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= 0001.2908.p (762 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... 1380 0.0 gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 99 1e-21 gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidogl... 89 2e-18 gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic pep... 69 2e-12 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 1380 bits (3572), Expect = 0.0, Method: Compositional matrix adjust. Identities = 670/731 (91%), Positives = 701/731 (95%) Query: 25 IPTAASAVPSFSEVQRDFLPSEASLLDRNGELLQRIRINMDERRLSWVKLEDVSPALRHA 84 +P AA AVPSF EVQRDFLPSEASLLDRNGELLQR+RINMDER+L+WV+LEDVSPALRHA Sbjct: 20 MPVAAHAVPSFKEVQRDFLPSEASLLDRNGELLQRMRINMDERKLAWVRLEDVSPALRHA 79 Query: 85 LIASEDRRFYQHSGIDWSAVAASAWGNLWNTKTRGASTITMQLAGLIYDNLRRKSGARSL 144 LIASEDRRFYQHSGIDWSAVAASAWGNLWN+KTRGASTITMQLAGLIYD+LRRKSGARSL Sbjct: 80 LIASEDRRFYQHSGIDWSAVAASAWGNLWNSKTRGASTITMQLAGLIYDDLRRKSGARSL 139 Query: 145 TQKVSQAWIAQSLERSWRKDQILEAYLNLVAFRGELVGVHALSRVMFRKHPSGLDQGEAA 204 TQKVSQAWIAQSLER+WRKDQILEAYLNLVAFRGELVGVHALSR+MF KHPSGLDQGEAA Sbjct: 140 TQKVSQAWIAQSLERNWRKDQILEAYLNLVAFRGELVGVHALSRIMFGKHPSGLDQGEAA 199 Query: 205 IAVALIRAPNATPRRVAERACAILKEEGAAEQCNGMDGRTELALARVSAKRDLPGTSDAP 264 IAVALIRAPNATPRRVA+RACAILKEEG EQCNGMDGRTELALARVSAKRDLPGTSDAP Sbjct: 200 IAVALIRAPNATPRRVADRACAILKEEGPGEQCNGMDGRTELALARVSAKRDLPGTSDAP 259 Query: 265 QLAPHLARKLLSAPGQQVRSTLDAPLQRFAAQALRHQLAALADRNIEDGSIIVIDNTSGE 324 QLAPHLARKLLSAPGQQ+RSTLDA LQRFA QALRHQLA LADRNIEDG+IIVIDN +G+ Sbjct: 260 QLAPHLARKLLSAPGQQLRSTLDARLQRFATQALRHQLAGLADRNIEDGAIIVIDNATGD 319 Query: 325 VLAWIGSSGSLSAAANVDGVVAQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS 384 VLAW+GSSG LSAAANVDGVVAQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS Sbjct: 320 VLAWVGSSGPLSAAANVDGVVAQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS 379 Query: 385 AGLYIPQNYDKQYKGLVSLRTSLGSSLNIPAVRTLVMVTPERFFRRLQALGFNLRESGDY 444 AGLYIPQNYDKQYKGLVSLRTSLGSSLNIPAVRTLVMVTPERFFRRLQALGFNLRESGDY Sbjct: 380 AGLYIPQNYDKQYKGLVSLRTSLGSSLNIPAVRTLVMVTPERFFRRLQALGFNLRESGDY 439 Query: 445 YGYSLALGSADVTLANLTNAYRVLANQGRYSPLRTRLDQARTPARTTPVMDADAAFIIGD 504 YGYSLALGSADVTLANL NAYRVLANQGRY+PLRTRLD+ARTPAR T VMDADAA+I+GD Sbjct: 440 YGYSLALGSADVTLANLANAYRVLANQGRYTPLRTRLDEARTPARATQVMDADAAYIVGD 499 Query: 505 ILSDRSARARTFGLENALSTRIWTAVKTGTSKDMRDNWCVGYSSRYTVGVWVGNASGAPM 564 ILSDRSARARTFGLENALSTRIWTAVKTGTSKDMRDNWCVGYS+RYTVGVWVGNASGAPM Sbjct: 500 ILSDRSARARTFGLENALSTRIWTAVKTGTSKDMRDNWCVGYSTRYTVGVWVGNASGAPM 559 Query: 565 WDVSGVTGAAPVWQALMQYLHERGREGGRDVRNAPPAKPAGVQAQAIRYEQEVEAARTEY 624 WDVSGVTGAAPVWQ +MQYLHERGR GGR+ N PPAKPAGVQAQ IRYEQEVEAARTEY Sbjct: 560 WDVSGVTGAAPVWQEVMQYLHERGRNGGREAGNGPPAKPAGVQAQMIRYEQEVEAARTEY 619 Query: 625 FLPGTAQSDIRIAHVREIRPAITYPTAGMLAALDPDIPPARQRIRFRAQGAPVGSRWRLD 684 FLPGTAQ++IR+AH R+IRPAITYPTAGMLAALDPDIPPARQRIRFRAQG P GSRW LD Sbjct: 620 FLPGTAQAEIRLAHARDIRPAITYPTAGMLAALDPDIPPARQRIRFRAQGVPAGSRWVLD 679 Query: 685 GKLIPQEVMQAGRVKAQKVSANTSATGEEELGFEWMPWPGKHVLVLQDQGGKELDSVRFE 744 GKL+PQEVMQAGRVKAQKVS N SA+GEEELGF+WMPWPGKHVLVLQD+GG+ELD VRFE Sbjct: 680 GKLMPQEVMQAGRVKAQKVSTNASASGEEELGFDWMPWPGKHVLVLQDKGGQELDRVRFE 739 Query: 745 VRGAVERPAGK 755 VRGAV RP K Sbjct: 740 VRGAVARPEEK 750 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 99.4 bits (246), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 83/253 (32%), Positives = 130/253 (51%), Gaps = 24/253 (9%) Query: 346 AQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATSAG-LYIPQNYDKQYKGLVSLR 404 A RQ GS+ KPF+Y ++EK L+ A++++D+P+ + G ++ P+NY +++G +S+R Sbjct: 463 AWRQPGSSFKPFIYSSSLEKG-LSPATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMR 521 Query: 405 TSLGSSLNIPAVRTLVMVTPERFFRRLQALGFNLRESGDYYGYSLALGSADVTLANLTNA 464 +L S+N+ ++R L V + + GF+ ++ Y +LALG+ +VT + A Sbjct: 522 RALQKSINLVSIRILERVGVKYAQEYITRFGFDADKNPPY--LTLALGAGNVTPLQMVGA 579 Query: 465 YRVLANQG-RYSP-LRTR--------LDQARTPA----RTTPVMDADAAFIIGDILSDRS 510 Y V AN G + +P L T+ L QA+ PA + V+DA AFI+ +L D Sbjct: 580 YSVFANGGYKINPYLITKVTDSNGEVLSQAK-PATADDESNRVIDARNAFIMDSMLRDVV 638 Query: 511 ARARTFGLENALS-TRIWTAVKTGTSKDMRDNWCVGYSSRYTVGVWVGNASGAPMWD-VS 568 ALS R A KTGT+ D D W GY T W+G + D + Sbjct: 639 RHGTAV---KALSLKRTDLAGKTGTTNDSMDAWFAGYQPGLTAIAWIGYDQPKSLGDRET 695 Query: 569 GVTGAAPVWQALM 581 G A PVW + M Sbjct: 696 GGGLALPVWISYM 708 Score = 84.0 bits (206), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 55/173 (31%), Positives = 87/173 (50%), Gaps = 15/173 (8%) Query: 66 ERRLSWVKLEDVSPALRHALIASEDRRFYQHSGIDWSAVAASAWGNLWNTKTRGASTITM 125 E R + V +D+ ++ A++A ED RFY+H G+D+ +A + + NL + GASTIT Sbjct: 67 EERRNLVHFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARATFSNL-SGGGGGASTITQ 125 Query: 126 QLAGLIYDNLRRKSGARSLTQKVSQAW-----IAQSLERSWRKDQILEAYLNLVAFRGEL 180 Q+A N S + QK ++ + +A +E + KDQILE Y+N + Sbjct: 126 QVA----RNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQRA 181 Query: 181 VGVHALSRVMFRKHPSGLDQGEAAIAVALIRAPNA-----TPRRVAERACAIL 228 G + +++ F K L EAA+ L +AP+A P+R R IL Sbjct: 182 YGFASAAQIYFGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYIL 234 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 88.6 bits (218), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 58/170 (34%), Positives = 93/170 (54%), Gaps = 11/170 (6%) Query: 66 ERRLSWVKLEDVSPALRHALIASEDRRFYQHSGIDWSAVA-ASAWGNLWNTKTRGASTIT 124 E + S VKL+D+ +++A++A ED RFY+H GIDW +A A L + ++GASTIT Sbjct: 85 EEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTIT 144 Query: 125 MQLAGLIYDNLRRKSGARSLTQKVSQAWIAQSLERSWRKDQILEAYLNLVAFRGELVGVH 184 MQ+A ++ + ++ ++K+ + +A +E + KDQILE Y+N + G Sbjct: 145 MQVARNVF-----LTKEKTFSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFA 199 Query: 185 ALSRVMFRKHPSGLDQGEAAIAVALIRAPNA-----TPRRVAERACAILK 229 A +R F K + EAA+ L +AP+A P+R R IL+ Sbjct: 200 AAARTYFGKDLKDVTLAEAAMLAGLPKAPSAYNPIVNPKRAHIRQQYILQ 249 Score = 73.6 bits (179), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 72/229 (31%), Positives = 112/229 (48%), Gaps = 24/229 (10%) Query: 346 AQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATSAGL--YIPQNYDKQYKGLVSL 403 A RQ GST KPF+Y A+EK + AS+++D+PV+ G + P++ D+ G +++ Sbjct: 476 AWRQPGSTFKPFIYSAALEKGF-APASIVNDAPVSYPAGPGQPNWEPRD-DETPAGPITV 533 Query: 404 RTSLGSSLNIPAVRTLVMV-TPERFFRRLQALGFNLRESGDYYGYSLALGSADVTLANLT 462 RT+L S+N+ A+RTL + P GF+ + Y +ALG+ L+ Sbjct: 534 RTALQKSVNLVAIRTLDYIGVPYAKDFITGTYGFDADKVPPY--LPMALGAGQTNPLQLS 591 Query: 463 NAYRVLANQGRYSPLRTRLDQARTPARTTPVMDADAAFIIGD----ILSDRSARARTFGL 518 AY V AN G ++ L T AR + A+ I+G+ ++S+R++ T L Sbjct: 592 AAYSVFANGGY--KVQPYLISQITDARGQALSKAE-PLIVGNGAPRVVSERNSYMMTSML 648 Query: 519 EN-------ALSTRIW---TAVKTGTSKDMRDNWCVGYSSRYTVGVWVG 557 ++ A S I A KTGT+ D D W GY VW+G Sbjct: 649 KSVAQGGTGARSNSIGRSDLAGKTGTTNDAVDGWFAGYQRTLATVVWMG 697 >gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic peptidoglycan transglycosylase [Herbaspirillum seropedicae SmR1] Length = 235 Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 62/201 (30%), Positives = 90/201 (44%), Gaps = 12/201 (5%) Query: 40 RDFLPSEASLLDRNGELLQRIRINMDERRLSWVKLEDVSPALRHALIASEDRRFYQHSGI 99 RD P S + + LLQ + + + WV +S L+ A+IASED F H G+ Sbjct: 34 RDHNPESTSFMRQQLALLQE-KDPKAQLQFRWVPYARISNNLKRAIIASEDSNFSSHDGV 92 Query: 100 DWSAVAASAWGNLWNTK-TRGASTITMQLAGLIYDNLRRKSGARSLTQKVSQAWIAQSLE 158 DW A+ + N K G STIT QLA ++ SG RS +K + I LE Sbjct: 93 DWEALQKAYEKNEKKGKVVAGGSTITQQLAKNLF-----LSGERSYLRKGQEFIITYMLE 147 Query: 159 RSWRKDQILEAYLNLVAFRGELVGVHALSRVMFRKHPSGLDQGEAAIAVALIRAPNATPR 218 K +I E YLN+V + + G A ++ +R + L +AA ++ P R Sbjct: 148 FLLDKQRIFEIYLNVVEWGNGVFGAEAAAQHYYRIPAASLGAEQAARLAVMLPRPRYYDR 207 Query: 219 R-----VAERACAILKEEGAA 234 +A R IL+ AA Sbjct: 208 NRGSGYLAARTSLILRRMNAA 228 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 0.132 0.386 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: 2,395,619 Number of extensions: 103575 Number of successful extensions: 352 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 344 Number of HSP's successfully gapped: 6 Length of query: 762 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 669 Effective length of database: 1,179,515 Effective search space: 789095535 Effective search space used: 789095535 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 (21.7 bits) S2: 134 (56.2 bits)