RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780456|ref|YP_003064869.1| 30S ribosomal protein S1 [Candidatus Liberibacter asiaticus str. psy62] (576 letters) >gnl|CDD|180520 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed. Length = 565 Score = 792 bits (2049), Expect = 0.0 Identities = 309/565 (54%), Positives = 410/565 (72%), Gaps = 5/565 (0%) Query: 1 MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFM 60 N E FA L EES + + E + KG VV ++KD V+VDVGLK EGRIP EF Sbjct: 5 AQNQNDMEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFK 64 Query: 61 GKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFN 120 + +KVGDEVEVYVER E+ FGE V SR+KA R W+K+E F GE +EGVI Sbjct: 65 NEQGELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVING 124 Query: 121 QVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL 180 +VKGG TVDLNG AFLP SQ+D+RPVRD PL + F+++K+DK+R NIVVSRRAVL Sbjct: 125 KVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRNNIVVSRRAVL 184 Query: 181 EESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKV 240 EE RAE+R E+++ LEEGQV+EG VKNITDYG FVDL GVDGLLH+TDI+W R+ HPS+V Sbjct: 185 EEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSEV 244 Query: 241 LSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFV 300 +++G +VKVK+++ ++E R+SLG+KQL ++PW+ ++ KY GSKV G VTN+TDYG FV Sbjct: 245 VNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFV 304 Query: 301 ELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPW 360 EL+ GIEGL H+S++SWTKKN HPSK++SVGQ+VEV++LE++ ++RISLGLKQ NPW Sbjct: 305 ELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPW 364 Query: 361 EEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDI 420 EEF++ +P G VEG+VKN TDFG F+GL+ +DG++HLSD+ W++ GE+ + Y KGD Sbjct: 365 EEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDE 424 Query: 421 VKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLID 480 V+AVVL +DV KERISLG+KQL + + +K +V+ V V + G V L D Sbjct: 425 VEAVVLKVDVEKERISLGIKQLEEDPFE--EFAKKHKKGSIVTGTVTEVKDKGAFVELED 482 Query: 481 HKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGA 540 G+ IR S+LSRDRV+ G V+A V+N+ +K+ ++SLSIKAL+ AEEK A Sbjct: 483 --GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEA 540 Query: 541 VAQFGS-SDSGASLGDILGMALKNR 564 +A++ S SDS +LGD+L ALK + Sbjct: 541 IAEYNSASDSKTTLGDLLKAALKGK 565 >gnl|CDD|162009 TIGR00717, rpsA, ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. Length = 516 Score = 538 bits (1387), Expect = e-153 Identities = 259/522 (49%), Positives = 364/522 (69%), Gaps = 6/522 (1%) Query: 9 EDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPI 68 E FA LLEES ++ + KG VV + KDTV VDVGLK EGRIP+ EF I Sbjct: 1 ESFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEF--LDAPLEI 58 Query: 69 KVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTV 128 +VGDEVEVY++R E+ FGE V SR+KA R +W K+E + G +EG I +VKGG V Sbjct: 59 QVGDEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIV 118 Query: 129 DLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQR 188 DLNG AFLP SQ+D++P++D+ L+ + F+I+K+D++R NIVVSRRA LEE R++ R Sbjct: 119 DLNGVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAR 178 Query: 189 SEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVK 248 E+++ L+EG V++G VKNITD+G FVDL GVDGLLH+TD++W R+ HPS+ + +GQ+VK Sbjct: 179 EELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVK 238 Query: 249 VKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEG 308 VK+I+ ++E RISL +KQL ++PW+ ++ K+ G K++G VTNLTDYGVFVE++ GIEG Sbjct: 239 VKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEG 298 Query: 309 LAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHP 368 L H+S++SW KKN HPSK++ G +VEV+IL+++P R+R+SLGLKQ NPWE+F + HP Sbjct: 299 LVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHP 358 Query: 369 PGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDI 428 G V G++K TDFG F+ L+ +DG+IHLSD+ W++ G + Y KGD ++AVVL + Sbjct: 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAV 418 Query: 429 DVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFI 488 D K+RISLGVKQL+ + + + + VV +V + + G V L G+ I Sbjct: 419 DKEKKRISLGVKQLTENPWEKF--AAKYKVGSVVKGKVTEIKDFGAFVELPG--GVEGLI 474 Query: 489 RRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 R S+LS +R + G V+A VV++ KK+ KVSLS+K Sbjct: 475 RNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516 Score = 202 bits (515), Expect = 2e-52 Identities = 125/425 (29%), Positives = 222/425 (52%), Gaps = 23/425 (5%) Query: 121 QVKGGMTVDLNGEVAFL-----PRSQIDIRPVRDVTPLMHEPQLFE--ILKMDKRRGNIV 173 + G V +N + F+ +I D + E + +++ R G V Sbjct: 20 SIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQVGDEVEVYLDRVEDRFGETV 79 Query: 174 VSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHR 233 +SR + R E ++ + EEG ++EG + G VDL+GV+ L + + Sbjct: 80 LSRE---KAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDVKP 136 Query: 234 ILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQL----EKNPWDDVQDKYVEGSKVSGV 289 I + IG+ +K KII+++Q+ + I + + +++ + EG V GV Sbjct: 137 IKDLDSL--IGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGV 194 Query: 290 VTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRIS 349 V N+TD+G FV+L G++GL HI+ +SW K+ HPS+ + VGQ+V+V +++ + + RIS Sbjct: 195 VKNITDFGAFVDL-GGVDGLLHITDMSW-KRVKHPSEYVKVGQEVKVKVIKFDKEKGRIS 252 Query: 350 LGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGE 409 L LKQ +PWE K P G ++ G V N TD+G+F+ ++E ++G++H+S++ W + Sbjct: 253 LSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNS 312 Query: 410 KVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISV 469 KGD V+ ++LDID + R+SLG+KQ + + + D V+ ++ + Sbjct: 313 HPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHP--VGDRVTGKIKKI 370 Query: 470 SEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGR-FSKGQIVDACVVNVSKKDGKVSLS 528 ++ G V L GI+ I SD+S D+ ++ + KG ++A V+ V K+ ++SL Sbjct: 371 TDFGAFVELEG--GIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLG 428 Query: 529 IKALE 533 +K L Sbjct: 429 VKQLT 433 Score = 45.5 bits (108), Expect = 4e-05 Identities = 57/260 (21%), Positives = 108/260 (41%), Gaps = 26/260 (10%) Query: 282 EGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEV 341 GS V G V + VFV++ EG + + + VG +VEV + V Sbjct: 18 PGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEF------LDAPLEIQVGDEVEVYLDRV 71 Query: 342 NPARKRISLGLKQAL-INPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGM---- 396 L ++A W + K++ G+ VEG++ K G + L+G+ Sbjct: 72 EDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIV----DLNGVEAFL 127 Query: 397 -IHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQL--SGSAPDVVDSV 453 D+ + + +I G +K ++ +D + I + + + + + Sbjct: 128 PGSQVDVKPIKDLDSLI-----GKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELL 182 Query: 454 SSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDA 513 +L++ DVV V ++++ G +D G++ + +D+S RV GQ V Sbjct: 183 ENLKEGDVVKGVVKNITDFGA---FVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKV 239 Query: 514 CVVNVSKKDGKVSLSIKALE 533 V+ K+ G++SLS+K L Sbjct: 240 KVIKFDKEKGRISLSLKQLG 259 >gnl|CDD|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed. Length = 647 Score = 344 bits (884), Expect = 5e-95 Identities = 145/344 (42%), Positives = 218/344 (63%), Gaps = 5/344 (1%) Query: 29 VTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTP---IKVGDEVEVYVERTENSF 85 + KG VV + ++ V VDVG K EG IP RE + +KVGDE+EV V + E+ Sbjct: 305 IVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDED 364 Query: 86 GEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIR 145 G V S+ +A RE W+++E F GE ++G + VKGG+ VD G AFLP S +++ Sbjct: 365 GYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELG 424 Query: 146 PVRDVTPLMHEPQLFEILKMD-KRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGT 204 V D++ + +I++ + KRR +V+SR+A+LEE + +++ E LEEG V+EG Sbjct: 425 YVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGE 484 Query: 205 VKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLG 264 VK +TD+G FVD+ GVDGLLHV++I+W R+ PS VL +G ++KV I+ I++E ++SL Sbjct: 485 VKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS 544 Query: 265 MKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHP 324 +K+L +PW++V++KY GS V G V + +G FVEL+ G++GL HISQISW K+ P Sbjct: 545 LKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISW-KRIDKP 603 Query: 325 SKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHP 368 +LS G++V+ ILEV+P KRI L +K+ P + Sbjct: 604 EDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPGDIEKVELE 647 Score = 182 bits (464), Expect = 2e-46 Identities = 106/368 (28%), Positives = 196/368 (53%), Gaps = 32/368 (8%) Query: 101 WEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEV-AFLPRSQIDIRPVRDVTPLMHEPQL 159 ++E + R G+ ++G + + + + VD+ + +P ++ + + + + Sbjct: 293 MNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDE 352 Query: 160 FE--ILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDL 217 E +LK++ G +V+S++ E + E+ + E G+ ++G VK + G+ VD Sbjct: 353 IEVKVLKLEDEDGYVVLSKKEADRE---KAWKELEEAFENGEPVKGKVKEVVKGGLLVDY 409 Query: 218 SGVDGLLHVTDIAWHRILHPSKVLS--IGQQVKVKIIRINQETHR-ISLGMKQL------ 268 GV L A H L + LS GQ+++VKII N++ + + L K + Sbjct: 410 GGVRAFLP----ASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKE 465 Query: 269 --EKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSK 326 ++ W+ ++ EG V G V LTD+G FV++ G++GL H+S+ISW + PS Sbjct: 466 KKKEETWNSLE----EGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISWGR-VEKPSD 519 Query: 327 ILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLF 386 +L VG +++V IL+++ K++SL LK+ L +PWE + +P G+ V G+V FG F Sbjct: 520 VLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAF 579 Query: 387 IGLDEHLDGMIHLSDLDWNR--PGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSG 444 + L+ +DG++H+S + W R E V++E G+ VKA +L++D ++RI L +K++ Sbjct: 580 VELEPGVDGLVHISQISWKRIDKPEDVLSE---GEEVKAKILEVDPEEKRIRLSIKEVEE 636 Query: 445 SAPDVVDS 452 D+ Sbjct: 637 EPGDIEKV 644 Score = 150 bits (382), Expect = 7e-37 Identities = 99/370 (26%), Positives = 191/370 (51%), Gaps = 25/370 (6%) Query: 181 EESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSG-VDGLLHVTDIAWHRILHPSK 239 E + E +E+ +++ G +++GTV ++ + VFVD+ +G++ + ++ I + Sbjct: 286 ENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKE 345 Query: 240 VLSIGQQVKVKIIRINQETHRISLGMKQLE-KNPWDDVQDKYVEGSKVSGVVTNLTDYGV 298 + +G +++VK++++ E + L K+ + + W ++++ + G V G V + G+ Sbjct: 346 SVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGL 405 Query: 299 FVELQSGIEGLAHISQISWTKKNIHPSKILS--VGQQVEVVILEVNPARKRISLGLKQAL 356 V+ G+ S + + + LS GQ++EV I+E N R++ + ++A+ Sbjct: 406 LVDY-GGVRAFLPASHVE-----LGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAI 459 Query: 357 INPW-----EEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKV 411 + EE S G VEGEVK TDFG F+ + +DG++H+S++ W R EK Sbjct: 460 LEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRV-EKP 517 Query: 412 IAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRK-NDVVSCEVISVS 470 GD +K +LDID +++SL +K+L PD ++V +V +V+ ++ Sbjct: 518 SDVLKVGDEIKVYILDIDKENKKLSLSLKKLL---PDPWENVEEKYPVGSIVLGKVVRIA 574 Query: 471 EGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIK 530 G V L G++ + S +S R+D+ S+G+ V A ++ V ++ ++ LSIK Sbjct: 575 PFGAFVEL--EPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632 Query: 531 ALEIAEEKGA 540 E+ EE G Sbjct: 633 --EVEEEPGD 640 Score = 64.2 bits (157), Expect = 9e-11 Identities = 63/312 (20%), Positives = 140/312 (44%), Gaps = 45/312 (14%) Query: 250 KIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGL 309 ++I+ E + + + ++++ + G V G V ++ + VFV++ EG+ Sbjct: 270 EVIKKMSELDNMEEVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGV 329 Query: 310 AHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQA-LINPWEEFSKSHP 368 + +++ + + + VG ++EV +L++ + L K+A W+E ++ Sbjct: 330 IPLRELTL-DEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFE 388 Query: 369 PGTEVEGEVKNKTDFGLFIGLDE--------HLDGMIHLSDLDWNRPGEKVIAEYAKGDI 420 G V+G+VK GL + H++ + ++ DL EY KG Sbjct: 389 NGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVE-LGYVEDLS----------EY-KGQE 436 Query: 421 VKAVVLDIDVGKERISLGVKQLSGSAPDVVDSV---------SSLRKNDVVSCEVISVSE 471 ++ +++ + + K++ S +++ +SL + DVV EV +++ Sbjct: 437 LEVKIIEFNRKRR------KKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTD 490 Query: 472 GGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKA 531 G + +D G++ + S++S RV++ G + ++++ K++ K+SLS+K Sbjct: 491 FG---AFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547 Query: 532 L-----EIAEEK 538 L E EEK Sbjct: 548 LLPDPWENVEEK 559 >gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed. Length = 390 Score = 328 bits (844), Expect = 2e-90 Identities = 149/361 (41%), Positives = 220/361 (60%), Gaps = 8/361 (2%) Query: 11 FATLLEESFTK-KDLAENCVTKGIVVGLEKDTVVVDV-GLKFEGRIPRREFMGKGQYTP- 67 EES K++ V G V+ +E V V++ G K EG IP E Sbjct: 1 MMEEFEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDIN 60 Query: 68 --IKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGG 125 +KVGDE+EVYV + E+ G + S+ + E W+K+E KF GE +E + VKGG Sbjct: 61 DVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGG 120 Query: 126 MTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRA 185 + VD+ G F+P S I R V D + + +I+++D + +++SRRAV+EE RA Sbjct: 121 LVVDVEGVRGFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERA 180 Query: 186 EQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQ 245 ++ E++ L+EG V+EGTV +TD+G FVD+ GVDGL+H+++++ R+ PS+V+S+GQ Sbjct: 181 AKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQ 240 Query: 246 QVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSG 305 +V+VK++ I+ ET RISL +K PW+ V++K EG + G V LTD+G FVE+ G Sbjct: 241 EVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPG 300 Query: 306 IEGLAHISQISWTKKNI-HPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFS 364 +EGL HISQIS K+I PS++L GQ+V+V +LEVN KRISL +K P EE Sbjct: 301 VEGLVHISQISH--KHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEED 358 Query: 365 K 365 + Sbjct: 359 R 359 Score = 181 bits (461), Expect = 5e-46 Identities = 97/289 (33%), Positives = 164/289 (56%), Gaps = 18/289 (6%) Query: 162 ILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVD 221 +LK++ GN+++S+R + E + ++ +K EEG+V+E V + G+ VD+ GV Sbjct: 73 VLKVEDGEGNLLLSKRRLEAE---KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVR 129 Query: 222 GLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEK----NPWDDVQ 277 G + + I+ + S G+ ++VKII ++ E +R+ L + + + +++ Sbjct: 130 GFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELL 187 Query: 278 DKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVV 337 EG V G V LTD+G FV++ G++GL HIS++S + PS+++SVGQ+VEV Sbjct: 188 SSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVE-KPSEVVSVGQEVEVK 245 Query: 338 ILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMI 397 +L ++ +RISL LK L PWE + P G +EG VK TDFG F+ + ++G++ Sbjct: 246 VLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLV 305 Query: 398 HLSDLDWNR---PGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLS 443 H+S + P E V+ E G VK VL+++ ++RISL +K L Sbjct: 306 HISQISHKHIATPSE-VLEE---GQEVKVKVLEVNEEEKRISLSIKALE 350 Score = 131 bits (331), Expect = 6e-31 Identities = 113/395 (28%), Positives = 199/395 (50%), Gaps = 36/395 (9%) Query: 192 VQKLEEGQVIEGTVKNITDYGVFVDLSG--VDGLLHVTDIAWHRILHPSKVLSIGQQVKV 249 V+++E G V+ G V + D VFV++ G V+G++ +++++ I + V+ +G +++V Sbjct: 12 VKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEV 71 Query: 250 KIIRINQETHRISLGMKQLEKNP-WDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEG 308 ++++ + L ++LE WD +++K+ EG V VT + G+ V++ G+ G Sbjct: 72 YVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV-EGVRG 130 Query: 309 LAHISQISWTKKNIHPSKILS--VGQQVEVVILEVNPARKRISLG----LKQALINPWEE 362 S IS + S G+ +EV I+E++P + R+ L +++ EE Sbjct: 131 FIPASLIS-----TRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEE 185 Query: 363 FSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNR---PGEKVIAEYAKGD 419 S G VEG V TDFG F+ + +DG++H+S+L R P E V + G Sbjct: 186 LLSSLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVV----SVGQ 240 Query: 420 IVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSS-LRKNDVVSCEVISVSEGGIEVSL 478 V+ VL ID ERISL +K + P + V L + DV+ V +++ G V + Sbjct: 241 EVEVKVLSIDWETERISLSLKD---TLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEV 297 Query: 479 IDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALE--IAE 536 + G+ + S +S + +GQ V V+ V++++ ++SLSIKALE AE Sbjct: 298 LP--GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAE 355 Query: 537 EKGAVAQF-----GSSDSGASLGDILGMALKNRGN 566 E+ ++ ++G SLGD++G LK Sbjct: 356 EEDRREEYRQYELPEEETGFSLGDLIGDKLKKLKL 390 Score = 40.6 bits (96), Expect = 0.001 Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 1/89 (1%) Query: 448 DVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSK 507 + ++SV + DVV+ EV+ V + + V++ +K I S+LS D ++ Sbjct: 7 ESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKV-EGVIPISELSNDHIEDINDVVKV 65 Query: 508 GQIVDACVVNVSKKDGKVSLSIKALEIAE 536 G ++ V+ V +G + LS + LE + Sbjct: 66 GDELEVYVLKVEDGEGNLLLSKRRLEAEK 94 >gnl|CDD|172339 PRK13806, rpsA, 30S ribosomal protein S1; Provisional. Length = 491 Score = 310 bits (797), Expect = 5e-85 Identities = 160/454 (35%), Positives = 248/454 (54%), Gaps = 11/454 (2%) Query: 5 NPSREDFATLLE--ESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGK 62 E FA LLE E K +L G V+ + +D+V VD G K +G + R E + Sbjct: 11 LDESESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDA 70 Query: 63 GQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQV 122 + VGDEVE+YV E S+ + + G +E + G +EG + Sbjct: 71 DGELTVAVGDEVELYVVSVNG--QEIRLSKALSGQGGA-AMLEEAYENGVPVEGKVTGTC 127 Query: 123 KGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEE 182 KGG V++ G AF P SQID+R V D + + F I ++++ NIVVSRRA+LE Sbjct: 128 KGGFNVEVLGRRAFCPVSQIDLRYVEDPESYVGQTFQFLITRVEENGRNIVVSRRALLER 187 Query: 183 SRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVL 241 + E ++ ++EG V+EGTV + +G FV+L+ GV+G++H+++++W R+ + + Sbjct: 188 EQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAV 247 Query: 242 SIGQQVKVKIIRINQETH----RISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYG 297 S+G V+VK++ I + RISL +KQ +PWD V D+ G KV+G V L +G Sbjct: 248 SVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFG 307 Query: 298 VFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALI 357 FVE+ GIEGL H+S++SWT++ P +++ G V V I +++PA++RISL L+ A Sbjct: 308 AFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEG 367 Query: 358 NPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAK 417 +PW + ++ PGT V G V+ + FGLF+ L + G++ S + + Sbjct: 368 DPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVIS-RAGKPATYEKLKP 426 Query: 418 GDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVD 451 GD V VV +ID K +ISL +GS D D Sbjct: 427 GDSVTLVVEEIDTAKRKISLAPAGAAGSGADDDD 460 >gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional. Length = 863 Score = 301 bits (772), Expect = 3e-82 Identities = 198/560 (35%), Positives = 301/560 (53%), Gaps = 29/560 (5%) Query: 15 LEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEV 74 L+E ++ + V G VV + TV VD+G K EGR+P EF P K GD V Sbjct: 310 LQERYSFEAPEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-----PPKAGDGV 364 Query: 75 EVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVI--FNQVKGGMTVDLN- 131 VYVER +G + S+ KA R G+ K+ R G +EG I + K G VDL Sbjct: 365 RVYVERV-TPYGPEL-SKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGA 422 Query: 132 GEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDK---RRGN--IVVSRRAVLEESRAE 186 G +AFLP SQ D + V L+ F I ++ + RGN IV++RR LEE + Sbjct: 423 GMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQ 482 Query: 187 QRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQ 246 R E + + G VK+ T +G F+DL G DGLLHV D++W + P + + GQ Sbjct: 483 AREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKKGQT 542 Query: 247 VKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGI 306 +++K+IR++Q RI+L +K + +PW + ++K+ V G VT + D+G F+EL GI Sbjct: 543 IELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGI 602 Query: 307 EGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKS 366 EGLAHIS+ SW KK PS ++ +G +VE +IL + R+SLGLKQ NPWEE Sbjct: 603 EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR 662 Query: 367 HPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVL 426 +P G + T+ G FI ++E +DG +H+ DL W + E G ++ +V+ Sbjct: 663 YPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVI 722 Query: 427 DIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINS 486 + D RI LGVKQLS + V + + V EV SV++ GI V + G+ Sbjct: 723 ECDPQARRIRLGVKQLSDNPWQVFANAYGV--GSTVEGEVSSVTDFGIFVRV--PGGVEG 778 Query: 487 FIRRSDLSRDRVDQDPG----RFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVA 542 +R+ L +R D DPG +++ G V A +V+++ KD KV+ S++ + ++ ++ Sbjct: 779 LVRKQHLVENR-DGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQRKVQRDELS 837 Query: 543 QFGSSDSGA-----SLGDIL 557 ++ S+ G +LGD++ Sbjct: 838 RYMSAPRGEDEGSFTLGDLM 857 >gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed. Length = 486 Score = 252 bits (645), Expect = 2e-67 Identities = 136/355 (38%), Positives = 221/355 (62%), Gaps = 13/355 (3%) Query: 7 SREDFATLLEES---FTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKG 63 S EDF ++++ F D+ E G VV +++D V++D+G K EG IP RE K Sbjct: 18 SAEDFLAAIDKTIKYFNDGDIVE-----GTVVKVDRDEVLLDIGYKTEGVIPSRELSIKH 72 Query: 64 QYTP---IKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFN 120 P ++VGDEVE V + E+ G + S+ +A E W IE + G + Sbjct: 73 DVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIE 132 Query: 121 QVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL 180 VKGG+ +D+ G FLP S +++R VRD+ P + + +I+++DK R N+V+SRRA L Sbjct: 133 VVKGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWL 191 Query: 181 EESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKV 240 E++++E RSE + +L++GQV +G V +I ++G FVDL GVDGL+HV++++W I HPS+V Sbjct: 192 EQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEV 251 Query: 241 LSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFV 300 + +GQ+V V+++ ++ + R+SL +K +++PW + G V G VT L +G FV Sbjct: 252 VEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFV 311 Query: 301 ELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQA 355 ++ GIEGL HIS+++ + P +++ VG +V V +++++ R+RISL LKQA Sbjct: 312 RVEEGIEGLVHISELAERHVEV-PEQVVQVGDEVFVKVIDIDLERRRISLSLKQA 365 Score = 124 bits (313), Expect = 7e-29 Identities = 91/275 (33%), Positives = 163/275 (59%), Gaps = 19/275 (6%) Query: 177 RAVLEESRAE-QR--SEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHR 233 R +L + RA+ +R I + E+ V+ GTV + G+ +D+ G+ G L + + R Sbjct: 99 RLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRR 157 Query: 234 I--LHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYV----EGSKVS 287 + L P IGQ+++ KII +++ + + L + + +V+ +++ +G Sbjct: 158 VRDLQPY----IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRK 213 Query: 288 GVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNI-HPSKILSVGQQVEVVILEVNPARK 346 GVV+++ ++G FV+L G++GL H+S++SW K+I HPS+++ VGQ+V V +L+V+ R+ Sbjct: 214 GVVSSIVNFGAFVDL-GGVDGLVHVSELSW--KHIDHPSEVVEVGQEVTVEVLDVDMDRE 270 Query: 347 RISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNR 406 R+SL LK +PW++F+++H G V G+V FG F+ ++E ++G++H+S+L R Sbjct: 271 RVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA-ER 329 Query: 407 PGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQ 441 E GD V V+DID+ + RISL +KQ Sbjct: 330 HVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364 >gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed. Length = 318 Score = 119 bits (299), Expect = 2e-27 Identities = 84/279 (30%), Positives = 136/279 (48%), Gaps = 20/279 (7%) Query: 7 SREDFATLLEE---SFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKG 63 + EDFA LL++ F D + G V LE ++D+G K +P +E Sbjct: 14 THEDFAALLDKYDYHFKPGD-----IVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINR 68 Query: 64 QYTPIKV---GDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFN 120 P +V + E ++ EN G+ S + WE++ + + +F Sbjct: 69 VEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFA 128 Query: 121 QVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL 180 +GG V + G F+P S I R ++ L+ E + L++D+ R +V+S R L Sbjct: 129 TNRGGALVRIEGLRGFIPGSHISTRKPKE--ELVGEELPLKFLEVDEERNRLVLSHRRAL 186 Query: 181 EESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKV 240 E + + +LE G+V+ GTV+ I YG F+D+ GV GLLH+++I+ I P V Sbjct: 187 VERK-------MNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSV 239 Query: 241 LSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDK 279 ++ ++KV II ++ E RISL KQLE P D ++D Sbjct: 240 FNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDP 278 Score = 65.2 bits (159), Expect = 5e-11 Identities = 66/259 (25%), Positives = 130/259 (50%), Gaps = 21/259 (8%) Query: 102 EKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVA-FLPRSQIDIRPVRDVTPLMH--EPQ 158 +K + F+ G+ + G +F+ G +D+ + A F+P ++ I V ++ E + Sbjct: 23 DKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETR 82 Query: 159 LFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLS 218 F IL + G + +S R + E RA +R +QK E + V G V + Sbjct: 83 EFFILSDENEDGQLTLSIRRI-EYMRAWERVRQLQK--EDATVRSEVFATNRGGALVRIE 139 Query: 219 GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQ--LEKNPWDDV 276 G+ G + + I+ + K +G+++ +K + +++E +R+ L ++ +E+ Sbjct: 140 GLRGFIPGSHISTRK----PKEELVGEELPLKFLEVDEERNRLVLSHRRALVERK----- 190 Query: 277 QDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIH-PSKILSVGQQVE 335 ++ G V G V + YG F+++ G+ GL HIS+IS ++I P + +V +++ Sbjct: 191 MNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEIS--HEHIETPHSVFNVNDEMK 247 Query: 336 VVILEVNPARKRISLGLKQ 354 V+I++++ R RISL KQ Sbjct: 248 VMIIDLDAERGRISLSTKQ 266 Score = 49.8 bits (119), Expect = 2e-06 Identities = 63/255 (24%), Positives = 122/255 (47%), Gaps = 13/255 (5%) Query: 198 GQVIEGTVKNITDYGVFVDLSG-VDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQ 256 G ++ GTV ++ G +D+ + + +++ +R+ P +VL + + I+ Sbjct: 32 GDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDEN 91 Query: 257 ETHRISLGMKQLE-KNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQI 315 E +++L ++++E W+ V+ E + V V G V ++ G+ G S I Sbjct: 92 EDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHI 150 Query: 316 SWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEG 375 S T+K K VG+++ + LEV+ R R+ L ++AL+ E G V G Sbjct: 151 S-TRK----PKEELVGEELPLKFLEVDEERNRLVLSHRRALV---ERKMNRLEVGEVVVG 202 Query: 376 EVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERI 435 V+ +G FI + + G++H+S++ E + + D +K +++D+D + RI Sbjct: 203 TVRGIKPYGAFIDIG-GVSGLLHISEISHEHI-ETPHSVFNVNDEMKVMIIDLDAERGRI 260 Query: 436 SLGVKQLSGSAPDVV 450 SL KQL D++ Sbjct: 261 SLSTKQLEPEPGDML 275 Score = 28.6 bits (64), Expect = 5.1 Identities = 13/57 (22%), Positives = 31/57 (54%) Query: 477 SLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALE 533 + ID G++ + S++S + ++ F+ + ++++ + G++SLS K LE Sbjct: 212 AFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLE 268 >gnl|CDD|183327 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional. Length = 693 Score = 88.6 bits (221), Expect = 4e-18 Identities = 32/81 (39%), Positives = 48/81 (59%), Gaps = 2/81 (2%) Query: 190 EIVQKLEEGQVIEGTVKNITDYGVFVD-LSGVDGLLHVTDIAWHRILHPSKVLSIGQQVK 248 I + E G++ EG V I D+G FV+ L G DGL+H+++IA R+ VL G +VK Sbjct: 614 GITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVK 673 Query: 249 VKIIRINQETHRISLGMKQLE 269 VK++ I+ + RI L K + Sbjct: 674 VKVLEID-KRGRIRLSRKAVL 693 Score = 70.5 bits (174), Expect = 1e-12 Identities = 26/69 (37%), Positives = 39/69 (56%), Gaps = 2/69 (2%) Query: 288 GVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKR 347 G V + D+G FVE+ G +GL HIS+I+ + +L G +V+V +LE++ R R Sbjct: 627 GKVVRIVDFGAFVEILPGKDGLVHISEIADERVE-KVEDVLKEGDEVKVKVLEIDK-RGR 684 Query: 348 ISLGLKQAL 356 I L K L Sbjct: 685 IRLSRKAVL 693 Score = 50.0 bits (121), Expect = 2e-06 Identities = 32/99 (32%), Positives = 48/99 (48%), Gaps = 14/99 (14%) Query: 344 ARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLD 403 A++RI + + E G EG+V DFG F+ + DG++H+S++ Sbjct: 608 AKERI-----EGITAEPEV-------GEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIA 655 Query: 404 WNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQL 442 R EKV +GD VK VL+ID + RI L K + Sbjct: 656 DER-VEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRKAV 692 Score = 30.0 bits (69), Expect = 1.7 Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 1/43 (2%) Query: 491 SDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALE 533 S+++ +RV++ +G V V+ + K+ G++ LS KA+ Sbjct: 652 SEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAVL 693 >gnl|CDD|128611 smart00316, S1, Ribosomal protein S1-like RNA-binding domain. Length = 72 Score = 78.4 bits (194), Expect = 5e-15 Identities = 32/72 (44%), Positives = 52/72 (72%), Gaps = 1/72 (1%) Query: 196 EEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRI 254 E G V+EGTV IT +G FVDL +GV+GL+ +++++ R+ P +VL +G +VKVK++ + Sbjct: 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60 Query: 255 NQETHRISLGMK 266 ++E RI L +K Sbjct: 61 DEEKGRIILSLK 72 Score = 72.6 bits (179), Expect = 3e-13 Identities = 31/72 (43%), Positives = 46/72 (63%), Gaps = 1/72 (1%) Query: 282 EGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEV 341 G V G VT +T +G FV+L +G+EGL IS++S K+ P ++L VG +V+V +L V Sbjct: 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSD-KRVKDPEEVLKVGDEVKVKVLSV 60 Query: 342 NPARKRISLGLK 353 + + RI L LK Sbjct: 61 DEEKGRIILSLK 72 Score = 61.9 bits (151), Expect = 5e-10 Identities = 27/72 (37%), Positives = 36/72 (50%), Gaps = 1/72 (1%) Query: 369 PGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDI 428 G VEG V T FG F+ L ++G+I +S+L R + GD VK VL + Sbjct: 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKR-VKDPEEVLKVGDEVKVKVLSV 60 Query: 429 DVGKERISLGVK 440 D K RI L +K Sbjct: 61 DEEKGRIILSLK 72 Score = 53.4 bits (129), Expect = 2e-07 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 2/74 (2%) Query: 457 RKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVV 516 DVV V ++ G V L + G+ I S+LS RV G V V+ Sbjct: 1 EVGDVVEGTVTEITPFGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVL 58 Query: 517 NVSKKDGKVSLSIK 530 +V ++ G++ LS+K Sbjct: 59 SVDEEKGRIILSLK 72 Score = 44.9 bits (107), Expect = 5e-05 Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 3/67 (4%) Query: 29 VTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTP---IKVGDEVEVYVERTENSF 85 V +G V + VD+G EG IP E K P +KVGDEV+V V + Sbjct: 5 VVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEK 64 Query: 86 GEAVFSR 92 G + S Sbjct: 65 GRIILSL 71 Score = 39.9 bits (94), Expect = 0.002 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 3/72 (4%) Query: 109 RAGERIEGVIFNQVKGGMTVDLNGEV-AFLPRSQIDIRPVRDVTP--LMHEPQLFEILKM 165 G+ +EG + G VDL V +P S++ + V+D + + ++L + Sbjct: 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60 Query: 166 DKRRGNIVVSRR 177 D+ +G I++S + Sbjct: 61 DEEKGRIILSLK 72 >gnl|CDD|163340 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family). Length = 684 Score = 77.9 bits (193), Expect = 6e-15 Identities = 31/75 (41%), Positives = 46/75 (61%), Gaps = 2/75 (2%) Query: 190 EIVQKLEEGQVIEGTVKNITDYGVFVD-LSGVDGLLHVTDIAWHRILHPSKVLSIGQQVK 248 I + E G++ EG V I D+G FV+ L G DGL+H+++IA R+ VL G +VK Sbjct: 611 GITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVK 670 Query: 249 VKIIRINQETHRISL 263 VK++ I+ + RI L Sbjct: 671 VKVLEID-KQGRIKL 684 Score = 56.0 bits (136), Expect = 2e-08 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 2/64 (3%) Query: 287 SGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARK 346 G V + D+G FVE+ G +GL HIS+I+ + +L G +V+V +LE++ + Sbjct: 623 EGKVVRIMDFGAFVEILPGKDGLVHISEIANERVE-KVEDVLKEGDEVKVKVLEID-KQG 680 Query: 347 RISL 350 RI L Sbjct: 681 RIKL 684 Score = 42.5 bits (101), Expect = 3e-04 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%) Query: 374 EGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDID 429 EG+V DFG F+ + DG++H+S++ R EKV +GD VK VL+ID Sbjct: 623 EGKVVRIMDFGAFVEILPGKDGLVHISEIANERV-EKVEDVLKEGDEVKVKVLEID 677 >gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated. Length = 123 Score = 65.5 bits (160), Expect = 4e-11 Identities = 34/91 (37%), Positives = 50/91 (54%), Gaps = 3/91 (3%) Query: 279 KYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWT-KKNIHPSKILSVGQQVEVV 337 +Y GS V+G VT + YG FV L +GL HIS+I+ K+IH LSVG +V+V Sbjct: 4 QYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIH--DFLSVGDEVKVK 61 Query: 338 ILEVNPARKRISLGLKQALINPWEEFSKSHP 368 +L V+ + +ISL ++ P + K Sbjct: 62 VLSVDEEKGKISLSIRATEEAPEAKRKKGKI 92 Score = 61.2 bits (149), Expect = 8e-10 Identities = 28/80 (35%), Positives = 46/80 (57%), Gaps = 1/80 (1%) Query: 194 KLEEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKII 252 + E G V+ G V I YG FV L GL+H+++I + LS+G +VKVK++ Sbjct: 4 QYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVL 63 Query: 253 RINQETHRISLGMKQLEKNP 272 +++E +ISL ++ E+ P Sbjct: 64 SVDEEKGKISLSIRATEEAP 83 Score = 42.0 bits (99), Expect = 4e-04 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%) Query: 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAK-GDIVKAVVLDI 428 G+ V G+V +G F+ LDE G++H+S++ K I ++ GD VK VL + Sbjct: 8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEI--THGFVKDIHDFLSVGDEVKVKVLSV 65 Query: 429 DVGKERISLGVK 440 D K +ISL ++ Sbjct: 66 DEEKGKISLSIR 77 Score = 32.3 bits (74), Expect = 0.39 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 4/49 (8%) Query: 506 SKGQIVDACVVNVSKKDGKVSLSIKALEIAEE----KGAVAQFGSSDSG 550 S G V V++V ++ GK+SLSI+A E A E KG + S+ G Sbjct: 53 SVGDEVKVKVLSVDEEKGKISLSIRATEEAPEAKRKKGKILIPNPSEQG 101 >gnl|CDD|181488 PRK08582, PRK08582, hypothetical protein; Provisional. Length = 139 Score = 62.8 bits (153), Expect = 2e-10 Identities = 39/103 (37%), Positives = 54/103 (52%), Gaps = 5/103 (4%) Query: 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTK-KNIHPSKILSVGQQVEVVILEV 341 GSK+ G VT +T++G FVEL G GL HIS+++ K+I+ L VG +VEV +L V Sbjct: 6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDIN--DHLKVGDEVEVKVLNV 63 Query: 342 NPARKRISLGLKQALINPWEEFSKSHPPGTEVEGE-VKNKTDF 383 K I L +K+A P + + G V K DF Sbjct: 64 EDDGK-IGLSIKKAKDRPKRQHDRPRHEDNRGGGNDVAPKEDF 105 Score = 45.8 bits (109), Expect = 3e-05 Identities = 24/79 (30%), Positives = 49/79 (62%), Gaps = 2/79 (2%) Query: 195 LEEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIR 253 +E G ++G V IT++G FV+L G GL+H++++A + + + L +G +V+VK++ Sbjct: 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLN 62 Query: 254 INQETHRISLGMKQLEKNP 272 + + +I L +K+ + P Sbjct: 63 VEDDG-KIGLSIKKAKDRP 80 Score = 32.7 bits (75), Expect = 0.25 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 6/74 (8%) Query: 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAK-GDIVKAVVLDI 428 G++++G+V T+FG F+ L E G++H+S++ N K I ++ K GD V+ VL++ Sbjct: 6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYV--KDINDHLKVGDEVEVKVLNV 63 Query: 429 -DVGKERISLGVKQ 441 D GK I L +K+ Sbjct: 64 EDDGK--IGLSIKK 75 >gnl|CDD|180268 PRK05807, PRK05807, hypothetical protein; Provisional. Length = 136 Score = 57.8 bits (140), Expect = 7e-09 Identities = 30/77 (38%), Positives = 50/77 (64%), Gaps = 1/77 (1%) Query: 195 LEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRI 254 L+ G ++EGTV NIT++G FV++ G GL+H++++A + + L +VKVK+I I Sbjct: 3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISI 62 Query: 255 NQETHRISLGMKQLEKN 271 + + +ISL +KQ K Sbjct: 63 D-DNGKISLSIKQAMKQ 78 Score = 48.2 bits (115), Expect = 5e-06 Identities = 30/98 (30%), Positives = 53/98 (54%), Gaps = 14/98 (14%) Query: 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTK-KNIHPSKILSVGQQVEVVILEV 341 GS + G V N+T++G FVE++ G GL HIS+++ T K+I + L +V+V ++ + Sbjct: 6 GSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIR--EHLKEQDKVKVKVISI 62 Query: 342 NPARKRISLGLKQALINP---------WEEFSKSHPPG 370 + +ISL +KQA+ W++ + G Sbjct: 63 DD-NGKISLSIKQAMKQKKSVKPAEIDWQKEKNKNNNG 99 Score = 37.4 bits (87), Expect = 0.010 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 5/73 (6%) Query: 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAK-GDIVKAVVLDI 428 G+ +EG V N T+FG F+ + E G++H+S++ K I E+ K D VK V+ I Sbjct: 6 GSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYV--KDIREHLKEQDKVKVKVISI 62 Query: 429 DVGKERISLGVKQ 441 D +ISL +KQ Sbjct: 63 D-DNGKISLSIKQ 74 >gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional. Length = 120 Score = 54.3 bits (131), Expect = 8e-08 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 3/72 (4%) Query: 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQI-SWTKKNIHPSKILSVGQQVEVVILEV 341 G K+ G +T + YG FV L++G GL HIS+I + NIH ++L VG++V V +++ Sbjct: 4 GDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIH--QLLKVGEEVLVQVVDF 61 Query: 342 NPARKRISLGLK 353 + + SL L+ Sbjct: 62 DEYTGKASLSLR 73 Score = 52.0 bits (125), Expect = 4e-07 Identities = 24/73 (32%), Positives = 46/73 (63%), Gaps = 1/73 (1%) Query: 198 GQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQ 256 G ++GT+ I YG FV L +G GL+H+++I I + ++L +G++V V+++ ++ Sbjct: 4 GDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDE 63 Query: 257 ETHRISLGMKQLE 269 T + SL ++ LE Sbjct: 64 YTGKASLSLRTLE 76 >gnl|CDD|179696 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated. Length = 262 Score = 52.1 bits (126), Expect = 4e-07 Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 3/74 (4%) Query: 196 EEGQVIEGTVKNITDYGVFVDL---SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKII 252 EEG+++ GTVK + D+G FV L G +G +H++++A + + + GQ+V K+I Sbjct: 7 EEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVI 66 Query: 253 RINQETHRISLGMK 266 R++ I L +K Sbjct: 67 RVDPRKGHIDLSLK 80 Score = 50.6 bits (122), Expect = 1e-06 Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 7/76 (9%) Query: 282 EGSKVSGVVTNLTDYGVFVELQ--SGIEGLAHISQIS--WTKKNIHPSKILSVGQQVEVV 337 EG V G V + D+G FV L G EG HIS+++ W KNI + GQ+V Sbjct: 8 EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWV-KNIR--DHVKEGQKVVCK 64 Query: 338 ILEVNPARKRISLGLK 353 ++ V+P + I L LK Sbjct: 65 VIRVDPRKGHIDLSLK 80 Score = 32.1 bits (74), Expect = 0.45 Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 21/83 (25%) Query: 369 PGTEVEGEVKNKTDFGLFIGLDEH--LDGMIHLSDL---------DWNRPGEKVIAEYAK 417 G V G VK DFG F+ LDE+ +G IH+S++ D + G+KV+ + Sbjct: 8 EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCK--- 64 Query: 418 GDIVKAVVLDIDVGKERISLGVK 440 V+ +D K I L +K Sbjct: 65 -------VIRVDPRKGHIDLSLK 80 >gnl|CDD|181471 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional. Length = 187 Score = 47.5 bits (114), Expect = 9e-06 Identities = 28/93 (30%), Positives = 45/93 (48%), Gaps = 16/93 (17%) Query: 191 IVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSK----------- 239 +V K E +V+EG V + ++G FV + VDGLLH++ I I + K Sbjct: 75 LVFKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKR 134 Query: 240 VLSIGQQVKVKIIRI-----NQETHRISLGMKQ 267 VL +G V+ +I+ + +I L M+Q Sbjct: 135 VLKVGDVVRARIVAVSLKERRPRGSKIGLTMRQ 167 Score = 35.6 bits (83), Expect = 0.033 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%) Query: 286 VSGVVTNLTDYGVFVELQSGIEGLAHISQIS 316 V G V + ++G FV + ++GL HISQI Sbjct: 85 VEGEVVEVVEFGAFVRI-GPVDGLLHISQIM 114 Score = 32.9 bits (76), Expect = 0.22 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 16/84 (19%) Query: 373 VEGEVKNKTDFGLFIGLDEHLDGMIHLS-------DLDWNRP---GEKVIAEYAKGDIVK 422 VEGEV +FG F+ + +DG++H+S D G++ GD+V+ Sbjct: 85 VEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVR 143 Query: 423 AVVLDI-----DVGKERISLGVKQ 441 A ++ + +I L ++Q Sbjct: 144 ARIVAVSLKERRPRGSKIGLTMRQ 167 >gnl|CDD|162678 TIGR02063, RNase_R, ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. Length = 709 Score = 46.5 bits (111), Expect = 2e-05 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 11/72 (15%) Query: 288 GVVTNLTDYGVFVEL-QSGIEGLAHISQISWTKKNIHP----------SKILSVGQQVEV 336 GV++ +T +G+FVEL + IEGL HIS + K+ +G +V+V Sbjct: 633 GVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKV 692 Query: 337 VILEVNPARKRI 348 +++ + +I Sbjct: 693 RVVKADLDTGKI 704 Score = 46.1 bits (110), Expect = 2e-05 Identities = 19/77 (24%), Positives = 43/77 (55%), Gaps = 13/77 (16%) Query: 198 GQVIEGTVKNITDYGVFVDL--SGVDGLLHVTDI---------AWHRILHPS--KVLSIG 244 G+ EG + +T +G+FV+L + ++GL+H++ + ++ KV +G Sbjct: 628 GEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLG 687 Query: 245 QQVKVKIIRINQETHRI 261 +VKV++++ + +T +I Sbjct: 688 DRVKVRVVKADLDTGKI 704 Score = 38.8 bits (91), Expect = 0.004 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 12/85 (14%) Query: 362 EFSKSHPPGTEVEGEVKNKTDFGLFIGLDE-HLDGMIHLSDLD-----WNRPGEKVIAE- 414 E+ G E EG + T FGLF+ L+ ++G++H+S L ++ G ++ E Sbjct: 621 EYMSEKI-GEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGER 679 Query: 415 ----YAKGDIVKAVVLDIDVGKERI 435 + GD VK V+ D+ +I Sbjct: 680 TGKVFRLGDRVKVRVVKADLDTGKI 704 >gnl|CDD|177797 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional. Length = 891 Score = 45.3 bits (107), Expect = 4e-05 Identities = 22/55 (40%), Positives = 33/55 (60%), Gaps = 5/55 (9%) Query: 290 VTNLTDYGVFVELQSGIEGLAHISQIS--WTKKNIHPSKILSVGQQVEVVILEVN 342 + ++ YG FVE+ G EGL HIS++S W K P VG +++V ++EVN Sbjct: 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAK---PEDAFKVGDRIDVKLIEVN 813 Score = 43.0 bits (101), Expect = 2e-04 Identities = 19/82 (23%), Positives = 43/82 (52%), Gaps = 2/82 (2%) Query: 205 VKNITDYGVFVDLS-GVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISL 263 +K+I YG FV+++ G +GL H+++++ + + P +G ++ VK+I +N + + L Sbjct: 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQ-LRL 820 Query: 264 GMKQLEKNPWDDVQDKYVEGSK 285 + L + + +G Sbjct: 821 SRRALLPEANSEKSSQKQQGGS 842 >gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase. Length = 719 Score = 43.3 bits (102), Expect = 2e-04 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 4/71 (5%) Query: 283 GSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSK---ILSVGQQVEVVIL 339 G + G V T +G FV L G +GL HISQI +LSVGQ+++V I Sbjct: 648 GERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIA 707 Query: 340 EVNPARKRISL 350 +++ R ++SL Sbjct: 708 DID-DRGKLSL 717 Score = 41.0 bits (96), Expect = 8e-04 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%) Query: 196 EEGQVIEGTVKNITDYGVFVDL-SGVDGLLHVTDI----AWHRILHPSKVLSIGQQVKVK 250 E G+ GTV T +G FV L G DGLLH++ I R+ + VLS+GQ+++V+ Sbjct: 646 EVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVE 705 Query: 251 IIRINQETHRISL 263 I I+ + ++SL Sbjct: 706 IADID-DRGKLSL 717 Score = 27.5 bits (61), Expect = 9.2 Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 3/63 (4%) Query: 370 GTEVEGEVKNKTDFGLFIGLDEHLDGMIHLS---DLDWNRPGEKVIAEYAKGDIVKAVVL 426 G G V T FG F+ L DG++H+S L + E V + G ++ + Sbjct: 648 GERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIA 707 Query: 427 DID 429 DID Sbjct: 708 DID 710 >gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE. Length = 179 Score = 39.4 bits (92), Expect = 0.003 Identities = 28/93 (30%), Positives = 45/93 (48%), Gaps = 16/93 (17%) Query: 191 IVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSK----------- 239 +V K E G+++EG V I ++G FV L DGL HV+ + + K Sbjct: 75 LVFKPELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKK 134 Query: 240 VLSIGQQVKVKIIRIN-----QETHRISLGMKQ 267 VL G +V+ +I+ ++ E +I L M+Q Sbjct: 135 VLDEGDKVRARIVALSLKDRRPEGSKIGLTMRQ 167 >gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. Length = 654 Score = 35.8 bits (83), Expect = 0.030 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 11/77 (14%) Query: 370 GTEVEGEVKNKTDFGLFIGLDEH-LDGMIHLSDLD-----WNRPGEKVIAE-----YAKG 418 GTE GE+ + T FG+F+ LD++ +DG+IH+S L +++ +I + Y G Sbjct: 573 GTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIG 632 Query: 419 DIVKAVVLDIDVGKERI 435 D V + ++++ I Sbjct: 633 DRVTVKLTEVNMETRSI 649 Score = 32.8 bits (75), Expect = 0.24 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 11/81 (13%) Query: 283 GSKVSGVVTNLTDYGVFVEL-QSGIEGLAHIS----------QISWTKKNIHPSKILSVG 331 G++ SG ++++T +G+FV L +GI+GL HIS Q K+ +G Sbjct: 573 GTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIG 632 Query: 332 QQVEVVILEVNPARKRISLGL 352 +V V + EVN + I L Sbjct: 633 DRVTVKLTEVNMETRSIIFEL 653 >gnl|CDD|181696 PRK09202, nusA, transcription elongation factor NusA; Validated. Length = 470 Score = 35.2 bits (82), Expect = 0.051 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 20/85 (23%) Query: 188 RSEIVQKLEE--------------GQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHR 233 + IVQK+ E G++I G VK + + VDL + +L + Sbjct: 111 KQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQI--- 167 Query: 234 ILHPSKVLSIGQQVKVKIIRINQET 258 P + G +V+ + + +E Sbjct: 168 ---PRENFRPGDRVRAYVYEVRKEA 189 Score = 34.5 bits (80), Expect = 0.084 Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 4/55 (7%) Query: 26 ENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVER 80 + G+V +E+ ++VD+G + E +PR+E + + + + GD V YV Sbjct: 134 VGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQIPRENF---RPGDRVRAYVYE 184 Score = 33.3 bits (77), Expect = 0.19 Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 19/87 (21%) Query: 68 IKVGDEVEVYVERTENSFGEAVFSRDKA----------LREGVWEKIEAKF--RAGERIE 115 +VGD +E +E + F R A +RE E++ ++ R GE I Sbjct: 87 AEVGDYIEEEIESVD-------FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIIT 139 Query: 116 GVIFNQVKGGMTVDLNGEVAFLPRSQI 142 GV+ +G + VDL A LPR + Sbjct: 140 GVVKRVERGNIIVDLGRAEAILPRKEQ 166 >gnl|CDD|185526 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional. Length = 319 Score = 34.6 bits (80), Expect = 0.064 Identities = 22/98 (22%), Positives = 54/98 (55%), Gaps = 3/98 (3%) Query: 196 EEGQVIEGTVKNITDYGVFVDL---SGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKII 252 EE ++ V IT+ G +V L ++G++ +++++ RI +K++ +G+ V ++ Sbjct: 16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVL 75 Query: 253 RINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVV 290 R+++E I L K++ + ++K+ + KV ++ Sbjct: 76 RVDKEKGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIM 113 Score = 31.2 bits (71), Expect = 0.84 Identities = 22/72 (30%), Positives = 38/72 (52%) Query: 459 NDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNV 518 +D+V +V+ ++E G VSL+++ I I S+LS+ R+ G+ V+ V Sbjct: 18 DDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRV 77 Query: 519 SKKDGKVSLSIK 530 K+ G + LS K Sbjct: 78 DKEKGYIDLSKK 89 Score = 27.7 bits (62), Expect = 8.4 Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 13/86 (15%) Query: 290 VTNLTDYGVFVEL--QSGIEGLAHISQISWTKKNIHP-SKILSVGQQVEVVILEVNPARK 346 V +T+ G +V L IEG+ +S++S K+ I +K++ VG+ VV+L V+ + Sbjct: 25 VVRITEMGAYVSLLEYDDIEGMILMSELS--KRRIRSINKLIRVGRHEVVVVLRVDKEKG 82 Query: 347 RISLGLKQALINPWEE------FSKS 366 I L K+ ++P + FSKS Sbjct: 83 YIDLSKKR--VSPEDIEACEEKFSKS 106 >gnl|CDD|183253 PRK11642, PRK11642, exoribonuclease R; Provisional. Length = 813 Score = 31.2 bits (71), Expect = 0.72 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 15/62 (24%) Query: 381 TDFGLFIGLDE-HLDGMIHLSDLD-----WNRPGEKVIAE-----YAKGDIVK----AVV 425 T FG F+ LD+ +DG++H+S LD +++ G+++I E Y GD V+ AV Sbjct: 655 TGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVN 714 Query: 426 LD 427 +D Sbjct: 715 MD 716 Score = 30.5 bits (69), Expect = 1.1 Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 13/88 (14%) Query: 198 GQVIEGTVKNITDYGVFVDLSG--VDGLLHVT---------DIAWHRILHPS--KVLSIG 244 G V +G + ++T +G FV L +DGL+HV+ D R++ S + +G Sbjct: 644 GNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLG 703 Query: 245 QQVKVKIIRINQETHRISLGMKQLEKNP 272 +V+V++ +N + +I + E+ P Sbjct: 704 DRVEVRVEAVNMDERKIDFSLISSERAP 731 Score = 29.3 bits (66), Expect = 2.9 Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 3/41 (7%) Query: 274 DDVQDKYVEGSKVSGVVTNLTDYGVFVELQS-GIEGLAHIS 313 D + D+ G+ GV++++T +G FV L I+GL H+S Sbjct: 637 DFMLDQV--GNVFKGVISSVTGFGFFVRLDDLFIDGLVHVS 675 >gnl|CDD|178056 PLN02437, PLN02437, ribonucleoside--diphosphate reductase large subunit. Length = 813 Score = 30.9 bits (70), Expect = 0.91 Identities = 12/26 (46%), Positives = 17/26 (65%) Query: 464 CEVISVSEGGIEVSLIDHKGINSFIR 489 C VIS S GGI +S+ + + S+IR Sbjct: 238 CAVISKSAGGIGLSVHNIRATGSYIR 263 >gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional. Length = 644 Score = 30.2 bits (69), Expect = 1.6 Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 6/54 (11%) Query: 463 SCEVISVSEGGIEVSLIDHKGINSFIRRSDLS--RDRVD--QDPGRFS-KGQIV 511 + E+I +S GG+ V L+++ G +FI S L RD + Q+ G KG+ V Sbjct: 566 AAEIIDISRGGMRVRLLEN-GAVAFIPASFLHAVRDELVCNQENGTVQIKGETV 618 >gnl|CDD|169002 PRK07546, PRK07546, hypothetical protein; Provisional. Length = 209 Score = 29.6 bits (67), Expect = 2.1 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 9/49 (18%) Query: 175 SRRAVLEESRAEQRSEIVQKL----EEGQVIEGTVKNITDYGVFVDLSG 219 +RRA + +RAE ++ E G+V EGT+ N+ F+D G Sbjct: 108 TRRAAYDAARAELPPAEADEVILLNERGEVCEGTITNV-----FLDRGG 151 >gnl|CDD|132427 TIGR03384, betaine_BetI, transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme. Length = 189 Score = 29.2 bits (66), Expect = 2.9 Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 2/47 (4%) Query: 154 MHEPQLFEILKMDKRR--GNIVVSRRAVLEESRAEQRSEIVQKLEEG 198 MH PQL + +++ RR N++ R +L +AE+ +E + L +G Sbjct: 114 MHSPQLARLQRINSRRLHSNLMSELRQLLPREQAERAAEGLAALIDG 160 >gnl|CDD|185269 PRK15371, PRK15371, effector protein YopJ; Provisional. Length = 287 Score = 28.5 bits (64), Expect = 5.0 Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 3/96 (3%) Query: 391 EHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVV 450 E L +I + D G + YA+ D+ L + + +K L S D+ Sbjct: 26 EELKNIITQLEDD-IADGSWIHKNYARTDLEVMPALVAQANNKYPEMNLK-LVTSPLDLS 83 Query: 451 DSVSSLRKNDVVSCE-VISVSEGGIEVSLIDHKGIN 485 + +N V S ++++ GGI S+ID+K I+ Sbjct: 84 IEIKETIENGVESSRFIVNMGSGGIHFSVIDYKHID 119 >gnl|CDD|162623 TIGR01953, NusA, transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids. Length = 341 Score = 28.4 bits (64), Expect = 5.2 Identities = 40/185 (21%), Positives = 79/185 (42%), Gaps = 24/185 (12%) Query: 91 SRDKAL-REGVWEKIEA--------KFRAGERIEGVIFNQVKGGMTVDLNGEV---AFLP 138 +++K + E V E IE F E +E V ++ G + V EV P Sbjct: 10 AKEKGISIETVIEAIEEALEQAYKKTFGQDENVE-VNIDRKTGDINVYRRKEVVEEVEDP 68 Query: 139 RSQIDIRPVRDVTPLMH--EPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQ--K 194 +I + R++ P + + EI + R +++ +L++ R +R + Sbjct: 69 SLEISLEDAREIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFS 128 Query: 195 LEEGQVIEGTVKNITDYG-VFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIR 253 +EG++I GTVK + G ++V+L +G+L + P + IG ++K + Sbjct: 129 SKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQI------PGEKFRIGDRIKAYVYE 182 Query: 254 INQET 258 + + Sbjct: 183 VRKTA 187 >gnl|CDD|152518 pfam12083, DUF3560, Domain of unknown function (DUF3560). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif. Length = 127 Score = 28.4 bits (64), Expect = 5.4 Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 6/43 (13%) Query: 57 REFMGKGQYTPIKVGDEVEV----YVERTENSFGEAVFSRDKA 95 E + GQ PI VG E +ER N+ G+AV ++DKA Sbjct: 36 AEAIPLGQ--PILVGHHSERRHRRDIERIHNTMGKAVEAQDKA 76 >gnl|CDD|181221 PRK08072, PRK08072, nicotinate-nucleotide pyrophosphorylase; Provisional. Length = 277 Score = 28.5 bits (64), Expect = 5.6 Identities = 27/90 (30%), Positives = 38/90 (42%), Gaps = 20/90 (22%) Query: 368 PPGTEVEGEVKNKTDFGLFIG----------LDEHLDGMIHLSDLDWNRPGEKVIAEYAK 417 P EG K G+F G LDE ++ +H D D + GE +IA Sbjct: 30 PDNLLGEGVFLAKDT-GVFAGRLVIEEGYKLLDERIEVELHKKDGDLVKKGE-IIAT--- 84 Query: 418 GDIVKAVVLDIDVGKERISLGVKQ-LSGSA 446 V+ V + G ER+ L + Q +SG A Sbjct: 85 ---VQGPVASLLTG-ERVILNLIQRMSGIA 110 >gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated. Length = 819 Score = 28.1 bits (63), Expect = 5.8 Identities = 16/58 (27%), Positives = 19/58 (32%), Gaps = 12/58 (20%) Query: 369 PGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEY--AKGDIVKAV 424 E+ G V LDE L G +L D EY A DI + V Sbjct: 772 EEEELTGSVY----------LDESLKGGAYLPSFDLKLNTSSFFREYRFASVDIKEQV 819 >gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit alpha; Provisional. Length = 1046 Score = 28.0 bits (62), Expect = 7.7 Identities = 35/169 (20%), Positives = 68/169 (40%), Gaps = 36/169 (21%) Query: 73 EVEVYVERTENSFGEAVFSRD--KALREGVWEKI---------------------EAKFR 109 E ++YV ++ + + RD KA R+ W+ + E FR Sbjct: 85 ESQLYVNGLQDVARDYIVYRDDRKAHRKKSWQSLSVIRRDGTVVHFNPMKISAALEKAFR 144 Query: 110 AGERIEGVIFNQVK---GGMTVDLNGEVAFL--PRSQIDIRPVRDVTPLMHEPQLFEILK 164 A ++IEG+ + V +T ++ E+ +IDI ++D+ E QL + Sbjct: 145 ATDKIEGMTPSSVLEEINALTQNIVEEILECCSQEDRIDIEKIQDIV----EQQLMVVGH 200 Query: 165 MDKRRGNIVVSR-RAVLEESRAE---QRSEIVQKLEEGQVIEGTVKNIT 209 D + I+ RA + +++ E I ++ E +G+ +T Sbjct: 201 YDVAKNYILYREARARVRDNKEEDGSTEKTIAEEAYEVLSKDGSTYTMT 249 >gnl|CDD|180379 PRK06065, PRK06065, acetyl-CoA acetyltransferase; Provisional. Length = 392 Score = 27.5 bits (61), Expect = 9.3 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%) Query: 121 QVKGGMTVD--LNGEVAFLPRSQIDIRPVRD 149 Q+ +TV+ L EV P +D+ PV D Sbjct: 188 QLGSKITVEDVLKSEVLVWPVQLLDVSPVSD 218 >gnl|CDD|162797 TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family. The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence difference separates members of TIGR02289, probable oligoendopeptidases of the M3 family that probably should not be designated PepF. Length = 587 Score = 27.7 bits (62), Expect = 9.7 Identities = 8/49 (16%), Positives = 17/49 (34%), Gaps = 3/49 (6%) Query: 79 ERTENSFGEA---VFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKG 124 E S +A + D +R+ ++ + + I N + G Sbjct: 183 EEETLSLEQALNLLRDPDAEVRKKAFKALLKAWEKNAPTLAAILNALAG 231 >gnl|CDD|181700 PRK09209, PRK09209, ribonucleotide-diphosphate reductase subunit alpha; Validated. Length = 761 Score = 27.4 bits (61), Expect = 9.7 Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%) Query: 527 LSIKA-LEIAEEKGAVAQFGSSD 548 L+I+A +E+A+EKGA F SD Sbjct: 579 LTIQASMELAKEKGAYPVFKGSD 601 >gnl|CDD|132501 TIGR03461, pabC_Proteo, aminodeoxychorismate lyase. Members of this protein family are aminodeoxychorismate lyase (ADC lyase), EC 4.1.3.38, the PabC protein of PABA biosynthesis. PABA (para-aminobenzoate) is a precursor of folate, needed for de novo purine biosynthesis. This enzyme is a pyridoxal-phosphate-binding protein in the class IV aminotransferase family (pfam01063). Length = 261 Score = 27.6 bits (62), Expect = 9.8 Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 6/32 (18%) Query: 197 EGQVIEGTVKNI---TDYGVF---VDLSGVDG 222 +G V+E T NI VF + GV G Sbjct: 166 DGNVVECTAANIFWRKGNQVFTPDLSYCGVAG 197 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.315 0.136 0.381 Gapped Lambda K H 0.267 0.0836 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 9,410,846 Number of extensions: 637684 Number of successful extensions: 1249 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1021 Number of HSP's successfully gapped: 117 Length of query: 576 Length of database: 5,994,473 Length adjustment: 99 Effective length of query: 477 Effective length of database: 3,855,281 Effective search space: 1838969037 Effective search space used: 1838969037 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 60 (26.7 bits)