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= 0001.4047.p (771 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 1546 0.0 gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidogl... 852 0.0 gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [H... 97 3e-21 gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic pep... 79 1e-15 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 1546 bits (4004), Expect = 0.0, Method: Compositional matrix adjust. Identities = 747/771 (96%), Positives = 760/771 (98%) Query: 1 MHWSLRILLGLFGTLFGLIVMALLGVAFIVALTYPKLPDLDTLTDYRPKIPLRIFSADGV 60 MHWSLRILLGL GT+FGL VM LLGV FIVALTYPKLPDLDTLTDYRPKIPLRIFSADGV Sbjct: 1 MHWSLRILLGLVGTIFGLAVMVLLGVTFIVALTYPKLPDLDTLTDYRPKIPLRIFSADGV 60 Query: 61 LIGEFGEERRNLVHFKDIPDIMKKAVLAIEDDRFYEHGGVDYQGILRATFSNLSGGGGGA 120 LIGEFGEERRNLVHFKDIP+IMKKAVLAIEDDRFYEHGGVDYQGI RATFSNLSGGGGGA Sbjct: 61 LIGEFGEERRNLVHFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARATFSNLSGGGGGA 120 Query: 121 STITQQVARNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQR 180 STITQQVARNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQR Sbjct: 121 STITQQVARNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQR 180 Query: 181 AYGFASAAQIYFGKQLKDITIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQL 240 AYGFASAAQIYFGKQLKD+TIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQL Sbjct: 181 AYGFASAAQIYFGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQL 240 Query: 241 GYITEAQYQEAKDEELRVKGDSSAFGMHAEYVAEMARQLIYAQYKDETYTRGLNVFTTIT 300 GYIT+AQYQ AKDEELRVKGDSSAFGMHAEYVAEMARQL+YAQYKDETYTRGLNVFTTIT Sbjct: 241 GYITDAQYQAAKDEELRVKGDSSAFGMHAEYVAEMARQLVYAQYKDETYTRGLNVFTTIT 300 Query: 301 KADQDAAYIALRRGIIDYERRHGYRGPEGYMDLPENASKEVVEDAVEVELADHPDSDDMV 360 K DQDAAYIALRRGIIDYERRHGYRGPEGYMDLPENA+K+ VEDAVEVELADHPDSDDMV Sbjct: 301 KTDQDAAYIALRRGIIDYERRHGYRGPEGYMDLPENATKDAVEDAVEVELADHPDSDDMV 360 Query: 361 AAVVLEAKPKEITAMLATGEEISISGAGLGFGANLLSDKAPPQKKIRRGAIIRVFQDGSN 420 +AVVLEAKPKEITAML+TGEEISISGAGLGFGANLLSDKAPPQKKIRRGAIIRVFQDG+N Sbjct: 361 SAVVLEAKPKEITAMLSTGEEISISGAGLGFGANLLSDKAPPQKKIRRGAIIRVFQDGNN 420 Query: 421 WIITQMPEVESAFVSVNSHDGAIRSLVGGFDFNRNKFNHVTQAWRQPGSSFKPFIYSSSL 480 WIITQMPEVESAFVSVNS DGAIRSLVGGFDFNRNKFNHVTQAWRQPGSSFKPFIYSSSL Sbjct: 421 WIITQMPEVESAFVSVNSQDGAIRSLVGGFDFNRNKFNHVTQAWRQPGSSFKPFIYSSSL 480 Query: 481 EKGLSPATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVG 540 EKGLSPATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVG Sbjct: 481 EKGLSPATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMRRALQKSINLVSIRILERVG 540 Query: 541 VKYAQEYITRFGFDADKNPPYLTLALGAGNVTPLQMVGAYSVFANGGYKINPYLITKVTD 600 VKYAQEYITRFGFDADKNPPYLTLALGAGNVTPLQMVGAYSVFANGGYKINPYLITKVTD Sbjct: 541 VKYAQEYITRFGFDADKNPPYLTLALGAGNVTPLQMVGAYSVFANGGYKINPYLITKVTD 600 Query: 601 NNGEVLSQAKPATADDESNRVIDARNAFIMDSMLRDVVRHGTAVKALSLKRTDLAGKTGT 660 +NGEVLSQAKPATADDESNRVIDARNAFIMDSMLRDVVRHGTAVKALSLKRTDLAGKTGT Sbjct: 601 SNGEVLSQAKPATADDESNRVIDARNAFIMDSMLRDVVRHGTAVKALSLKRTDLAGKTGT 660 Query: 661 TNDSMDAWFAGYQPGLTAIAWIGYDQPKSLGDRETGGGLALPVWISYMSKALKDVPNVDR 720 TNDSMDAWFAGYQPGLTAIAWIGYDQPKSLGDRETGGGLALPVWISYMSKALKDVPNVDR Sbjct: 661 TNDSMDAWFAGYQPGLTAIAWIGYDQPKSLGDRETGGGLALPVWISYMSKALKDVPNVDR 720 Query: 721 KVPDGVIESGGEYYYAEFPPSAMVRDLGMGDHGGMTPEEEKAKTQMKNELF 771 KVPDG+IESGGEYYYAEFPPSAMVRDLGMGD G+TPEEEKAKTQMKNELF Sbjct: 721 KVPDGLIESGGEYYYAEFPPSAMVRDLGMGDRSGLTPEEEKAKTQMKNELF 771 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 852 bits (2202), Expect = 0.0, Method: Compositional matrix adjust. Identities = 435/761 (57%), Positives = 567/761 (74%), Gaps = 21/761 (2%) Query: 14 TLFGLIVMALLGVAFIVALTYPKLPDLDTLTDYRPKIPLRIFSADGVLIGEFGEERRNLV 73 ++ GL V L V + + P+LP L+ +TDYRPK+PLRI+S D VL+GEFGEE+R+LV Sbjct: 32 SILGLGVAGALLVVYALIFINPRLPSLELITDYRPKVPLRIWSEDKVLLGEFGEEKRSLV 91 Query: 74 HFKDIPDIMKKAVLAIEDDRFYEHGGVDYQGILRATFSNLSGGGG--GASTITQQVARNF 131 DIP MK AVLAIED RFYEHGG+D+ GI RA +++ G GASTIT QVARN Sbjct: 92 KLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTITMQVARNV 151 Query: 132 FLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQRAYGFASAAQIY 191 FLT E TF +K YE+ LA KIE+ LTKDQILEVYMNQIYLGQRA+GFA+AA+ Y Sbjct: 152 FLT-KEKTFSRK-----LYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFAAAARTY 205 Query: 192 FGKQLKDITIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQLGYITEAQYQEA 251 FGK LKD+T+AEAAMLAGLPKAPSAYNP+VNPKRAH RQQYIL RM +G+IT+AQY++A Sbjct: 206 FGKDLKDVTLAEAAMLAGLPKAPSAYNPIVNPKRAHIRQQYILQRMLDVGFITKAQYEKA 265 Query: 252 KDEELRVKGDSSAFGMHAEYVAEMARQLIYAQYKDETYTRGLNVFTTITKADQDAAYIAL 311 EEL+V+ S + +HAEYV EM RQ++YAQYK++TYT+G NV+TT+ ADQ AAY+A+ Sbjct: 266 AKEELKVRAPGSQYNIHAEYVNEMVRQMVYAQYKEDTYTQGFNVYTTVNAADQQAAYLAV 325 Query: 312 RRGIIDYERRHGYRGPEGYMDLPENASKEVVEDAVEVELADHPDSDDMVAAVVLEAKPKE 371 R+G++DY+RRHGYRGPE ++LP NA A++ + DHPD+DD++AAVV+ A PK+ Sbjct: 326 RKGVMDYDRRHGYRGPEETIELPANAEDRAA--AIDDVMDDHPDNDDILAAVVVAASPKQ 383 Query: 372 ITAMLATGEEISISGAGLGFGANLLSDKAPPQKKIRRGAIIRVFQDG-SNWIITQMPEVE 430 I A+L +G++ISI G L F A+ LS+KA +I GA+IRV QD NW + Q+P+VE Sbjct: 384 IDAVLRSGDKISIKGEALRFVASALSEKAKKDIRIGPGALIRVMQDAKQNWQVAQLPQVE 443 Query: 431 SAFVSVNSHDGAIRSLVGGFDFNRNKFNHVTQAWRQPGSSFKPFIYSSSLEKGLSPATII 490 +A VSV DGAIR+LVGGFDF +N FNHVTQAWRQPGS+FKPFIYS++LEKG +PA+I+ Sbjct: 444 AALVSVVPQDGAIRALVGGFDFTQNNFNHVTQAWRQPGSTFKPFIYSAALEKGFAPASIV 503 Query: 491 NDAPLTFTQTGGQV-WQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQEYIT 549 NDAP+++ GQ W+P++ GPI++R ALQKS+NLV+IR L+ +GV YA+++IT Sbjct: 504 NDAPVSYPAGPGQPNWEPRD-DETPAGPITVRTALQKSVNLVAIRTLDYIGVPYAKDFIT 562 Query: 550 -RFGFDADKNPPYLTLALGAGNVTPLQMVGAYSVFANGGYKINPYLITKVTDNNGEVLSQ 608 +GFDADK PPYL +ALGAG PLQ+ AYSVFANGGYK+ PYLI+++TD G+ LS+ Sbjct: 563 GTYGFDADKVPPYLPMALGAGQTNPLQLSAAYSVFANGGYKVQPYLISQITDARGQALSK 622 Query: 609 AKPATADDESNRVIDARNAFIMDSMLRDVVRHGTAVKALSLKRTDLAGKTGTTNDSMDAW 668 A+P + + RV+ RN+++M SML+ V + GT ++ S+ R+DLAGKTGTTND++D W Sbjct: 623 AEPLIVGNGAPRVVSERNSYMMTSMLKSVAQGGTGARSNSIGRSDLAGKTGTTNDAVDGW 682 Query: 669 FAGYQPGLTAIAWIGYDQPKSLGDRETGGGLALPVWISYMSKALKDVPNVDRKVPDGVIE 728 FAGYQ L + W+GYDQPKSLG +E G LALP+W+ YM+KALK VP D VP+G+ Sbjct: 683 FAGYQRTLATVVWMGYDQPKSLGSKEFGAQLALPIWVDYMAKALKGVPQFDLPVPEGIRF 742 Query: 729 SGGEYYYAEFPP-SAMVRDLG------MGDHGGMTPEEEKA 762 GE YY F P + +V ++G + + G TP + A Sbjct: 743 IDGEPYYDNFTPNNGLVTNVGVTVVDAISNFFGWTPSQAPA 783 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 97.4 bits (241), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 80/252 (31%), Positives = 127/252 (50%), Gaps = 22/252 (8%) Query: 463 AWRQPGSSFKPFIYSSSLEKG-LSPATIINDAPLTFTQTGGQVWQPKNYGGKFEGPISMR 521 A RQ GS+ KPF+Y ++EK L+ A++++D+P+ + G ++ P+NY +++G +S+R Sbjct: 341 AQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATSAG-LYIPQNYDKQYKGLVSLR 399 Query: 522 RALQKSINLVSIRILERVGVKYAQEYITRFGFDADKNPPY--LTLALGAGNVTPLQMVGA 579 +L S+N+ ++R L V + + GF+ ++ Y +LALG+ +VT + A Sbjct: 400 TSLGSSLNIPAVRTLVMVTPERFFRRLQALGFNLRESGDYYGYSLALGSADVTLANLANA 459 Query: 580 YSVFANGGYKINPYLITKVTDNNGEVLSQAKPATADDESNRVIDARNAFIMDSMLRDVVR 639 Y V AN G + P L T++ + PA A +V+DA A+I+ +L D Sbjct: 460 YRVLANQG-RYTP-LRTRLDEAR-------TPARA----TQVMDADAAYIVGDILSDRSA 506 Query: 640 HGTAV---KALSLKRTDLAGKTGTTNDSMDAWFAGYQPGLTAIAWIGYDQPKSLGDRETG 696 ALS R A KTGT+ D D W GY T W+G + D +G Sbjct: 507 RARTFGLENALS-TRIWTAVKTGTSKDMRDNWCVGYSTRYTVGVWVGNASGAPMWD-VSG 564 Query: 697 GGLALPVWISYM 708 A PVW M Sbjct: 565 VTGAAPVWQEVM 576 Score = 82.8 bits (203), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 53/172 (30%), Positives = 84/172 (48%), Gaps = 13/172 (7%) Query: 67 EERRNLVHFKDIPDIMKKAVLAIEDDRFYEHGGVDYQGILRATFSNL-SGGGGGASTITQ 125 E + V +D+ ++ A++A ED RFY+H G+D+ + + + NL + GASTIT Sbjct: 61 ERKLAWVRLEDVSPALRHALIASEDRRFYQHSGIDWSAVAASAWGNLWNSKTRGASTITM 120 Query: 126 QVARNFFLTSNEPTFLQKATRKFFYEIPLAW---KIENNLTKDQILEVYMNQIYLGQRAY 182 Q+A + + + R ++ AW +E N KDQILE Y+N + Sbjct: 121 QLAGLIY----DDLRRKSGARSLTQKVSQAWIAQSLERNWRKDQILEAYLNLVAFRGELV 176 Query: 183 GFASAAQIYFGKQLKDITIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYIL 234 G + ++I FGK + EAA+ L +AP+A P+R R IL Sbjct: 177 GVHALSRIMFGKHPSGLDQGEAAIAVALIRAPNA-----TPRRVADRACAIL 223 >gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic peptidoglycan transglycosylase [Herbaspirillum seropedicae SmR1] Length = 235 Score = 79.3 bits (194), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 56/167 (33%), Positives = 85/167 (50%), Gaps = 8/167 (4%) Query: 73 VHFKDIPDIMKKAVLAIEDDRFYEHGGVDYQGILRATFSNLSGGG--GGASTITQQVARN 130 V + I + +K+A++A ED F H GVD++ + +A N G G STITQQ+A+N Sbjct: 65 VPYARISNNLKRAIIASEDSNFSSHDGVDWEALQKAYEKNEKKGKVVAGGSTITQQLAKN 124 Query: 131 FFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQRAYGFASAAQI 190 FL S E ++L+K E + + +E L K +I E+Y+N + G +G +AAQ Sbjct: 125 LFL-SGERSYLRKGQ-----EFIITYMLEFLLDKQRIFEIYLNVVEWGNGVFGAEAAAQH 178 Query: 191 YFGKQLKDITIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRM 237 Y+ + +AA LA + P Y+ AR IL RM Sbjct: 179 YYRIPAASLGAEQAARLAVMLPRPRYYDRNRGSGYLAARTSLILRRM 225 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 0.136 0.398 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: 2,473,386 Number of extensions: 109006 Number of successful extensions: 310 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 300 Number of HSP's successfully gapped: 6 Length of query: 771 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 678 Effective length of database: 1,179,515 Effective search space: 799711170 Effective search space used: 799711170 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)