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= 0098.0003.p (431 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... 580 e-167 gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 74 2e-14 gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidogl... 69 6e-13 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 580 bits (1496), Expect = e-167, Method: Compositional matrix adjust. Identities = 288/401 (71%), Positives = 334/401 (83%), Gaps = 15/401 (3%) Query: 20 VPGIVLAVPGFAEVQQSFRSSEASMVDRHGELIQQLRLNPNERRLSWIALEDISPALRNA 79 +P AVP F EVQ+ F SEAS++DR+GEL+Q++R+N +ER+L+W+ LED+SPALR+A Sbjct: 20 MPVAAHAVPSFKEVQRDFLPSEASLLDRNGELLQRMRINMDERKLAWVRLEDVSPALRHA 79 Query: 80 LIASEDRRFYQHSGVDWNAVAASAWGNLWNTPPPPPPP---------------PPSARSM 124 LIASEDRRFYQHSG+DW+AVAASAWGNLWN+ ARS+ Sbjct: 80 LIASEDRRFYQHSGIDWSAVAASAWGNLWNSKTRGASTITMQLAGLIYDDLRRKSGARSL 139 Query: 125 TQKVSQVFIAQSLERNWRKDQILEAYLNLVSFRGELVGVHALSRVLFGKHPSGLNQSEAA 184 TQKVSQ +IAQSLERNWRKDQILEAYLNLV+FRGELVGVHALSR++FGKHPSGL+Q EAA Sbjct: 140 TQKVSQAWIAQSLERNWRKDQILEAYLNLVAFRGELVGVHALSRIMFGKHPSGLDQGEAA 199 Query: 185 IAVALIRAPNARPAKVSERACAILKEQQAPQECNGLQGRTELVLARATAKGEVSGAATAP 244 IAVALIRAPNA P +V++RACAILKE+ ++CNG+ GRTEL LAR +AK ++ G + AP Sbjct: 200 IAVALIRAPNATPRRVADRACAILKEEGPGEQCNGMDGRTELALARVSAKRDLPGTSDAP 259 Query: 245 QLAPHLGRKLLKDAGKTIRSTLDAATQRFASDALRQQLSALVERNIEDGAVVVIDNASGD 304 QLAPHL RKLL G+ +RSTLDA QRFA+ ALR QL+ L +RNIEDGA++VIDNA+GD Sbjct: 260 QLAPHLARKLLSAPGQQLRSTLDARLQRFATQALRHQLAGLADRNIEDGAIIVIDNATGD 319 Query: 305 VLAWVGSSGSLSGAAQVDGVQALRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS 364 VLAWVGSSG LS AA VDGV A RQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS Sbjct: 320 VLAWVGSSGPLSAAANVDGVVAQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATS 379 Query: 365 AGLYIPQNYDKQFKGLVSMRTALGSSLNIPAVRTLVTVTPE 405 AGLYIPQNYDKQ+KGLVS+RT+LGSSLNIPAVRTLV VTPE Sbjct: 380 AGLYIPQNYDKQYKGLVSLRTSLGSSLNIPAVRTLVMVTPE 420 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 74.3 bits (181), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 50/169 (29%), Positives = 80/169 (47%), Gaps = 30/169 (17%) Query: 61 ERRLSWIALEDISPALRNALIASEDRRFYQHSGVDWNAVAASAWGNLWNTPPPPPPPPPS 120 E R + + +DI ++ A++A ED RFY+H GVD+ +A + + NL Sbjct: 67 EERRNLVHFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARATFSNLSGGGG-------G 119 Query: 121 ARSMTQKVSQVF----------------------IAQSLERNWRKDQILEAYLNLVSFRG 158 A ++TQ+V++ F +A +E N KDQILE Y+N + Sbjct: 120 ASTITQQVARNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQ 179 Query: 159 ELVGVHALSRVLFGKHPSGLNQSEAAIAVALIRAPNA-RPAKVSERACA 206 G + +++ FGK L +EAA+ L +AP+A P +RA A Sbjct: 180 RAYGFASAAQIYFGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHA 228 Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 31/77 (40%), Positives = 53/77 (68%), Gaps = 2/77 (2%) Query: 324 VQALRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATSAG-LYIPQNYDKQFKGLVS 382 QA RQ GS+ KPF+Y ++EK L+ A++++D+P+ + G ++ P+NY +F+G +S Sbjct: 461 TQAWRQPGSSFKPFIYSSSLEKG-LSPATIINDAPLTFTQTGGQVWQPKNYGGKFEGPIS 519 Query: 383 MRTALGSSLNIPAVRTL 399 MR AL S+N+ ++R L Sbjct: 520 MRRALQKSINLVSIRIL 536 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 69.3 bits (168), Expect = 6e-13, Method: Compositional matrix adjust. Identities = 48/170 (28%), Positives = 83/170 (48%), Gaps = 29/170 (17%) Query: 61 ERRLSWIALEDISPALRNALIASEDRRFYQHSGVDWNAVA----------ASAWG----- 105 E + S + L+DI ++NA++A ED RFY+H G+DW +A +++ G Sbjct: 85 EEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTIT 144 Query: 106 -----NLWNTPPPPPPPPPSARSMTQKVSQVFIAQSLERNWRKDQILEAYLNLVSFRGEL 160 N++ T ++ ++K+ +V +A +E KDQILE Y+N + Sbjct: 145 MQVARNVFLT---------KEKTFSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQRA 195 Query: 161 VGVHALSRVLFGKHPSGLNQSEAAIAVALIRAPNARPAKVSERACAILKE 210 G A +R FGK + +EAA+ L +AP+A V+ + I ++ Sbjct: 196 FGFAAAARTYFGKDLKDVTLAEAAMLAGLPKAPSAYNPIVNPKRAHIRQQ 245 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 0.317 0.131 0.380 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: 1,246,588 Number of extensions: 48323 Number of successful extensions: 242 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 240 Number of HSP's successfully gapped: 4 Length of query: 431 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 343 Effective length of database: 1,203,190 Effective search space: 412694170 Effective search space used: 412694170 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: 132 (55.5 bits)