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= 0002.0066.p (251 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic pep... 389 e-109 gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidogl... 91 1e-19 gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 82 5e-17 gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [H... 74 1e-14 >gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic peptidoglycan transglycosylase [Herbaspirillum seropedicae SmR1] Length = 235 Score = 389 bits (1000), Expect = e-109, Method: Compositional matrix adjust. Identities = 192/231 (83%), Positives = 208/231 (90%) Query: 1 MKLLRKLFLWLIVLPITLLFLLQLYFFVQIWWWVDHNPGSTSFMRHQLSLLQEKNPNAQL 60 MK LRKL W++VLP+ L+ L+QLYFFVQIWWW DHNP STSFMR QL+LLQEK+P AQL Sbjct: 1 MKSLRKLLFWIVVLPLVLVLLMQLYFFVQIWWWRDHNPESTSFMRQQLALLQEKDPKAQL 60 Query: 61 QFKWVPYNRISNNLKRAIIASEDSNFSEHEGVDWDALQKAYEKNTRKGKVVAGGSTITQQ 120 QF+WVPY RISNNLKRAIIASEDSNFS H+GVDW+ALQKAYEKN +KGKVVAGGSTITQQ Sbjct: 61 QFRWVPYARISNNLKRAIIASEDSNFSSHDGVDWEALQKAYEKNEKKGKVVAGGSTITQQ 120 Query: 121 LAKNLFLSGERSYLRKAQEFIITYMLEFLMDKQRIFEIYLNVVEWGNGVFGAEAASLHYY 180 LAKNLFLSGERSYLRK QEFIITYMLEFL+DKQRIFEIYLNVVEWGNGVFGAEAA+ HYY Sbjct: 121 LAKNLFLSGERSYLRKGQEFIITYMLEFLLDKQRIFEIYLNVVEWGNGVFGAEAAAQHYY 180 Query: 181 GAPAANLGPSQAARLAVMLPRPRFYDKNPGSAYLANRTGLILRRMNAAELP 231 PAA+LG QAARLAVMLPRPR+YD+N GS YLA RT LILRRMNAA LP Sbjct: 181 RIPAASLGAEQAARLAVMLPRPRYYDRNRGSGYLAARTSLILRRMNAATLP 231 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 90.5 bits (223), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 56/163 (34%), Positives = 92/163 (56%), Gaps = 4/163 (2%) Query: 65 VPYNRISNNLKRAIIASEDSNFSEHEGVDWDALQKAYEKNTRKGKVVAGGSTITQQLAKN 124 V + I ++K A++A ED F EH G+DW + +A + +G G STIT Q+A+N Sbjct: 91 VKLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTITMQVARN 150 Query: 125 LFLSGERSYLRKAQEFIITYMLEFLMDKQRIFEIYLNVVEWGNGVFGAEAASLHYYGAPA 184 +FL+ E+++ RK E ++ +E + K +I E+Y+N + G FG AA+ Y+G Sbjct: 151 VFLTKEKTFSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFAAAARTYFGKDL 210 Query: 185 ANLGPSQAARLAVMLPRPRFYDK--NPGSAYLANRTGLILRRM 225 ++ ++AA LA + P Y+ NP A++ R IL+RM Sbjct: 211 KDVTLAEAAMLAGLPKAPSAYNPIVNPKRAHI--RQQYILQRM 251 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 81.6 bits (200), Expect = 5e-17, Method: Compositional matrix adjust. Identities = 59/169 (34%), Positives = 90/169 (53%), Gaps = 12/169 (7%) Query: 65 VPYNRISNNLKRAIIASEDSNFSEHEGVDWDALQKAYEKNTRKGKVVAGGSTITQQLAKN 124 V + I +K+A++A ED F EH GVD+ + +A N G G STITQQ+A+N Sbjct: 73 VHFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARATFSNLSGGG--GGASTITQQVARN 130 Query: 125 LFL-SGERSYLRKAQ-----EFIITYMLEFLMDKQRIFEIYLNVVEWGNGVFGAEAASLH 178 FL S E ++L+KA E + + +E + K +I E+Y+N + G +G +A+ Sbjct: 131 FFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQRAYGFASAAQI 190 Query: 179 YYGAPAANLGPSQAARLAVMLPRPRFYDK--NPGSAYLANRTGLILRRM 225 Y+G +L ++AA LA + P Y+ NP A+ R IL RM Sbjct: 191 YFGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHA--RQQYILLRM 237 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 73.6 bits (179), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 71/220 (32%), Positives = 99/220 (45%), Gaps = 25/220 (11%) Query: 35 DHNPGSTSFMRHQLSLLQEKNPN-AQLQFKWVPYNRISNNLKRAIIASEDSNFSEHEGVD 93 D P S + LLQ N + + WV +S L+ A+IASED F +H G+D Sbjct: 36 DFLPSEASLLDRNGELLQRMRINMDERKLAWVRLEDVSPALRHALIASEDRRFYQHSGID 95 Query: 94 WDALQKAYEKNTRKGKVVAGGSTITQQLAKNLF-----LSGERSYLRKAQEFIITYMLEF 148 W A+ + N K G STIT QLA ++ SG RS +K + I LE Sbjct: 96 WSAVAASAWGNLWNSK-TRGASTITMQLAGLIYDDLRRKSGARSLTQKVSQAWIAQSLER 154 Query: 149 LMDKQRIFEIYLNVVEWGNGVFGAEAASLHYYGAPAANLGPSQAARLAVMLPR-----PR 203 K +I E YLN+V + + G A S +G + L +AA +AV L R PR Sbjct: 155 NWRKDQILEAYLNLVAFRGELVGVHALSRIMFGKHPSGLDQGEAA-IAVALIRAPNATPR 213 Query: 204 ---------FYDKNPGSAY--LANRTGLILRRMNAA-ELP 231 ++ PG + RT L L R++A +LP Sbjct: 214 RVADRACAILKEEGPGEQCNGMDGRTELALARVSAKRDLP 253 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 0.321 0.135 0.411 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: 690,075 Number of extensions: 25950 Number of successful extensions: 109 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 106 Number of HSP's successfully gapped: 4 Length of query: 251 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 168 Effective length of database: 1,226,865 Effective search space: 206113320 Effective search space used: 206113320 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 (21.9 bits) S2: 129 (54.3 bits)