RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780316|ref|YP_003064729.1| phenylalanyl-tRNA synthetase subunit beta [Candidatus Liberibacter asiaticus str. psy62] (805 letters) >gnl|CDD|179078 PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta; Reviewed. Length = 791 Score = 880 bits (2276), Expect = 0.0 Identities = 320/813 (39%), Positives = 467/813 (57%), Gaps = 31/813 (3%) Query: 1 MKFTLSWLKDHLDTDVSLEKICDTLTSIGLEVEKVDNR-EALSPFTIVKVLSVERNPDLD 59 MKF+LSWLK++++ D+S E++ + LT IGLEVE V++ LS + KVL E++P+ D Sbjct: 1 MKFSLSWLKEYVNPDISSEELAEALTMIGLEVEGVEDVAAGLSGVVVGKVLECEKHPNAD 60 Query: 60 ----CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIEST 115 C ++D G+ + +Q+VCGAPNVR G A PG+ +P + K+RG+ES Sbjct: 61 KLRVC---QVDVGE-EPLQIVCGAPNVRAGDKVPVALPGAVLP-GGFKIKKAKLRGVESE 115 Query: 116 GMMCSEKELMLSDDSASIMELPIDAPVGGRLSDYLELSDPIIDVSLTPNRSDCIGVRGIA 175 GM+CS EL LSDD I+ELP DAPVG +YL L D +I++SLTPNR+DC+ VRGIA Sbjct: 116 GMLCSASELGLSDDHDGIIELPEDAPVGTDAREYLGLDDTVIEISLTPNRADCLSVRGIA 175 Query: 176 LDLVAAGLGKLKEINISCPLSSESIPLEIKFDLDDSSLCKGFAMCCVKGVRNNVA-PNWM 234 +L A LK I +I ++ +++D LC +A +KGV+N P W+ Sbjct: 176 RELAALLGLPLKLPEI--EPVPATIDDKLPVEIEDPDLCPRYAGRVIKGVKNIAPSPLWL 233 Query: 235 RQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRISDVLTVRRACSGEKILALDNQE 294 ++RL+A G+R I+ +VDITNYV L+ G P H FD +I + VRRA GEK+ LD +E Sbjct: 234 QERLRAAGIRPINNVVDITNYVMLELGQPLHAFDLDKIGGGIVVRRAKEGEKLTTLDGKE 293 Query: 295 YDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIIT 354 L P+++VIA D + ++AG++GG+ + +NTT+VL+E A +DP++I ++ + LG+ T Sbjct: 294 RTLDPEDLVIADDKKPLALAGVMGGEDSEVTENTTNVLLESAYFDPVSIRKTARRLGLRT 353 Query: 355 DSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNITYKPRKIVFMNSEVKRL 414 D+ YRFERGVD + L+ +LIL L GG + + K I + RL Sbjct: 354 DASYRFERGVDPALTLLALERATALILELGGGEVVEGVVDVYPLPKEPTITLRLERINRL 413 Query: 415 SGIDVPIEDSLRILERLGFSVIGEY-DKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIK 473 G ++ E+ + IL+RLGF V D V+VPSWR D+E + DLVEE+ RIYG D I Sbjct: 414 LGTEISDEEIVDILKRLGFEVTEVDGDGLTVTVPSWRFDIEIEEDLVEEVARIYGYDNIP 473 Query: 474 SEPLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRELEI 533 S P L+ Q R ++R LA+ EV+ +SF+S E + LFG L + Sbjct: 474 STPPVAALT--MGGLTEAQRLLRRLRRALAALGYQEVITYSFVSPEDAKLFGLNPEPLLL 531 Query: 534 LNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYE-NDTPEGQKYMAAGIR 592 LNPIS ++S MRTSLLPGLL+A N++R D A+FE+ V+ + + AG+ Sbjct: 532 LNPISEELSVMRTSLLPGLLEAVAYNLNRGNKDVALFEIGRVFLPDGDLPREPEHLAGVL 591 Query: 593 KGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPFVSLDSLRFESGAPSWYHPGR 652 G+ E W K R VD FD K D +++E + + HPGR Sbjct: 592 TGNRVEES----WGGK-----RPVDFFDLKGDVEALLEALGLPEVEFVAEFEAAALHPGR 642 Query: 653 SGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHLSS 712 S I V+G+ GE HP +L L FE+ LD++ + +K K K +S Sbjct: 643 SAEIYL-DGKVIGFIGELHPKVLKKLDLPGRTYVFELDLDALLEAARKLPKYKP---ISK 698 Query: 713 LHPVKRDLAFIVDQHIPAGTLVNIIKNVDR-LIDDVTVFDVFQGKSLGEGKKSVAIQVLI 771 V+RDLA +VD+ +PA ++ IK L++ V +FDV++GK +GEGKKS+A ++ Sbjct: 699 FPAVRRDLALVVDEDVPAADILKAIKKAGGKLLESVELFDVYEGKGIGEGKKSLAFRLTF 758 Query: 772 QPLKDTFRDDDIRILMDRIVENVVKKTNAVLRS 804 Q T D++I MD+IV + +K A LR Sbjct: 759 QDPDRTLTDEEINAAMDKIVAALEEKFGAELRG 791 >gnl|CDD|161895 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end, however. Length = 798 Score = 648 bits (1674), Expect = 0.0 Identities = 297/814 (36%), Positives = 470/814 (57%), Gaps = 27/814 (3%) Query: 1 MKFTLSWLKDHLD-TDVSLEKICDTLTSIGLEVEKVDN-REALSPFTIVKVLSVERNPDL 58 MK +L WL++++ +++ E+I + LTSIGLEVE V + L + KVL VE +P+ Sbjct: 1 MKISLKWLREYVPLSEIDNEEIAEALTSIGLEVEAVIPFSKPLKGVVVGKVLEVEPHPNA 60 Query: 59 D-CAILRIDTGKHQEIQVVCGAPNVRVGLLGVWAPPGSCIPENNMIVNVRKIRGIESTGM 117 D + ++D G+ + +Q+VCGAPNV G A PG+ +P N + + K+RG+ES GM Sbjct: 61 DKLKVCKVDIGEKEMLQIVCGAPNVEAGKKVAVALPGAKLP-NGLKIKKSKLRGVESEGM 119 Query: 118 MCSEKELMLSDDSASIMELPIDAPVGGRLSDYLELSDPIIDVSLTPNRSDCIGVRGIALD 177 +CSE EL L + S I+ L DAP+G +++YL L D II+VS+TPNR DC+ + GIA + Sbjct: 120 LCSEDELGLDEKSDGIIVLDEDAPLGTDIAEYLGLDDDIIEVSITPNRGDCLSILGIARE 179 Query: 178 LVAAGLGKLKEINISCPLSSESIPLEIKFDLDDSSLCKGFAMCCVKGVRNNVAPNWMRQR 237 L A L+ P ++E+I K +++D +C + +KGV+ +P W+++R Sbjct: 180 LAALFDLPLETPVPFEPETTETIDEGFKIEIEDPEVCPFYLGRVIKGVKVKPSPLWLKER 239 Query: 238 LKAVGLRSISALVDITNYVSLDRGYPSHVFDASRIS-DVLTVRRACSGEKILALDNQEYD 296 L+ G+R I+ +VDITNYV L+ G P H FDA +I + VR A GE LD +E + Sbjct: 240 LRRSGIRPINNIVDITNYVMLELGQPLHAFDADKIEGSNIEVRSAKEGESFTTLDGKERE 299 Query: 297 LSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDS 356 L ++VIA D + +IAG++GGK +G D TT++ +E A ++P I ++ + LGI TDS Sbjct: 300 LKKGDLVIADDKKPLAIAGVMGGKESGVTDTTTNIFLESAYFNPERIRKTARRLGISTDS 359 Query: 357 RYRFERGVDLQGMIPVLKHIVSLILSLCGG-TASDICIARNITYKPRKIVFMNSEVKRLS 415 YRFERGVD + L ++LIL + GG S + K +KI ++ ++ Sbjct: 360 SYRFERGVDPELTELALDRALNLILEIFGGEVISVVSDVYKEKAKEKKISLRIKKLNKIL 419 Query: 416 GIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSE 475 GI + E+ IL+RLGF V + D +EV+VPS+R D+ + DL+EEI RIYG D I +E Sbjct: 420 GISLSDEEVRDILKRLGFKVEKQKDGWEVTVPSYRHDITIEEDLIEEIARIYGYDNIPAE 479 Query: 476 PLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRE--LEI 533 PL ++ +K N R ++ +L + EV+ +S +S E++ F + E +EI Sbjct: 480 PLSVSSKLNKNN--ENYLLLRKLRTLLVGLGLNEVITYSLVSSEKAEKFNFPKLENLVEI 537 Query: 534 LNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYEND--TPEGQKYMAAGI 591 NP+S + S +RTSLLP LL+ N +R D IFE+ V+ D + Q +A I Sbjct: 538 KNPLSNERSVLRTSLLPSLLEVLAYNQNRKNKDVKIFEIGKVFAKDGLGVKEQLRLAILI 597 Query: 592 RKGSSGIEGSGRLWSDKSEERCRFVDLFDAKADALSVIEPF-VSLDSLRFESGAPSWYHP 650 SG E + W+ K E+ VD +D K D S++E +S D + HP Sbjct: 598 ----SG-EKNPSSWNHKEEK----VDFYDLKGDVESLLELLGLSDDVYFKNTAENEELHP 648 Query: 651 GRSGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSIPISQKKRTKTKKVVHL 710 G+S I + + G+ GE HP I + L P E+ LD + S KK K + + Sbjct: 649 GQSATIYLKGKKI-GFIGELHPEIAKKYDLKEPTFVAELDLDRLLESLKKVPKYRP---I 704 Query: 711 SSLHPVKRDLAFIVDQHIPAGTLVNIIKNVD-RLIDDVTVFDVFQGKSLGEGKKSVAIQV 769 S V RD++F+V + +PA ++ +IK L+++V +FDV++GK++GEGKKS+A+++ Sbjct: 705 SKFPAVTRDISFLVPKDVPANEIIKLIKKSGLELLEEVELFDVYEGKNIGEGKKSLALRL 764 Query: 770 LIQPLKDTFRDDDIRILMDRIVENVVKKTNAVLR 803 +++ + T D++I ++++++ + +K A LR Sbjct: 765 VLRDKERTLTDEEINKIVEKVLNLLKEKLGAELR 798 >gnl|CDD|129106 smart00873, B3_4, B3/4 domain. This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins. Length = 174 Score = 176 bits (449), Expect = 2e-44 Identities = 65/171 (38%), Positives = 105/171 (61%), Gaps = 2/171 (1%) Query: 217 FAMCCVKGVRNNV-APNWMRQRLKAVGLRSISALVDITNYVSLDRGYPSHVFDASRIS-D 274 + ++GV+N +P W+++RL G+R I+ +VDITNYVSL+ G P H FD +I Sbjct: 4 YLGRVIRGVKNTRPSPEWLQERLHRAGIRPINNVVDITNYVSLETGQPLHAFDLDKIKGK 63 Query: 275 VLTVRRACSGEKILALDNQEYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVE 334 + +RRA GE LD +EY+L ++VIA D ++AG++GG+ + +NTT++ +E Sbjct: 64 DIPLRRAKEGETFETLDGKEYELDEGDLVIADDEGPLALAGVMGGEESEVTENTTNIFLE 123 Query: 335 VALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIPVLKHIVSLILSLCG 385 A++ P I + + L + TD+ RFERGVD + + L +L+L +CG Sbjct: 124 PAIFSPRTIRITARTLNLFTDASGRFERGVDPELVELALDRAAALLLEICG 174 >gnl|CDD|181993 PRK09616, pheT, phenylalanyl-tRNA synthetase subunit beta; Reviewed. Length = 552 Score = 131 bits (332), Expect = 6e-31 Identities = 98/413 (23%), Positives = 174/413 (42%), Gaps = 66/413 (15%) Query: 294 EYDLSPDNVVIASDGRIQSIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGII 353 ++D P +++ S+G + S II + + T ++ ++V D + + L II Sbjct: 190 DFDRYP--LIVDSEGNVLSFPPIINSELTRVTEGTRNLFIDVTGTDLEAVLLA---LNII 244 Query: 354 TDSRYRFERGVDLQGMIPVLKHIVSLILSLCGGTASDICIARNITYKPRKIVFMNSEVKR 413 + ERG G I +K +I T D PR + + Sbjct: 245 ATALA--ERG----GTIESVK----VIYPDGELTTPD--------LTPRTREVSVEYINK 286 Query: 414 LSGIDVPIEDSLRILERLGFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIK 473 L GID+ E+ + +LER+ + DK +V+VP +R D+ + D++E++ YG + ++ Sbjct: 287 LLGIDLSAEEIIELLERMRYDAEIGDDKVKVTVPPYRVDILHEVDVIEDVAIAYGYNNLE 346 Query: 474 SEPLPLTQV--EDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLFGGGQRE- 530 E + + R ++ ++ EV+N++ S+E VLF E Sbjct: 347 PELPKVFTIGRLHPIEKL-----ERAIRDLMVGLGFQEVMNFTLTSEE--VLFEKMNLEP 399 Query: 531 ----LEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQKY 586 +E+LNPIS D + +RTSLLP LL+ N R IFE+ V D Sbjct: 400 EEDYVEVLNPISEDYTVVRTSLLPSLLEFLSNNKHREYPQ-KIFEIGDVVLIDESTETGT 458 Query: 587 MAAGIRKGSSGIEGSGRLWSDKSEERCRFVDLFDAKA---DALSVIEPFV-SLD-SLRFE 641 ++E + + ++A + SV++ + L E Sbjct: 459 ---------------------RTERKLAAA-IAHSEASFTEIKSVVQALLRELGIEYEVE 496 Query: 642 SGAPSWYHPGRSGIIKTSAEIVLGYFGEFHPNILDFFGLSNPICGFEVYLDSI 694 + PGR I + + + G GE HP +L+ FG+ P+ FE+ L+++ Sbjct: 497 ESEHPSFIPGRCADILVNGKKI-GVIGEIHPEVLENFGIEVPVVAFEIDLEAL 548 >gnl|CDD|161894 TIGR00471, pheT_arch, phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes. Length = 551 Score = 86.0 bits (213), Expect = 3e-17 Identities = 120/573 (20%), Positives = 212/573 (36%), Gaps = 103/573 (17%) Query: 153 SDPIIDVSLTPNRSDCIGVRGIALDLVAAGLGKLKE-INISCPLSSESI-PLEIKFDLDD 210 P I V PNR D + V G+A L+ + I L S ++K +D+ Sbjct: 40 ESPEIKVEFNPNRPDLLSVEGLAR--------SLRGYLGIEKGLKSYDSKKGDVKLTVDE 91 Query: 211 SSL-CKGFA-MCCVKGVRNN--VAPNWM--RQRLKAVGLRSISALVDITNYVSLDRGYPS 264 S L + F VKG+ N V + + +++L R+ V I + LD+ Sbjct: 92 SVLQIRPFITGAVVKGIILNDKVLESLIELQEKLHWNIGRNRR-KVAIGIH-DLDKVEFP 149 Query: 265 HVFDASRISDV----LTVRRACSGEKILAL--DNQEY-------DLSPDNVVIASDGRIQ 311 + A + + L + + ++IL Y D P +++ S + Sbjct: 150 FHYKAVSPNGIKFVPLNSDQEMTPDEILEEHPKGIRYAHIIEDSDKFP--LILDSKDDVL 207 Query: 312 SIAGIIGGKHAGCDDNTTDVLVEVALWDPINIARSGKNLGIITDSRYRFERGVDLQGMIP 371 S+ II + NT ++L++V D L I +RG ++ Sbjct: 208 SMPPIINSELTKLTVNTRNLLIDVTGTDK-TAVE--ITLNIACTMFA--DRGDGRITVVE 262 Query: 372 VLKHIVSLILSLCGGTASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILERL 431 V + L PR + + L G+++ ++ L+++ Sbjct: 263 VERPDEHLGQP---------------NLAPRFMEVSVEYINSLLGLNLSADEIAHSLKKM 307 Query: 432 GFSVIGEYDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQI-KSEPLPLTQVEDKRNLSL 490 + +K +V +P++R D+ + D++E++ YG + PL T L Sbjct: 308 RLDAVQSDEKLKVVIPAYRVDILHEVDIIEDVAIGYGYNNFPPELPLINTIGR----LKP 363 Query: 491 QQSRTRYVKRVLASRAMMEVVNWSFISKEQSVLF--GGGQRELEILNPISADMSNMRTSL 548 + ++ ++ EV+ + S+E + ++++ NP + + + +RTSL Sbjct: 364 LNKVSDIIREIMVGLGFQEVIPLTLTSEEVNFKRMRIEDNNDVKVANPKTLEYTIVRTSL 423 Query: 549 LPGLLKATGRNVDRAIADFAIFEVSHVYENDTPEGQKYMAAGIRKGSSGIEGSGRLWSDK 608 LPGLL+ N + IFE+ V D DK Sbjct: 424 LPGLLETLSENKHHELPQ-KIFEIGDVVVKD---------------------------DK 455 Query: 609 SEERCR-FVDLFDAKADA---LSVIEPFVSLDSLRFESGAPSW--------YHPGRSGII 656 SE R R L + + I+ V +L E G + PGR I Sbjct: 456 SETRSRVVTKLAVGITHSEANFNEIKSIV--AALARELGIEYEIEESEHPSFIPGRGAKI 513 Query: 657 KTSAEIVLGYFGEFHPNILDFFGLSNPICGFEV 689 + + G+FGE HP +L F L P+ FEV Sbjct: 514 VFEGKAI-GHFGEIHPEVLTNFELEFPVSAFEV 545 >gnl|CDD|129107 smart00874, B5, tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits. Length = 71 Score = 84.5 bits (210), Expect = 1e-16 Identities = 33/70 (47%), Positives = 45/70 (64%), Gaps = 2/70 (2%) Query: 401 PRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSV--IGEYDKFEVSVPSWRQDVEEKAD 458 PR I + RL G+D+ E+ IL+RLGF V G+ D EV+VPS+R D+ +AD Sbjct: 1 PRTITLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSGDDDTLEVTVPSYRFDILIEAD 60 Query: 459 LVEEILRIYG 468 L+EE+ RIYG Sbjct: 61 LIEEVARIYG 70 Score = 30.2 bits (69), Expect = 2.1 Identities = 11/41 (26%), Positives = 19/41 (46%) Query: 1 MKFTLSWLKDHLDTDVSLEKICDTLTSIGLEVEKVDNREAL 41 + + L D+S E+I + L +G EVE + + L Sbjct: 4 ITLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSGDDDTL 44 >gnl|CDD|177906 PLN02265, PLN02265, probable phenylalanyl-tRNA synthetase beta chain. Length = 597 Score = 73.6 bits (181), Expect = 2e-13 Identities = 82/305 (26%), Positives = 118/305 (38%), Gaps = 59/305 (19%) Query: 409 SEVKRLSGIDVPIEDSLRILER--LGFSVIGEYD-KFEVSVPSWRQDVEEKADLVEEILR 465 S + G+ + E+ +L + L + VSVP R D+ D+ E++ Sbjct: 317 SYINSSIGVSLDAEEVASLLNKMQLQAEQSSDDGCTIRVSVPPTRSDILHPCDVAEDVAI 376 Query: 466 IYGVDQIKSE---------PLPLTQVEDKRNLSLQQSRTRYVKRVLASRAMMEVVNWSFI 516 YG + I PL Q D ++ +A EV+ W Sbjct: 377 AYGYNNIPKRKPKSMTVGKQQPLNQFSDL------------LRAEVAMAGFTEVLTWILC 424 Query: 517 SKEQSVLFGGGQRE------LEILNPISADMSNMRTSLLPGLLKATGRNVDRAIADFAIF 570 S +++ F RE + I NP SAD +RTSLLPGLLK G N D +F Sbjct: 425 SHKEN--FAMLNREDDGNSAVIIGNPRSADFEVVRTSLLPGLLKTLGHNKDAPKP-IKLF 481 Query: 571 EVSHVYENDTPE-----GQKYMAAGIRKGSSGIEGSGRLWSDKSEE--RCRFVDLFDAKA 623 EVS V D + + +AA +SG E L D+ E FV++ D Sbjct: 482 EVSDVVLLDESKDVGARNSRRLAALYCGTTSGFEVIHGL-VDRIMEVLGIPFVEIGDNNG 540 Query: 624 DALSVIEPFVSLDSLRFESGAPSWYHPGR-SGIIKTSAEIVLGYFGEFHPNILDFFGLSN 682 + S P Y PGR + II + G FG HP +L+ F + + Sbjct: 541 YYVE-------------PSNEPE-YFPGRQASIIYKGKHV--GTFGIVHPEVLNNFDIPD 584 Query: 683 PICGF 687 P C F Sbjct: 585 P-CSF 588 >gnl|CDD|183389 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed. Length = 648 Score = 34.4 bits (80), Expect = 0.11 Identities = 26/119 (21%), Positives = 56/119 (47%), Gaps = 23/119 (19%) Query: 33 EKVDNREALSPFTIVKVLSVERNPDLDCAI-LRIDTGKHQEIQVVCGAPNVRVGLLGVWA 91 +KV+ R + +VL E+ D + L++D G+ + Q+V G + + Sbjct: 549 DKVELR-------VAEVLEAEKVEKSDKLLKLQVDLGEEEPRQIVSG--------IAKFY 593 Query: 92 PPGSCIPENNMIV-NV--RKIRGIESTGMMCSEKELMLSDDSASIMELPIDAPVGGRLS 147 PP + + ++V N+ K+ G ES GM+ + ++ D +++ + + P G ++ Sbjct: 594 PPEELVGKKVVVVANLKPAKLMGEESQGMILAAED----DGKLTLLTVDKEVPNGSKVK 648 >gnl|CDD|172756 PRK14268, PRK14268, phosphate ABC transporter ATP-binding protein; Provisional. Length = 258 Score = 32.7 bits (74), Expect = 0.43 Identities = 14/29 (48%), Positives = 18/29 (62%) Query: 378 SLILSLCGGTASDICIARNITYKPRKIVF 406 S LSL GG +CIAR + KP+ I+F Sbjct: 150 SPALSLSGGQQQRLCIARTLAVKPKIILF 178 >gnl|CDD|182690 PRK10742, PRK10742, putative methyltransferase; Provisional. Length = 250 Score = 31.7 bits (72), Expect = 0.70 Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 3/34 (8%) Query: 233 WMRQRLKAVGLRSISALVDIT---NYVSLDRGYP 263 W+++RL+ + S++AL DIT V LD +P Sbjct: 142 WLQERLQLIHASSLTALTDITPRPQVVYLDPMFP 175 >gnl|CDD|181525 PRK08655, PRK08655, prephenate dehydrogenase; Provisional. Length = 437 Score = 31.1 bits (71), Expect = 1.2 Identities = 20/119 (16%), Positives = 52/119 (43%), Gaps = 21/119 (17%) Query: 688 EVYLDSIPISQKKRTKTKKVVHLS-------------SLHPVKRDLAFIVDQHIPAGTLV 734 +V D + + + + K+ ++ +L RD++ + + ++ Sbjct: 320 KVTPDYVTLKKNNKEIKLKISNIRLLSEKELREWKKKNLEKYVRDISVLFPKGADPEVIL 379 Query: 735 NIIKNVDRLIDDVTVFDVFQGKSLGEGKKSVAIQVLIQPLKDTFRDDDIRILMDRIVEN 793 +++ N+ + D + + DV+ GK + EG SV ++ + F +D+ ++ I+E Sbjct: 380 DLLDNLKHVFD-IEIIDVYSGKQIEEGYLSVTFRITV------FGKEDLE-NVEEILEG 430 >gnl|CDD|180976 PRK07431, PRK07431, aspartate kinase; Provisional. Length = 587 Score = 30.7 bits (70), Expect = 1.4 Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 4/45 (8%) Query: 138 IDAPVGGR----LSDYLELSDPIIDVSLTPNRSDCIGVRGIALDL 178 IDA G + + + EL D I+++ T + D VRG+ALD Sbjct: 393 IDAEDGDKALRAVCEAFELEDSQIEINPTASGQDEPEVRGVALDR 437 >gnl|CDD|163306 TIGR03527, selenium_YedF, selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis. Length = 194 Score = 29.9 bits (68), Expect = 2.4 Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 1/36 (2%) Query: 401 PRKIVFMNSEVKRLSGIDVPIEDSLRILERLGFSVI 436 P++I+F+N VK L+ + + L+ LE+ G ++ Sbjct: 121 PKRILFVNGGVK-LTTEGSEVLEDLKELEKKGVEIL 155 >gnl|CDD|132490 TIGR03449, mycothiol_MshA, UDP-N-acetylglucosamine: 1L-myo-inositol-1-phosphate 1-alpha-D-N-acetylglucosaminyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species. Length = 405 Score = 29.7 bits (67), Expect = 2.8 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 6/68 (8%) Query: 573 SHVYENDTPEGQKYMAAGIRKGSSGI-EGSGRLWSDKSEERCRFVDLFDAKADALSVIEP 631 + + + DTPE R G + + + RL ++ EE V +DA D + V+ P Sbjct: 140 AALADGDTPE-----PEARRIGEQQLVDNADRLIANTDEEARDLVRHYDADPDRIDVVAP 194 Query: 632 FVSLDSLR 639 L+ R Sbjct: 195 GADLERFR 202 >gnl|CDD|184583 PRK14237, PRK14237, phosphate transporter ATP-binding protein; Provisional. Length = 267 Score = 29.7 bits (67), Expect = 3.1 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%) Query: 381 LSLCGGTASDICIARNITYKPRKIVFMNSEVKRLSGIDV-PIEDSL 425 L+L GG +CIAR I KP I+ M+ L I +E+++ Sbjct: 162 LTLSGGQQQRLCIARAIAVKP-DILLMDEPASALDPISTMQLEETM 206 >gnl|CDD|163014 TIGR02778, ligD_pol, DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain. Length = 245 Score = 29.6 bits (67), Expect = 3.7 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 10/54 (18%) Query: 193 CPLSSESIPLEIKFDLD-DSSLCKGFAMCCVKGVRNNVAPNWMRQRLKAVGLRS 245 + + P I FDLD + + + A +R+ L +GL S Sbjct: 106 ARIDAPEKPDRIVFDLDPGPGV--AWKLVVE-------AAQLIRELLDELGLES 150 >gnl|CDD|128425 smart00115, CASc, Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues. Length = 241 Score = 29.5 bits (67), Expect = 3.8 Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 9/76 (11%) Query: 7 WLKDHLDTDVSLEKICDTLTSIGLEVEKVDNREALSPFTIVKVL-SVERNP---DLDCAI 62 L TDV E + + S+G EV +N A +++ L P D D + Sbjct: 21 SLPRRNGTDVDAENLTELFQSLGYEVHVKNNLTAEE---MLEELKEFAERPEHSDSDSFV 77 Query: 63 LRIDTGKHQEIQVVCG 78 + + H E + G Sbjct: 78 CVLLS--HGEEGGIYG 91 >gnl|CDD|179264 PRK01254, PRK01254, hypothetical protein; Provisional. Length = 707 Score = 28.9 bits (65), Expect = 4.8 Identities = 17/36 (47%), Positives = 17/36 (47%), Gaps = 10/36 (27%) Query: 597 GIEGSGR------LWSDKSEERCRFVDLFDAKADAL 626 GIE S R WSDK R L DAKAD L Sbjct: 156 GIEASLRRIAHYDYWSDK----VRRSVLVDAKADIL 187 >gnl|CDD|162807 TIGR02323, CP_lyasePhnK, phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se. Length = 253 Score = 29.0 bits (65), Expect = 5.1 Identities = 35/105 (33%), Positives = 53/105 (50%), Gaps = 15/105 (14%) Query: 385 GGTASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIE----DSLRILER-LGFSVI-GE 438 GG + IARN+ +PR +VFM+ G+DV ++ D LR L R LG +VI Sbjct: 151 GGMQQRLQIARNLVTRPR-LVFMDEPT---GGLDVSVQARLLDLLRGLVRDLGLAVIIVT 206 Query: 439 YDKFEVSVPSWRQDVEEKADLVEEILRIYGVDQIKSEPL-PLTQV 482 +D + + R V ++ +VE L DQ+ +P P TQ+ Sbjct: 207 HDLGVARLLAQRLLVMQQGRVVESGL----TDQVLDDPQHPYTQL 247 >gnl|CDD|184597 PRK14270, PRK14270, phosphate ABC transporter ATP-binding protein; Provisional. Length = 251 Score = 28.8 bits (64), Expect = 5.7 Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 2/44 (4%) Query: 381 LSLCGGTASDICIARNITYKPRKIVFMNSEVKRLSGID-VPIED 423 L L GG +CIAR I KP ++ M+ L I + IED Sbjct: 146 LKLSGGQQQRLCIARTIAVKP-DVILMDEPTSALDPISTLKIED 188 >gnl|CDD|181145 PRK07850, PRK07850, acetyl-CoA acetyltransferase; Provisional. Length = 387 Score = 28.5 bits (64), Expect = 7.5 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 7/50 (14%) Query: 417 IDVPIEDSLRILERLGFSVIGEYDKFEV-----SVP-SWRQDVEEKADLV 460 +D P++ + ++LE+ G IG+ D E+ SV SW Q E D V Sbjct: 284 LDGPVQATAKVLEKAGMK-IGDIDLVEINEAFASVVLSWAQVHEPDMDKV 332 >gnl|CDD|184588 PRK14243, PRK14243, phosphate transporter ATP-binding protein; Provisional. Length = 264 Score = 28.2 bits (63), Expect = 7.6 Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 6/49 (12%) Query: 381 LSLCGGTASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIEDSLRILE 429 LSL GG +CIAR I +P +++ M+ L PI +LRI E Sbjct: 150 LSLSGGQQQRLCIARAIAVQP-EVILMDEPCSALD----PIS-TLRIEE 192 >gnl|CDD|162242 TIGR01187, potA, spermidine/putrescine ABC transporter ATP-binding subunit. This model describes spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Polyamines like spermidine and putrescine play vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included). Length = 325 Score = 27.8 bits (62), Expect = 9.8 Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 9/59 (15%) Query: 383 LCGGTASDICIARNITYKPRKIVFMNSEVKRLSGIDVPIEDSL-----RILERLGFSVI 436 L GG + +AR + +KP KI+ ++ + LS +D + D + I E+LG + + Sbjct: 101 LSGGQQQRVALARALVFKP-KILLLD---EPLSALDKKLRDQMQLELKTIQEQLGITFV 155 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 0.320 0.138 0.400 Gapped Lambda K H 0.267 0.0650 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 13,261,423 Number of extensions: 896431 Number of successful extensions: 1666 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1636 Number of HSP's successfully gapped: 48 Length of query: 805 Length of database: 5,994,473 Length adjustment: 101 Effective length of query: 704 Effective length of database: 3,812,065 Effective search space: 2683693760 Effective search space used: 2683693760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 61 (27.4 bits)