BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0005.0090.p (728 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [H... 1048 0.0 gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 101 2e-22 gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidogl... 93 8e-20 gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic pep... 62 2e-10 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 1048 bits (2710), Expect = 0.0, Method: Compositional matrix adjust. Identities = 517/702 (73%), Positives = 592/702 (84%), Gaps = 26/702 (3%) Query: 20 VPGIALAVPGFAEVQQSVRSSDASMFDRHGELIQQLRLNPNERRLSWIALEDISPALRNA 79 +P A AVP F EVQ+ S+AS+ DR+GEL+Q++R+N +ER+L+W+ LED+SPALR+A Sbjct: 20 MPVAAHAVPSFKEVQRDFLPSEASLLDRNGELLQRMRINMDERKLAWVRLEDVSPALRHA 79 Query: 80 LIASEDRRFYQHSGVDWNAVAASAWGNLWNTKTRGASTITMQLAGLIYDDLRRKSSARSM 139 LIASEDRRFYQHSG+DW+AVAASAWGNLWN+KTRGASTITMQLAGLIYDDLRRKS ARS+ Sbjct: 80 LIASEDRRFYQHSGIDWSAVAASAWGNLWNSKTRGASTITMQLAGLIYDDLRRKSGARSL 139 Query: 140 TQKVSQVFIAQSLERNWRKDQILEAYLNLVSFRGELVGVHALSRVLFGKHPSGLNQSEAA 199 TQKVSQ +IAQSLERNWRKDQILEAYLNLV+FRGELVGVHALSR++FGKHPSGL+Q EAA Sbjct: 140 TQKVSQAWIAQSLERNWRKDQILEAYLNLVAFRGELVGVHALSRIMFGKHPSGLDQGEAA 199 Query: 200 IAVALIRAPNAKPAKVSERACAILKEQQAPQECNGLQGRTELVLARATAKGELSGAGTAP 259 IAVALIRAPNA P +V++RACAILKE+ ++CNG+ GRTEL LAR +AK +L G AP Sbjct: 200 IAVALIRAPNATPRRVADRACAILKEEGPGEQCNGMDGRTELALARVSAKRDLPGTSDAP 259 Query: 260 QLAPHLGRKLLKDAGKPVYSTIDAATQRFASDALRRQLSALVERNIEDGAVVVIDNASGD 319 QLAPHL RKLL G+ + ST+DA QRFA+ ALR QL+ L +RNIEDGA++VIDNA+GD Sbjct: 260 QLAPHLARKLLSAPGQQLRSTLDARLQRFATQALRHQLAGLADRNIEDGAIIVIDNATGD 319 Query: 320 VLAWVGSSGSLSGAAQVDGVQALRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS 379 VLAWVGSSG LS AA VDGV A RQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS Sbjct: 320 VLAWVGSSGPLSAAANVDGVVAQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS 379 Query: 380 AGLYIPQNYDKQFKGLVSMRTALGSSLNIPAVRTLVTVTPERFFRRLQSLGFNLRESGDY 439 AGLYIPQNYDKQ+KGLVS+RT+LGSSLNIPAVRTLV VTPERFFRRLQ+LGFNLRESGDY Sbjct: 380 AGLYIPQNYDKQYKGLVSLRTSLGSSLNIPAVRTLVMVTPERFFRRLQALGFNLRESGDY 439 Query: 440 YGYSLALGSADVSLLSLTNAYRALANQGRYSSVRTTTSDPR--AAYQQAMDGSASFIVGD 497 YGYSLALGSADV+L +L NAYR LANQGRY+ +RT + R A Q MD A++IVGD Sbjct: 440 YGYSLALGSADVTLANLANAYRVLANQGRYTPLRTRLDEARTPARATQVMDADAAYIVGD 499 Query: 498 ILSDRSARARTFGLESALSTRIWTAVKTGTSKDMRDNWCVGFSSRYTVGVWVGNASGAPM 557 ILSDRSARARTFGLE+ALSTRIWTAVKTGTSKDMRDNWCVG+S+RYTVGVWVGNASGAPM Sbjct: 500 ILSDRSARARTFGLENALSTRIWTAVKTGTSKDMRDNWCVGYSTRYTVGVWVGNASGAPM 559 Query: 558 WDVSGVTGAAPVWQEVMQYLH-------RQSGSQEPARPASVIAQPVQFENRLEAARTEY 610 WDVSGVTGAAPVWQEVMQYLH R++G+ PA+PA V AQ +++E +EAARTEY Sbjct: 560 WDVSGVTGAAPVWQEVMQYLHERGRNGGREAGNGPPAKPAGVQAQMIRYEQEVEAARTEY 619 Query: 611 FLPGTQQSLLRVAKSNDIAPAISYPTPGMLVAIDPDIPPAHQRLRFSAQGVKQGS-WVLD 669 FLPGT Q+ +R+A + DI PAI+YPT GML A+DPDIPPA QR+RF AQGV GS WVLD Sbjct: 620 FLPGTAQAEIRLAHARDIRPAITYPTAGMLAALDPDIPPARQRIRFRAQGVPAGSRWVLD 679 Query: 670 GKSL--------------VRTAGKKTG--DLGYDWMPWPGKH 695 GK + V T +G +LG+DWMPWPGKH Sbjct: 680 GKLMPQEVMQAGRVKAQKVSTNASASGEEELGFDWMPWPGKH 721 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 101 bits (252), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 108/397 (27%), Positives = 174/397 (43%), Gaps = 50/397 (12%) Query: 197 EAAIAVALIRAPNAKPAKVSERACAILKEQQAPQECNGLQGRTELVLARATAKGELSGAG 256 E A+ V L P++ + A++ E + P+E + E + +SGAG Sbjct: 343 EDAVEVELADHPDS-----DDMVSAVVLEAK-PKEITAMLSTGEEI--------SISGAG 388 Query: 257 TAPQLAPHLGRKLLKDAGKPVYSTIDAATQRFASDALRRQLSALVERNIEDGAVVVIDNA 316 G LL D P A R D ++ + E + A V +++ Sbjct: 389 LG------FGANLLSDKAPPQKKIRRGAIIRVFQDGNNWIITQMPEV---ESAFVSVNSQ 439 Query: 317 SGDVLAWVGSSGSLSGAAQVDGV-QALRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVN 375 G + + VG G + + V QA RQ GS+ KPF+Y ++EK L+ A++++D+P+ Sbjct: 440 DGAIRSLVG--GFDFNRNKFNHVTQAWRQPGSSFKPFIYSSSLEKG-LSPATIINDAPLT 496 Query: 376 LATSAG-LYIPQNYDKQFKGLVSMRTALGSSLNIPAVRTLVTVTPERFFRRLQSLGFNLR 434 + G ++ P+NY +F+G +SMR AL S+N+ ++R L V + + GF+ Sbjct: 497 FTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQEYITRFGFDAD 556 Query: 435 ESGDYYGYSLALGSADVSLLSLTNAYRALANQGR----YSSVRTTTSDPRAAYQ------ 484 ++ Y +LALG+ +V+ L + AY AN G Y + T S+ Q Sbjct: 557 KNPPY--LTLALGAGNVTPLQMVGAYSVFANGGYKINPYLITKVTDSNGEVLSQAKPATA 614 Query: 485 -----QAMDGSASFIVGDILSDRSARARTFGLESALS-TRIWTAVKTGTSKDMRDNWCVG 538 + +D +FI+ +L D ALS R A KTGT+ D D W G Sbjct: 615 DDESNRVIDARNAFIMDSMLRDVVRHGTAV---KALSLKRTDLAGKTGTTNDSMDAWFAG 671 Query: 539 FSSRYTVGVWVGNASGAPMWD-VSGVTGAAPVWQEVM 574 + T W+G + D +G A PVW M Sbjct: 672 YQPGLTAIAWIGYDQPKSLGDRETGGGLALPVWISYM 708 Score = 92.4 bits (228), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 81/267 (30%), Positives = 126/267 (47%), Gaps = 22/267 (8%) Query: 44 MFDRHGELIQQLRLNPNERRLSWIALEDISPALRNALIASEDRRFYQHSGVDWNAVAASA 103 +F G LI + E R + + +DI ++ A++A ED RFY+H GVD+ +A + Sbjct: 54 IFSADGVLIGEF----GEERRNLVHFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARAT 109 Query: 104 WGNLWNTKTRGASTITMQLAGLIYDDLRRKSSARSMTQKV-SQVFIAQSLERNWRKDQIL 162 + NL + GASTIT Q+A + + + T+K ++ +A +E N KDQIL Sbjct: 110 FSNL-SGGGGGASTITQQVARNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQIL 168 Query: 163 EAYLNLVSFRGELVGVHALSRVLFGKHPSGLNQSEAAIAVALIRAPNA-KPAKVSERACA 221 E Y+N + G + +++ FGK L +EAA+ L +AP+A P +RA A Sbjct: 169 EVYMNQIYLGQRAYGFASAAQIYFGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHA 228 Query: 222 ILKEQQAPQECNGLQGRTELVLARAT-----AKGELSGAGTAPQLAPHLGRKLL----KD 272 ++Q L T+ A KG+ S G + + R+L+ KD Sbjct: 229 --RQQYILLRMRQLGYITDAQYQAAKDEELRVKGDSSAFGMHAEYVAEMARQLVYAQYKD 286 Query: 273 A----GKPVYSTIDAATQRFASDALRR 295 G V++TI Q A ALRR Sbjct: 287 ETYTRGLNVFTTITKTDQDAAYIALRR 313 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 92.8 bits (229), Expect = 8e-20, Method: Compositional matrix adjust. Identities = 78/250 (31%), Positives = 129/250 (51%), Gaps = 22/250 (8%) Query: 61 ERRLSWIALEDISPALRNALIASEDRRFYQHSGVDWNAVA-ASAWGNLWNTKTRGASTIT 119 E + S + L+DI ++NA++A ED RFY+H G+DW +A A L + ++GASTIT Sbjct: 85 EEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTIT 144 Query: 120 MQLAGLIYDDLRRKSSARSMTQKVSQVFIAQSLERNWRKDQILEAYLNLVSFRGELVGVH 179 MQ+A ++ + ++ ++K+ +V +A +E KDQILE Y+N + G Sbjct: 145 MQVARNVF-----LTKEKTFSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFA 199 Query: 180 ALSRVLFGKHPSGLNQSEAAIAVALIRAPNAKPAKVSERACAILKEQQAPQECNGLQGRT 239 A +R FGK + +EAA+ L +AP+A V+ + I ++Q Q + T Sbjct: 200 AAARTYFGKDLKDVTLAEAAMLAGLPKAPSAYNPIVNPKRAHI-RQQYILQRMLDVGFIT 258 Query: 240 ELVLARATAKGELSGAGTAPQLAPH------LGRKLL-----KDA---GKPVYSTIDAAT 285 + +A AK EL Q H + R+++ +D G VY+T++AA Sbjct: 259 KAQYEKA-AKEELKVRAPGSQYNIHAEYVNEMVRQMVYAQYKEDTYTQGFNVYTTVNAAD 317 Query: 286 QRFASDALRR 295 Q+ A A+R+ Sbjct: 318 QQAAYLAVRK 327 Score = 84.3 bits (207), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 80/253 (31%), Positives = 121/253 (47%), Gaps = 23/253 (9%) Query: 340 QALRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATSAGL--YIPQNYDKQFKGLVS 397 QA RQ GST KPF+Y A+EK + AS+++D+PV+ G + P++ D+ G ++ Sbjct: 475 QAWRQPGSTFKPFIYSAALEKGF-APASIVNDAPVSYPAGPGQPNWEPRD-DETPAGPIT 532 Query: 398 MRTALGSSLNIPAVRTLVTV-TPERFFRRLQSLGFNLRESGDYYGYSLALGSADVSLLSL 456 +RTAL S+N+ A+RTL + P + GF+ + Y +ALG+ + L L Sbjct: 533 VRTALQKSVNLVAIRTLDYIGVPYAKDFITGTYGFDADKVPPY--LPMALGAGQTNPLQL 590 Query: 457 TNAYRALANQGRYSSVRTTTSDPRAAYQQAMDGSASFIVGD----ILSDRSARARTFGLE 512 + AY AN G Y S A QA+ + IVG+ ++S+R++ T L+ Sbjct: 591 SAAYSVFANGG-YKVQPYLISQITDARGQALSKAEPLIVGNGAPRVVSERNSYMMTSMLK 649 Query: 513 S-------ALSTRIW---TAVKTGTSKDMRDNWCVGFSSRYTVGVWVGNASGAPMWDVS- 561 S A S I A KTGT+ D D W G+ VW+G + Sbjct: 650 SVAQGGTGARSNSIGRSDLAGKTGTTNDAVDGWFAGYQRTLATVVWMGYDQPKSLGSKEF 709 Query: 562 GVTGAAPVWQEVM 574 G A P+W + M Sbjct: 710 GAQLALPIWVDYM 722 >gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic peptidoglycan transglycosylase [Herbaspirillum seropedicae SmR1] Length = 235 Score = 61.6 bits (148), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 50/146 (34%), Positives = 70/146 (47%), Gaps = 7/146 (4%) Query: 63 RLSWIALEDISPALRNALIASEDRRFYQHSGVDWNAVAASAWGNLWNTK-TRGASTITMQ 121 + W+ IS L+ A+IASED F H GVDW A+ + N K G STIT Q Sbjct: 61 QFRWVPYARISNNLKRAIIASEDSNFSSHDGVDWEALQKAYEKNEKKGKVVAGGSTITQQ 120 Query: 122 LAGLIYDDLRRKSSARSMTQKVSQVFIAQSLERNWRKDQILEAYLNLVSFRGELVGVHAL 181 LA ++ S RS +K + I LE K +I E YLN+V + + G A Sbjct: 121 LAKNLF-----LSGERSYLRKGQEFIITYMLEFLLDKQRIFEIYLNVVEWGNGVFGAEAA 175 Query: 182 SRVLFGKHPSGLNQSEAA-IAVALIR 206 ++ + + L +AA +AV L R Sbjct: 176 AQHYYRIPAASLGAEQAARLAVMLPR 201 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.318 0.131 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 2,299,050 Number of extensions: 97926 Number of successful extensions: 378 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 366 Number of HSP's successfully gapped: 6 Length of query: 728 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 636 Effective length of database: 1,184,250 Effective search space: 753183000 Effective search space used: 753183000 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: 41 (21.8 bits) S2: 134 (56.2 bits)