~~Al~QI~~k~Y~~~ 76 (101) T pfam08011 27 TNKGRIDLTLKPTYTYIYIFEFKYIKVKDSDKEIAEEALEQIKEYGYAEK 76 (101) T ss_pred CCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCHHH T ss_conf 69994649999748819999999638643101568999999997674088 No 69 >TIGR01823 PabB-fungal para-aminobenzoate synthase; InterPro: IPR010117 This entry represents the fungal clade of para-aminobenzoate synthase, which acts on chorismate to form para-aminobenzoic acid (PABA), a precursor of folate.. Probab=32.90 E-value=31 Score=14.48 Aligned_cols=73 Identities=15% Similarity=0.200 Sum_probs=54.8 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCEECCCCCC Q ss_conf 8666672576445620134678763022005999999999954389999999999999999978-984785232058887 Q gi|254780124|r 224 NDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNA-GDEIQGYQLVEGRKG 302 (388) Q Consensus 224 ~g~~CrfC~~k~~Cra~a~~~l~~~~~~p~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~-G~~~~g~Klv~gr~~ 302 (388) -.++|.+=|.|++-+.-.+.+|+.|. --+.++-|++|.+--+|+|.+=+ ++-+.+ +..||-+==||-- | T Consensus 632 ~d~~~~~~PiKGTvkk~~~M~lekAr--~iL~~~KemgEnlMI~DLIRnDL-------y~l~~~~~VhVeel~sVeeh-~ 701 (851) T TIGR01823 632 RDDRLKLKPIKGTVKKEEDMSLEKAR--KILKSEKEMGENLMILDLIRNDL-------YELVKKNDVHVEELLSVEEH-A 701 (851) T ss_pred CCCCEEECCCCCEECCCCCCCHHHHH--HHHCCCCHHHHHHHHHHHHHHHH-------HHHCCCCCEECCCCCEEHHH-H T ss_conf 56722322563022107886889999--87268410467878999887538-------98607897422530000112-1 Q ss_pred CCCCC Q ss_conf 86116 Q gi|254780124|r 303 NRSFK 307 (388) Q Consensus 303 ~r~~~ 307 (388) |.|. T Consensus 702 -~VYq 705 (851) T TIGR01823 702 -RVYQ 705 (851) T ss_pred -HHEE T ss_conf -2300 No 70 >PRK06642 single-stranded DNA-binding protein; Provisional Probab=32.66 E-value=21 Score=15.54 Aligned_cols=35 Identities=14% Similarity=0.319 Sum_probs=20.1 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHH Q ss_conf 999999999999997898478523205888786116989 Q gi|254780124|r 272 SYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDIN 310 (388) Q Consensus 272 ~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~ 310 (388) -|-+...+.+..-+.+|..+ +|+||-..|.|+|.+ T Consensus 59 ~~~k~~ae~~~~yl~KG~~V----~VeG~L~~r~y~dkd 93 (152) T PRK06642 59 IFSEGLVSVVERYVTKGSKL----YIEGSLQTRKWNDNS 93 (152) T ss_pred HHHHHHHHHHHHHCCCCCEE----EEEEEEEECCCCCCC T ss_conf 63389999999865688889----996678753559899 No 71 >COG0372 GltA Citrate synthase [Energy production and conversion] Probab=32.21 E-value=33 Score=14.24 Aligned_cols=51 Identities=24% Similarity=0.376 Sum_probs=31.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHH Q ss_conf 9999999954389999999999999999978984785232058887861169899999998 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLT 317 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~ 317 (388) ++++.+.|.. +.+-.+++++|..+.+.+|+.++|| |.|.|++-|==+++++ T Consensus 235 ne~v~~ml~e---i~~~~~~~~~~v~~~l~~~~~imGF-------GHRVYk~~DPRa~~lk 285 (390) T COG0372 235 NEAVMKMLEE---IGSSGESAEAYVRKALDRKERIMGF-------GHRVYKNYDPRAKVLK 285 (390) T ss_pred HHHHHHHHHH---HCCCCHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHH T ss_conf 8999999999---6213232999999998569976788-------9776789995599999 No 72 >cd06106 ScCit3_like Saccharomyces cerevisiae (Sc) 2-methylcitrate synthase Cit3-like. 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate and CoA. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with OAA to form citrate and CoA, the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the a Probab=31.10 E-value=35 Score=14.12 Aligned_cols=56 Identities=20% Similarity=0.265 Sum_probs=34.7 Q ss_pred CHHHHHHHH-HHHHHHHHH--HHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 999999999-543899999--999999999999789847852320588878611698999999986 Q gi|254780124|r 256 TTVELSKAY-SSISLIKSY--VKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 256 ~~~e~~~~l-~~~~~l~~w--~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) -++++-+-+ ...+.|.+| .++|++|+.+.+.+|+.++|| |.|.|+..|-=+..+++ T Consensus 273 ANq~Vl~~l~~m~~~ig~~~~~e~v~~yv~~~l~~g~~i~Gf-------GHrVyk~~DPRa~~lk~ 331 (428) T cd06106 273 AAQEVLRWILEMQKNIGSKATDQDIRDYLWKTLKSGRVVPGY-------GHAVLRKPDPRFTALME 331 (428) T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCEEECC-------CEECCCCCCCHHHHHHH T ss_conf 589999999999998089876899999999854469863202-------60103579947999999 No 73 >PRK09234 fbiC FO synthase; Reviewed Probab=30.85 E-value=35 Score=14.09 Aligned_cols=19 Identities=21% Similarity=0.558 Sum_probs=12.5 Q ss_pred CCCCCCCCCCCCCCCCCCC Q ss_conf 7766788866667257644 Q gi|254780124|r 217 SLEHYGVNDDSCRFCRAKV 235 (388) Q Consensus 217 ~~~~~~~~g~~CrfC~~k~ 235 (388) +..+...+.-.|+||.|.. T Consensus 533 NINyTNVC~~~C~FCAF~r 551 (846) T PRK09234 533 NINFTNICYTGCRFCAFAQ 551 (846) T ss_pred CCCHHHHHHCCCCCCCCCC T ss_conf 7638877551797351447 No 74 >cd06110 BSuCS-II_like Bacillus subtilis (Bs) citrate synthase (CS)-II_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-II, the major CS of the gram-positive bacterium Bacillus subtilis. A mutation in the gene which encodes BsCS-II (citZ gene) has been described which resulted in a significant loss of CS activity, partial glutamate auxotrophy, and a sporulation deficiency, a Probab=30.42 E-value=36 Score=14.04 Aligned_cols=51 Identities=22% Similarity=0.310 Sum_probs=32.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 99999999543899999999999999999789847852320588878611698999999986 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) ++++.+.|..+ .+ .++|++|..+.+.+|+.+||| |.|.|++.|-=+..|+. T Consensus 219 n~~v~~ml~~i---~~-~~~v~~~i~~~l~~~~~i~GF-------GHrvY~~~DPRa~~l~~ 269 (356) T cd06110 219 NERVMKMLLEI---GS-VDNVAAYVKDKLANKEKIMGF-------GHRVYKTGDPRAKHLRE 269 (356) T ss_pred HHHHHHHHHHH---CC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH T ss_conf 99999999984---88-667999999998378988888-------87668888957999999 No 75 >TIGR01793 cit_synth_euk citrate (Si)-synthase, eukaryotic; InterPro: IPR010109 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry includes both mitochondrial and peroxisomal forms of citrate synthase. Peroxisomal forms of the enzyme, recognized by the C-terminal targeting motif SKL, act in the glyoxylate cycle. Eukaryotic homologs include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans (Emericella nidulans).; GO: 0004108 citrate (Si)-synthase activity, 0044262 cellular carbohydrate metabolic process. Probab=30.10 E-value=35 Score=14.12 Aligned_cols=50 Identities=24% Similarity=0.339 Sum_probs=30.9 Q ss_pred HHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHCCCCCCHH Q ss_conf 9999999999978984785232058887861169899999998616510000 Q gi|254780124|r 275 KACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFK 326 (388) Q Consensus 275 ~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~~~~~~~~ 326 (388) +.+|+|.=..+++|+-||||==--=|..-.+|+-+- +=+|+..=-|++|+ T Consensus 299 eqlKdy~WktLnsG~VVPGYGHaVLRkTDPRY~cQR--EFALk~LPdDplFk 348 (430) T TIGR01793 299 EQLKDYVWKTLNSGKVVPGYGHAVLRKTDPRYICQR--EFALKHLPDDPLFK 348 (430) T ss_pred HHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCHH--HHHHHCCCCCHHHH T ss_conf 678999997605895425766520268898843128--88833178961568 No 76 >COG1801 Uncharacterized conserved protein [Function unknown] Probab=29.69 E-value=37 Score=13.96 Aligned_cols=32 Identities=22% Similarity=0.248 Sum_probs=21.7 Q ss_pred CCCCCCCCHHHHHC-CCHHHHHHCCCCCCCCHH Q ss_conf 75618423677871-832388621389998988 Q gi|254780124|r 4 HAFLSASSSHRWLK-CPIAPTLESKIPQTTSIY 35 (388) Q Consensus 4 HA~LSpSs~~rwl~-CP~s~~Le~~~pd~~S~a 35 (388) +|..|+....||.. -|.-.+.+-+.|..-+-. T Consensus 47 Ya~p~~~t~~~W~~~~p~~FrFsvK~~~~iTH~ 79 (263) T COG1801 47 YAPPSPETVLRWAEETPDDFRFSVKAPRAITHQ 79 (263) T ss_pred CCCCCHHHHHHHHHHCCCCEEEEEEECCCCCCH T ss_conf 479997999999985899869999855011455 No 77 >KOG0649 consensus Probab=28.98 E-value=27 Score=14.81 Aligned_cols=25 Identities=20% Similarity=0.129 Sum_probs=18.6 Q ss_pred CCEEEEEEEECCCCCCC-CCCCCHHH Q ss_conf 99799998113688767-44668799 Q gi|254780124|r 123 STQWIIVDFKYGAGVPV-KAENNTQL 147 (388) Q Consensus 123 dg~l~IiDyKtGk~~~v-~a~~n~QL 147 (388) ||+.+|.|.||++.+.+ +...|+-+ T Consensus 177 DGtvRvWd~kt~k~v~~ie~yk~~~~ 202 (325) T KOG0649 177 DGTVRVWDTKTQKHVSMIEPYKNPNL 202 (325) T ss_pred CCCEEEEECCCCCEEEEECCCCCHHH T ss_conf 76179876265533677304457211 No 78 >PRK08207 coproporphyrinogen III oxidase; Provisional Probab=28.65 E-value=38 Score=13.85 Aligned_cols=17 Identities=29% Similarity=0.380 Sum_probs=14.2 Q ss_pred CCCCCHHHHHHHHHHHH Q ss_conf 00599999999995438 Q gi|254780124|r 252 PSTNTTVELSKAYSSIS 268 (388) Q Consensus 252 p~~l~~~e~~~~l~~~~ 268 (388) |..|+.+++..|+..+. T Consensus 238 PS~Ls~~ql~~ll~~i~ 254 (497) T PRK08207 238 PTSITAEEFEKLLEEIY 254 (497) T ss_pred CCCCCHHHHHHHHHHHH T ss_conf 00299999999999999 No 79 >TIGR01084 mutY A/G-specific adenine glycosylase; InterPro: IPR005760 The DNA repair enzyme MutY plays an important role in the prevention of DNA mutations resulting from the presence of the oxidatively damaged lesion 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxoG). 8-OxoG can mispair with 2'-deoxycytidine 5'-triphosphate or with 2'-deoxyadenosine triphosphate during DNA replication, forming C*8-oxoG and A*8-oxoG mispairs. Human MutY is responsible for recognition and removal of the inappropriately inserted adenine in an A=8-oxoG mispair. If unrepaired, the A=8-oxoG mispairs can result in deleterious C:G to A:T transversions. Multiple forms of mammalian MutY are formed by alternative splicing and locate to the nucleus or mitochondrion, where they have been shown to interact with several other proteins involved in the repair of DNA damage . The HhH-GPD domain within the protein binds the phosphate backbone of the substrate. This family represents bacterial MutY and a limited number of murine homologs. In rat, the Escherichia coli MutY DNA glycosylase homolog (MYH) is induced in response to mitochondrial DNA damage . ; GO: 0019104 DNA N-glycosylase activity, 0006284 base-excision repair, 0005622 intracellular. Probab=27.72 E-value=35 Score=14.06 Aligned_cols=38 Identities=16% Similarity=0.250 Sum_probs=24.7 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH Q ss_conf 99998577653047766788866667257644562013467876 Q gi|254780124|r 204 GTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLE 247 (388) Q Consensus 204 a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l~~ 247 (388) .+.+++.-|..+. +....|.-||....|-|..+.+-.. T Consensus 191 nqalmDlGA~iC~------rk~P~C~~CPl~~~C~A~~~~~~~~ 228 (297) T TIGR01084 191 NQALMDLGALICT------RKKPKCDLCPLQDFCLAYKQGTPEE 228 (297) T ss_pred HHHHHHCCCCCCC------CCCCCCCCCCHHHHHHHHHCCCHHH T ss_conf 8899862361037------8478545487066555654277111 No 80 >pfam09856 DUF2083 Predicted transcriptional regulator (DUF2083). This domain is found in various prokaryotic transcriptional regulatory proteins belonging to the XRE family. Its exact function is, as yet, unknown. Probab=27.04 E-value=34 Score=14.14 Aligned_cols=24 Identities=25% Similarity=0.528 Sum_probs=18.5 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHH Q ss_conf 7888666672576445620134678 Q gi|254780124|r 221 YGVNDDSCRFCRAKVRCPALSRHVL 245 (388) Q Consensus 221 ~~~~g~~CrfC~~k~~Cra~a~~~l 245 (388) ..+-|-.||-|+ +.-|++||+--+ T Consensus 117 ~~pIG~sCRiC~-R~~C~qRa~Ppi 140 (156) T pfam09856 117 ATPIGVGCRLCE-RADCPQRAFPPL 140 (156) T ss_pred CCCCCCCCCCCC-CCCCCHHCCCCC T ss_conf 562137411469-889733218988 No 81 >PRK13627 carnitine operon protein CaiE; Provisional Probab=26.84 E-value=28 Score=14.73 Aligned_cols=21 Identities=19% Similarity=0.181 Sum_probs=11.2 Q ss_pred HHHEECCCCCCEECCCCCCCH Q ss_conf 300156789826630788620 Q gi|254780124|r 353 QELITRGDGKPVIAPRDIPTN 373 (388) Q Consensus 353 ~~~i~k~~gkp~l~p~~d~~~ 373 (388) .+|-+..++.|.|-..++.+| T Consensus 174 ~Pl~~~e~~r~~~~~~~~~~p 194 (196) T PRK13627 174 QPLTQMEENRPRLQGTTDVTP 194 (196) T ss_pred CCCCCCCCCCCCCCCCCCCCC T ss_conf 886446799863357656687 No 82 >COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair] Probab=25.99 E-value=42 Score=13.54 Aligned_cols=37 Identities=27% Similarity=0.280 Sum_probs=19.4 Q ss_pred EEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHH Q ss_conf 9999999985-997999981136887674466879999999 Q gi|254780124|r 113 TGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYAC 152 (388) Q Consensus 113 ~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYAL 152 (388) .|.+|.+-++ +|...||.+|-++.-+ +|. .||.=|-. T Consensus 160 ~G~vDilg~De~G~~viiElKR~ka~~-~Av--~QL~RYv~ 197 (253) T COG1637 160 IGKVDILGRDERGNIVIIELKRRKAGL-SAV--SQLKRYVE 197 (253) T ss_pred CCEEEEEEECCCCCEEEEEEECCCCCC-HHH--HHHHHHHH T ss_conf 425679988689999999994254771-089--99999999 No 83 >cd06115 AthCS_per_like Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains three Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3 which are involved in the glyoxylate cycle. AthCYS1, in addition to a peroxisomal targeting sequence, has a predicted secretory signal peptide; it may be targeted to both the secretory pathway and the peroxisomes and is thought to be located in the extracellular matrix. AthCSY1 is expr Probab=25.08 E-value=44 Score=13.43 Aligned_cols=52 Identities=13% Similarity=0.279 Sum_probs=34.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHC Q ss_conf 999999995438999999999999999997898478523205888786116989999999861 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSV 319 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~ 319 (388) ++++.+.|. .|.+ .++|++|..+.+.+|+.++|| |.|.|+..|-=+..|+.. T Consensus 258 ne~v~~ml~---ei~s-~~~v~~~i~~~l~~~~rimGf-------GHrVYk~~DPRa~ilk~~ 309 (410) T cd06115 258 NEAVLRMLA---EIGT-VENIPAFIEGVKNRKRKLSGF-------GHRVYKNYDPRAKIIKKL 309 (410) T ss_pred HHHHHHHHH---HHCC-HHHHHHHHHHHHCCCCCCCCC-------CCCCCCCCCCHHHHHHHH T ss_conf 899999999---9647-223799999987167876778-------987688888277999999 No 84 >PRK08173 DNA topoisomerase III; Validated Probab=24.45 E-value=45 Score=13.36 Aligned_cols=32 Identities=13% Similarity=0.205 Sum_probs=23.6 Q ss_pred HCCCCHHHHHHHHHHCCCCHHHHHHHHHHEECCCCCC Q ss_conf 0138988999974000242678987530015678982 Q gi|254780124|r 327 RILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKP 363 (388) Q Consensus 327 ~~l~~~~~~ek~~~~~~~~~~~~~~l~~~i~k~~gkp 363 (388) .+.||+.||.||+.+.+ -++|.+|+-+..|+| T Consensus 766 ~k~i~~~~~~kLl~~gk-----T~li~gF~S~k~gr~ 797 (857) T PRK08173 766 QQEISREQMAKLLTDGK-----TDLLPGFKSSRTGRN 797 (857) T ss_pred CCCCCHHHHHHHHHCCC-----CCHHCCCEECCCCCC T ss_conf 98789999999997599-----103203343778996 No 85 >cd06118 citrate_synt_like_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and Probab=24.43 E-value=45 Score=13.36 Aligned_cols=46 Identities=22% Similarity=0.419 Sum_probs=30.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 543899999999999999999789847852320588878611698999999986 Q gi|254780124|r 265 SSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 265 ~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) ...+.+.+ .++++++..+.+.+|+.++|| |.|.|++.|-=+.+|+. T Consensus 224 ~~l~~i~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~l~~ 269 (358) T cd06118 224 KMLLEIGT-PENVEAYIWKKLANKRRIMGF-------GHRVYKTYDPRAKILKE 269 (358) T ss_pred HHHHHHCC-HHHHHHHHHHHHCCCCCCCCC-------CCCCCCCCCCHHHHHHH T ss_conf 99999688-565899999974046777787-------87657889955899999 No 86 >pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown. Probab=24.40 E-value=45 Score=13.35 Aligned_cols=59 Identities=19% Similarity=0.241 Sum_probs=37.4 Q ss_pred EEEEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEC Q ss_conf 589999999985-9979999811368876744668799999999998438356765138999998304 Q gi|254780124|r 111 GATGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRV 177 (388) Q Consensus 111 ~~~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~ 177 (388) .-.|.+|.+-++ +|.+.||..|--++ +.+.-.||.=|--...+. +. ...|+..+.-|.. T Consensus 133 T~~G~VDil~~D~~G~~VvVEvKRr~a---~idaV~QL~RYve~l~rd----~~-~~~VRGIlvAp~I 192 (228) T pfam01939 133 IAHGIVDILGKDEDGNIVILELKRRKA---DLHAVSQLKRYVDSLKED----YV-EAKVRGVLVAPSI 192 (228) T ss_pred CCCCCEEEEEECCCCCEEEEEEEEECC---CHHHHHHHHHHHHHHHHC----CC-CCCCEEEEECCCC T ss_conf 588736689987999999999974037---820799999999998655----48-8860399999858 No 87 >KOG2457 consensus Probab=23.50 E-value=27 Score=14.87 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=18.5 Q ss_pred CCCCCCCCCCCCCCCCCHHH--HHH Q ss_conf 88866667257644562013--467 Q gi|254780124|r 222 GVNDDSCRFCRAKVRCPALS--RHV 244 (388) Q Consensus 222 ~~~g~~CrfC~~k~~Cra~a--~~~ 244 (388) +|....|.-||..++|||+. |.| T Consensus 290 Tpq~P~CS~CPvss~CrA~q~~Eqn 314 (555) T KOG2457 290 TPQKPSCSSCPVSSQCRAFQLSEQN 314 (555) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHC T ss_conf 5799876778728899887676423 No 88 >TIGR01311 glycerol_kin glycerol kinase; InterPro: IPR005999 Glycerol kinase (2.7.1.30 from EC) is a bacterial sugar kinase which catalyzes the Mg-ATP-dependent phosphorylation of glycerol to yield glycerol 3-phosphate. The enzyme from Escherichia coli is an allosteric regulatory enzyme whose activity is inhibited by fructose 1,6-bisphosphate (FBP) and the glucose-specific phosphocarrier of the phosphoenolpyruvate:glycose phosphotransferase system, IIA(Glc), structural studies suggest a nucleophilic in-line transfer mechanism for the ATP-dependent phosphorylation of glycerol by glycerol kinase .; GO: 0004370 glycerol kinase activity, 0006072 glycerol-3-phosphate metabolic process. Probab=23.35 E-value=19 Score=15.90 Aligned_cols=37 Identities=19% Similarity=0.123 Sum_probs=22.7 Q ss_pred EEEEEEEEEEEE---ECC---EEEEEEEECCCCC-----CCCCCCCHHH Q ss_conf 058999999998---599---7999981136887-----6744668799 Q gi|254780124|r 110 PGATGTADILIF---NST---QWIIVDFKYGAGV-----PVKAENNTQL 147 (388) Q Consensus 110 ~~~~GtiD~I~~---~dg---~l~IiDyKtGk~~-----~v~a~~n~QL 147 (388) --+|||||.-++ .+| ..||.|+ |.-+. ...-+.+.+| T Consensus 163 ~LlFGTiDTWL~WnLTGG~nG~~HvTDv-tNASRT~LfNl~tl~WD~eL 210 (518) T TIGR01311 163 ELLFGTIDTWLIWNLTGGVNGKVHVTDV-TNASRTMLFNLHTLEWDDEL 210 (518) T ss_pred CCEECCCHHHHHHHHCCCCCCCEEECCC-CCHHHHHHCCCHHHHHHHHH T ss_conf 8433250246675315897886553378-61468764140121000899 No 89 >TIGR00770 Dcu transporter, anaerobic C4-dicarboxylate uptake (Dcu) family; InterPro: IPR004668 These proteins are members of the C4-Dicarboxylate Uptake (Dcu) family. Most proteins in this family are predicted to have 12 GES predicted transmembrane regions; however the one member whose membrane topology has been experimentally determined has 10 transmembrane regions, with both the N- and C-termini localized to the periplasm . The DcuA and DcuB proteins are involved in the transport of aspartate, malate, fumarate and succinate in many species , , , and are thought to function as antiporters with any two of these substrates. Since DcuA is encoded in an operon with the gene for aspartase, and DcuB is encoded in an operon with the gene for fumarase, their physiological functions may be to catalyze aspartate:fumarate and fumarate:malate exchange during the anaerobic utilization of aspartate and fumarate, respectively . The Escherichia coli DcuA and DcuB proteins have very different expression patterns . DcuA is constitutively expressed; DcuB is strongly induced anaerobically by FNR and C4-dicarboxylates, while it is repressed by nitrate and subject to CRP-mediated catabolite repression.; GO: 0015556 C4-dicarboxylate transmembrane transporter activity, 0015740 C4-dicarboxylate transport, 0016021 integral to membrane. Probab=23.15 E-value=29 Score=14.64 Aligned_cols=11 Identities=9% Similarity=0.175 Sum_probs=5.5 Q ss_pred HHHHHHHCCCC Q ss_conf 99999724576 Q gi|254780124|r 45 LLAHCLEQGVD 55 (388) Q Consensus 45 llE~~l~~~l~ 55 (388) ++|.+||+.-+ T Consensus 72 iAEKlLRrnPK 82 (447) T TIGR00770 72 IAEKLLRRNPK 82 (447) T ss_pred HHHHHHCCCCC T ss_conf 99897416997 No 90 >COG2810 Predicted type IV restriction endonuclease [Defense mechanisms] Probab=22.88 E-value=48 Score=13.16 Aligned_cols=73 Identities=21% Similarity=0.206 Sum_probs=41.0 Q ss_pred HHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECC-EEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC Q ss_conf 9998503787368877553200044058999999998599-799998113688767446687999999999984383567 Q gi|254780124|r 85 LAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNST-QWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFG 163 (388) Q Consensus 85 ~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg-~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~ 163 (388) +.+..+..++.----||+=+... .-|++|...+.|| ....+.-|.+. ...+.+.-|+.-||.-.-..++...+ T Consensus 32 lp~L~slGwdi~nPkEV~PEe~t----~~GraDyalikd~kvfafieak~ls--~~~akd~qq~~~Yav~~Gv~~~iVtn 105 (284) T COG2810 32 LPFLSSLGWDIDNPKEVRPEEKT----EEGRADYALIKDGKVFAFIEAKNLS--VNPAKDVQQLAKYAVDKGVEVGIVTN 105 (284) T ss_pred HHHHHHCCCCCCCCCCCCCCCCC----CCCCCCEEEEECCCEEEEEECCCCC--CCCHHHHHHHHHHHHHCCCEEEEEEC T ss_conf 99999707778990205864245----5576544888569389987211347--57268999999998852837999967 No 91 >KOG3300 consensus Probab=22.40 E-value=50 Score=13.10 Aligned_cols=33 Identities=6% Similarity=0.183 Sum_probs=23.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCC Q ss_conf 389999999999999999978984785232058 Q gi|254780124|r 267 ISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEG 299 (388) Q Consensus 267 ~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~g 299 (388) +..=..|++.++.+...++.-=+.|||||+=|- T Consensus 80 AErDr~~l~~lrkn~eeEaeiMKdVPgWkvGEp 112 (146) T KOG3300 80 AERDRRFLSELRKNLEEEAEIMKDVPGWKVGEP 112 (146) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 887799999999868889999704998623765 No 92 >cd06111 DsCS_like Cold-active citrate synthase (CS) from an Antarctic bacterial strain DS2-3R (Ds)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. DsCS, compared with CS from the hyperthermophile Pyrococcus furiosus (not included in this group), has an increase in the size of surface loops, a higher proline content in the loop regions, a more accessible active site, and a highe Probab=22.18 E-value=50 Score=13.07 Aligned_cols=50 Identities=14% Similarity=0.251 Sum_probs=31.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHH Q ss_conf 9999999954389999999999999999978984785232058887861169899999998 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLT 317 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~ 317 (388) ++.+.+.| +++.+ .+++++|..+.+.+|+.++|| |.|.|++.|-=+..|+ T Consensus 219 n~~v~~ml---~ei~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~l~ 268 (362) T cd06111 219 NEAVMHMM---LEIDD-PEKAAQWMLDALARKEKVMGF-------GHRVYKSGDSRVPTME 268 (362) T ss_pred HHHHHHHH---HHHCC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCCHHHHH T ss_conf 89999999---98378-122699999998468877888-------8755778895059999 No 93 >TIGR02187 GlrX_arch Glutaredoxin-like domain protein; InterPro: IPR011903 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.. Probab=21.98 E-value=32 Score=14.32 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=11.7 Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 6666725764456201346787630 Q gi|254780124|r 225 DDSCRFCRAKVRCPALSRHVLLEAT 249 (388) Q Consensus 225 g~~CrfC~~k~~Cra~a~~~l~~~~ 249 (388) ...|-|||... +.-|+++++. T Consensus 156 TPtCPYCP~AV----~mAH~fA~~~ 176 (237) T TIGR02187 156 TPTCPYCPRAV----LMAHKFALAN 176 (237) T ss_pred ECCCCCHHHHH----HHHHHHHHHC T ss_conf 56899725799----9999999835 No 94 >COG3894 Uncharacterized metal-binding protein [General function prediction only] Probab=21.89 E-value=27 Score=14.84 Aligned_cols=24 Identities=33% Similarity=0.331 Sum_probs=19.0 Q ss_pred EEEEEEEECCCCCCCCCCCCHHHH Q ss_conf 799998113688767446687999 Q gi|254780124|r 125 QWIIVDFKYGAGVPVKAENNTQLM 148 (388) Q Consensus 125 ~l~IiDyKtGk~~~v~a~~n~QL~ 148 (388) ..++||+|+|+-+.+.-..|+|++ T Consensus 177 ~aqlVDL~sgevv~t~~T~n~ql~ 200 (614) T COG3894 177 RAQLVDLKSGEVVATVITSNPQLP 200 (614) T ss_pred EEEEEECCCCCEEEEEECCCCCCC T ss_conf 257875167867886522589877 No 95 >PRK04247 hypothetical protein; Provisional Probab=21.56 E-value=51 Score=12.99 Aligned_cols=56 Identities=16% Similarity=0.204 Sum_probs=29.8 Q ss_pred EEEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEE Q ss_conf 89999999985-997999981136887674466879999999999843835676513899999830 Q gi|254780124|r 112 ATGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPR 176 (388) Q Consensus 112 ~~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr 176 (388) -.|.+|.+-++ +|.+.||..|-.++- .+.-.||.=|--...... ...|+..+.-|. T Consensus 158 ~~G~VDil~~D~~G~~V~VEvKR~ra~---idaV~QL~RYve~l~~~~------~~~VRGIlvAp~ 214 (250) T PRK04247 158 PAGIIDILGRDKEGNLVVLELKRRRAG---LSAVSQLKRYVEAYREEL------GAKVRGILVAPS 214 (250) T ss_pred CCCCEEEEEECCCCCEEEEEEEECCCC---CCHHHHHHHHHHHHHHHC------CCCCEEEEECCC T ss_conf 988464899879989999999713378---147999999999987636------998219999885 No 96 >cd06100 CCL_ACL-C Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CC Probab=21.51 E-value=52 Score=12.99 Aligned_cols=56 Identities=13% Similarity=0.111 Sum_probs=31.2 Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHC Q ss_conf 999999995438-999999999999999997898478523205888786116989999999861 Q gi|254780124|r 257 TVELSKAYSSIS-LIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSV 319 (388) Q Consensus 257 ~~e~~~~l~~~~-~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~ 319 (388) ++...+.+..+. .-.....++..++.+....|+.+||| | .|.|++.|--...|++. T Consensus 84 ~e~~~~ml~~~~~~~~~~~~~~~~~v~~~~~~~~~ipGf----G---H~vyk~~DPRa~~L~~~ 140 (227) T cd06100 84 GEGAARLFKEAVDSGDALDAAAAEFVAEYRAAKKRIPGF----G---HPVHKNPDPRVPRLLEL 140 (227) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCC----C---CCCCCCCCCHHHHHHHH T ss_conf 699999999998647762889999999998659977788----9---88799999459999999 No 97 >cd06103 ScCS-like Saccharomyces cerevisiae (Sc) citrate synthase (CS)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homo Probab=21.24 E-value=52 Score=12.95 Aligned_cols=55 Identities=16% Similarity=0.247 Sum_probs=33.4 Q ss_pred HHHHHHHHHHH-HHHHH--HHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH Q ss_conf 99999999543-89999--9999999999999789847852320588878611698999999986 Q gi|254780124|r 257 TVELSKAYSSI-SLIKS--YVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS 318 (388) Q Consensus 257 ~~e~~~~l~~~-~~l~~--w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~ 318 (388) ++++-+.|..+ +.+-. -.+.|++|+.+.+.+|+.++|| |.|.|+..|-=+..+++ T Consensus 274 Ne~Vl~ml~~i~~~~g~~~s~e~v~~~v~~~l~~~~~imGf-------GHrVYk~~DPRa~ilk~ 331 (426) T cd06103 274 NQEVLKWLLKMQKELGKDVSDEELEKYIWDTLNSGRVVPGY-------GHAVLRKTDPRFTCQRE 331 (426) T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH T ss_conf 89999999999987288888899999999987169943267-------87657789946999999 No 98 >PRK12350 citrate synthase 2; Provisional Probab=21.12 E-value=53 Score=12.93 Aligned_cols=52 Identities=13% Similarity=0.302 Sum_probs=33.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHC Q ss_conf 999999995438999999999999999997898478523205888786116989999999861 Q gi|254780124|r 257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSV 319 (388) Q Consensus 257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~ 319 (388) ++.+.+.|..+ .+ .++++++..+.+..|+.++|| |.|.|++.|-=+.+|+.. T Consensus 206 ne~v~~ml~~i---~~-~~~~~~~i~~~l~~~~rimGF-------GHrVYk~~DPRa~~lk~~ 257 (352) T PRK12350 206 PGRVLPMLDAI---ER-TGDARGWVKGALDRGERLMGF-------GHRVYRAEDPRARVLRAA 257 (352) T ss_pred HHHHHHHHHHH---CC-CCCHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHHH T ss_conf 99999999984---67-002899999998536765567-------887788899358999999 No 99 >PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional Probab=20.45 E-value=54 Score=12.84 Aligned_cols=19 Identities=11% Similarity=0.401 Sum_probs=8.5 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 3899999999999999999 Q gi|254780124|r 267 ISLIKSYVKACEDEMFKRL 285 (388) Q Consensus 267 ~~~l~~w~~~v~~~a~~~~ 285 (388) +++|....+.|-+.+++++ T Consensus 47 IPElReRik~vAe~~~~~v 65 (185) T PRK04424 47 IPELRERIKHVAEKNYDKV 65 (185) T ss_pred CHHHHHHHHHHHHHHHHHH T ss_conf 8789999999999747640 No 100 >pfam05813 Orthopox_F7 Orthopoxvirus F7 protein. Probab=20.01 E-value=33 Score=14.24 Aligned_cols=14 Identities=43% Similarity=0.914 Sum_probs=7.2 Q ss_pred CCC-CCCCCCCCCCH Q ss_conf 666-72576445620 Q gi|254780124|r 226 DSC-RFCRAKVRCPA 239 (388) Q Consensus 226 ~~C-rfC~~k~~Cra 239 (388) +.| |||++|.--.- T Consensus 7 sccgrfcdaknknk~ 21 (82) T pfam05813 7 SCCGRFCDAKNKNKN 21 (82) T ss_pred CHHHHHCCCCCCCCC T ss_conf 222102033333532 Done!