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= 0001.1201.p (824 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidogl... 1520 0.0 gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 879 0.0 gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [H... 99 2e-21 gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic pep... 88 3e-18 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 1520 bits (3936), Expect = 0.0, Method: Compositional matrix adjust. Identities = 754/829 (90%), Positives = 788/829 (95%), Gaps = 12/829 (1%) Query: 1 MPFSSLPD-----LRRQRGFLSINVAKFIGLSILGLGVAGALLVVYALIFINPRLPSLDL 55 MP +LP L RQRGFL+ N+AKFIGLSILGLGVAGALLVVYALIFINPRLPSL+L Sbjct: 1 MPLPTLPRPHSRPLTRQRGFLNPNIAKFIGLSILGLGVAGALLVVYALIFINPRLPSLEL 60 Query: 56 ITDYRPKVPLRIWSADKVLLGEFGEEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDW 115 ITDYRPKVPLRIWS DKVLLGEFGEEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDW Sbjct: 61 ITDYRPKVPLRIWSEDKVLLGEFGEEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDW 120 Query: 116 IGIARALVTDVLRGSASQGASTITMQVARNVFLTKEKTLSRKLYEVLLANKIEHALTKDQ 175 IGIARALVTDVLRGSASQGASTITMQVARNVFLTKEKT SRKLYEVLLANKIEHALTKDQ Sbjct: 121 IGIARALVTDVLRGSASQGASTITMQVARNVFLTKEKTFSRKLYEVLLANKIEHALTKDQ 180 Query: 176 ILEVYMNQIYLGQRAFGFAAAARTYFGKDLKDITLAEAAMLAGLPKAPSAYNPIVNPKRA 235 ILEVYMNQIYLGQRAFGFAAAARTYFGKDLKD+TLAEAAMLAGLPKAPSAYNPIVNPKRA Sbjct: 181 ILEVYMNQIYLGQRAFGFAAAARTYFGKDLKDVTLAEAAMLAGLPKAPSAYNPIVNPKRA 240 Query: 236 HIRQQYILQRMLDVGFITQAQYDKASKEELKVRAPGSQYTVHAEYVNEMVRQMVYAQYKE 295 HIRQQYILQRMLDVGFIT+AQY+KA+KEELKVRAPGSQY +HAEYVNEMVRQMVYAQYKE Sbjct: 241 HIRQQYILQRMLDVGFITKAQYEKAAKEELKVRAPGSQYNIHAEYVNEMVRQMVYAQYKE 300 Query: 296 DTYTQGFNVYTTVNAADQQAAYQAVRKGVMDYDRRHGYRGPEETIELPANAEDRASAIDD 355 DTYTQGFNVYTTVNAADQQAAY AVRKGVMDYDRRHGYRGPEETIELPANAEDRA+AIDD Sbjct: 301 DTYTQGFNVYTTVNAADQQAAYLAVRKGVMDYDRRHGYRGPEETIELPANAEDRAAAIDD 360 Query: 356 VMDDHPDNDDILAAVVVAANPKQIDAVLRSGDKISIKGEALRFVAAALSEKAKKDIRIAP 415 VMDDHPDNDDILAAVVVAA+PKQIDAVLRSGDKISIKGEALRFVA+ALSEKAKKDIRI P Sbjct: 361 VMDDHPDNDDILAAVVVAASPKQIDAVLRSGDKISIKGEALRFVASALSEKAKKDIRIGP 420 Query: 416 GALIRVMQDAKQNWQVVQLPQVEAALVSVVPQDGAIRALVGGFDFTQNNFNHVTQAWRQP 475 GALIRVMQDAKQNWQV QLPQVEAALVSVVPQDGAIRALVGGFDFTQNNFNHVTQAWRQP Sbjct: 421 GALIRVMQDAKQNWQVAQLPQVEAALVSVVPQDGAIRALVGGFDFTQNNFNHVTQAWRQP 480 Query: 476 GSTFKPFIYSAALEKGFAPASIVNDAPVSYPAGPGQPNWEPKDDETPAGPMTVRTALQKS 535 GSTFKPFIYSAALEKGFAPASIVNDAPVSYPAGPGQPNWEP+DDETPAGP+TVRTALQKS Sbjct: 481 GSTFKPFIYSAALEKGFAPASIVNDAPVSYPAGPGQPNWEPRDDETPAGPITVRTALQKS 540 Query: 536 VNLVAIRTLDYIGVPYARDFITGTYGFDTDKVPPYLPMALGAGQTNPLQLSAAYSVFANG 595 VNLVAIRTLDYIGVPYA+DFITGTYGFD DKVPPYLPMALGAGQTNPLQLSAAYSVFANG Sbjct: 541 VNLVAIRTLDYIGVPYAKDFITGTYGFDADKVPPYLPMALGAGQTNPLQLSAAYSVFANG 600 Query: 596 GYKIQPYLISQITDARGKVLSKADPLIVGNGAPRVVAERNSYIMTNLLRSVAQAGTGARS 655 GYK+QPYLISQITDARG+ LSKA+PLIVGNGAPRVV+ERNSY+MT++L+SVAQ GTGARS Sbjct: 601 GYKVQPYLISQITDARGQALSKAEPLIVGNGAPRVVSERNSYMMTSMLKSVAQGGTGARS 660 Query: 656 NSIGRTDLAGKTGTTNDAVDGWFAGYQHTLATVAWMGYDQPKSLGSKEFGAQLALPIWVD 715 NSIGR+DLAGKTGTTNDAVDGWFAGYQ TLATV WMGYDQPKSLGSKEFGAQLALPIWVD Sbjct: 661 NSIGRSDLAGKTGTTNDAVDGWFAGYQRTLATVVWMGYDQPKSLGSKEFGAQLALPIWVD 720 Query: 716 YMAKALKGVPQFDQPVPDGIRFIDGEPYYDNFTPNNGLVTNVGVTAGDALANFFGWTTNQ 775 YMAKALKGVPQFD PVP+GIRFIDGEPYYDNFTPNNGLVTNVGVT DA++NFFGWT +Q Sbjct: 721 YMAKALKGVPQFDLPVPEGIRFIDGEPYYDNFTPNNGLVTNVGVTVVDAISNFFGWTPSQ 780 Query: 776 TPATPANNQPAPNVPGSAPGGPGAAPGTSANRPQSESARRFLDNTNQGH 824 PATP + QP PNVPG+ AP T+ R +E+ARRFLD+TNQGH Sbjct: 781 APATPGSTQPEPNVPGT-------APATNGTRAPNENARRFLDSTNQGH 822 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 879 bits (2270), Expect = 0.0, Method: Compositional matrix adjust. Identities = 437/742 (58%), Positives = 559/742 (75%), Gaps = 15/742 (2%) Query: 27 SILGLGVAGALLVVYALIFINPRLPSLDLITDYRPKVPLRIWSADKVLLGEFGEEKRSLV 86 +I GL V L V + + P+LP LD +TDYRPK+PLRI+SAD VL+GEFGEE+R+LV Sbjct: 14 TIFGLAVMVLLGVTFIVALTYPKLPDLDTLTDYRPKIPLRIFSADGVLIGEFGEERRNLV 73 Query: 87 KLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTITMQVARNV 146 DIP MK AVLAIED RFYEHGG+D+ GIARA +++ G GASTIT QVARN Sbjct: 74 HFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARATFSNLSGGGG--GASTITQQVARNF 131 Query: 147 FLTK------EKTLSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFAAAARTY 200 FLT +K + YE+ LA KIE+ LTKDQILEVYMNQIYLGQRA+GFA+AA+ Y Sbjct: 132 FLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQRAYGFASAAQIY 191 Query: 201 FGKDLKDITLAEAAMLAGLPKAPSAYNPIVNPKRAHIRQQYILQRMLDVGFITQAQYDKA 260 FGK LKD+T+AEAAMLAGLPKAPSAYNP+VNPKRAH RQQYIL RM +G+IT AQY A Sbjct: 192 FGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQLGYITDAQYQAA 251 Query: 261 SKEELKVRAPGSQYTVHAEYVNEMVRQMVYAQYKEDTYTQGFNVYTTVNAADQQAAYQAV 320 EEL+V+ S + +HAEYV EM RQ+VYAQYK++TYT+G NV+TT+ DQ AAY A+ Sbjct: 252 KDEELRVKGDSSAFGMHAEYVAEMARQLVYAQYKDETYTRGLNVFTTITKTDQDAAYIAL 311 Query: 321 RKGVMDYDRRHGYRGPEETIELPANAEDRA--SAIDDVMDDHPDNDDILAAVVVAANPKQ 378 R+G++DY+RRHGYRGPE ++LP NA A A++ + DHPD+DD+++AVV+ A PK+ Sbjct: 312 RRGIIDYERRHGYRGPEGYMDLPENATKDAVEDAVEVELADHPDSDDMVSAVVLEAKPKE 371 Query: 379 IDAVLRSGDKISIKGEALRFVAAALSEKAKKDIRIAPGALIRVMQDAKQNWQVVQLPQVE 438 I A+L +G++ISI G L F A LS+KA +I GA+IRV QD NW + Q+P+VE Sbjct: 372 ITAMLSTGEEISISGAGLGFGANLLSDKAPPQKKIRRGAIIRVFQDG-NNWIITQMPEVE 430 Query: 439 AALVSVVPQDGAIRALVGGFDFTQNNFNHVTQAWRQPGSTFKPFIYSAALEKGFAPASIV 498 +A VSV QDGAIR+LVGGFDF +N FNHVTQAWRQPGS+FKPFIYS++LEKG +PA+I+ Sbjct: 431 SAFVSVNSQDGAIRSLVGGFDFNRNKFNHVTQAWRQPGSSFKPFIYSSSLEKGLSPATII 490 Query: 499 NDAPVSYPAGPGQPNWEPKD-DETPAGPMTVRTALQKSVNLVAIRTLDYIGVPYARDFIT 557 NDAP+++ GQ W+PK+ GP+++R ALQKS+NLV+IR L+ +GV YA+++IT Sbjct: 491 NDAPLTFTQTGGQV-WQPKNYGGKFEGPISMRRALQKSINLVSIRILERVGVKYAQEYIT 549 Query: 558 GTYGFDTDKVPPYLPMALGAGQTNPLQLSAAYSVFANGGYKIQPYLISQITDARGKVLSK 617 +GFD DK PPYL +ALGAG PLQ+ AYSVFANGGYKI PYLI+++TD+ G+VLS+ Sbjct: 550 -RFGFDADKNPPYLTLALGAGNVTPLQMVGAYSVFANGGYKINPYLITKVTDSNGEVLSQ 608 Query: 618 ADPLIVGNGAPRVVAERNSYIMTNLLRSVAQAGTGARSNSIGRTDLAGKTGTTNDAVDGW 677 A P + + RV+ RN++IM ++LR V + GT ++ S+ RTDLAGKTGTTND++D W Sbjct: 609 AKPATADDESNRVIDARNAFIMDSMLRDVVRHGTAVKALSLKRTDLAGKTGTTNDSMDAW 668 Query: 678 FAGYQHTLATVAWMGYDQPKSLGSKEFGAQLALPIWVDYMAKALKGVPQFDQPVPDGIRF 737 FAGYQ L +AW+GYDQPKSLG +E G LALP+W+ YM+KALK VP D+ VPDG+ Sbjct: 669 FAGYQPGLTAIAWIGYDQPKSLGDRETGGGLALPVWISYMSKALKDVPNVDRKVPDGLIE 728 Query: 738 IDGEPYYDNFTPNNGLVTNVGV 759 GE YY F P + +V ++G+ Sbjct: 729 SGGEYYYAEFPP-SAMVRDLGM 749 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 98.6 bits (244), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 60/170 (35%), Positives = 94/170 (55%), Gaps = 11/170 (6%) Query: 80 EEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTIT 139 E K + V+L+D+ +++A++A ED RFY+H GIDW +A A L S ++GASTIT Sbjct: 61 ERKLAWVRLEDVSPALRHALIASEDRRFYQHSGIDWSAVA-ASAWGNLWNSKTRGASTIT 119 Query: 140 MQVARNVF-----LTKEKTLSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFA 194 MQ+A ++ + ++L++K+ + +A +E KDQILE Y+N + G Sbjct: 120 MQLAGLIYDDLRRKSGARSLTQKVSQAWIAQSLERNWRKDQILEAYLNLVAFRGELVGVH 179 Query: 195 AAARTYFGKDLKDITLAEAAMLAGLPKAPSAYNPIVNPKRAHIRQQYILQ 244 A +R FGK + EAA+ L +AP+A P+R R IL+ Sbjct: 180 ALSRIMFGKHPSGLDQGEAAIAVALIRAPNA-----TPRRVADRACAILK 224 Score = 75.5 bits (184), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 99/326 (30%), Positives = 146/326 (44%), Gaps = 43/326 (13%) Query: 414 APGALIRVMQDAK-QNWQVVQLPQVEAALVSVVPQDGAI----------RALVG--GFDF 460 APG +R DA+ Q + L A L +DGAI A VG G Sbjct: 272 APGQQLRSTLDARLQRFATQALRHQLAGLADRNIEDGAIIVIDNATGDVLAWVGSSGPLS 331 Query: 461 TQNNFNHVTQAWRQPGSTFKPFIYSAALEKGF-APASIVNDAPVSYPAGPGQPNWEPKD- 518 N + V A RQ GST KPF+Y A+EK + AS+++D+PV+ G + P++ Sbjct: 332 AAANVDGVV-AQRQAGSTLKPFLYELAIEKKWLTAASLLDDSPVNLATSAGL--YIPQNY 388 Query: 519 DETPAGPMTVRTALQKSVNLVAIRTLDYIGVPYARDFIT-GTYGFDTDKVPPY--LPMAL 575 D+ G +++RT+L S+N+ A+RTL + V R F GF+ + Y +AL Sbjct: 389 DKQYKGLVSLRTSLGSSLNIPAVRTL--VMVTPERFFRRLQALGFNLRESGDYYGYSLAL 446 Query: 576 GAGQTNPLQLSAAYSVFANGGY--KIQPYLISQITDARGKVLSKAD-PLIVGNGAPRVVA 632 G+ L+ AY V AN G ++ L T AR + AD IVG+ +++ Sbjct: 447 GSADVTLANLANAYRVLANQGRYTPLRTRLDEARTPARATQVMDADAAYIVGD----ILS 502 Query: 633 ERNSYIMTNLLRSVAQAGTGARSNSIG-RTDLAGKTGTTNDAVDGWFAGYQHTLATVAWM 691 +R+ A+A T N++ R A KTGT+ D D W GY W+ Sbjct: 503 DRS-----------ARARTFGLENALSTRIWTAVKTGTSKDMRDNWCVGYSTRYTVGVWV 551 Query: 692 GYDQPKSLGSKEFGAQLALPIWVDYM 717 G + G A P+W + M Sbjct: 552 GNASGAPMWDVS-GVTGAAPVWQEVM 576 >gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic peptidoglycan transglycosylase [Herbaspirillum seropedicae SmR1] Length = 235 Score = 87.8 bits (216), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 52/156 (33%), Positives = 81/156 (51%) Query: 91 IPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLRGSASQGASTITMQVARNVFLTK 150 I ++K A++A ED F H G+DW + +A + +G G STIT Q+A+N+FL+ Sbjct: 70 ISNNLKRAIIASEDSNFSSHDGVDWEALQKAYEKNEKKGKVVAGGSTITQQLAKNLFLSG 129 Query: 151 EKTLSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQRAFGFAAAARTYFGKDLKDITL 210 E++ RK E ++ +E L K +I E+Y+N + G FG AAA+ Y+ + Sbjct: 130 ERSYLRKGQEFIITYMLEFLLDKQRIFEIYLNVVEWGNGVFGAEAAAQHYYRIPAASLGA 189 Query: 211 AEAAMLAGLPKAPSAYNPIVNPKRAHIRQQYILQRM 246 +AA LA + P Y+ R IL+RM Sbjct: 190 EQAARLAVMLPRPRYYDRNRGSGYLAARTSLILRRM 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 0.317 0.134 0.395 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: 2,398,573 Number of extensions: 99325 Number of successful extensions: 312 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 301 Number of HSP's successfully gapped: 5 Length of query: 824 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 731 Effective length of database: 1,179,515 Effective search space: 862225465 Effective search space used: 862225465 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: 135 (56.6 bits)