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= 0002.0608.p (459 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... 580 e-166 gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidogl... 360 e-100 gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [H... 72 1e-13 gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic pep... 66 7e-12 >gi|300310721|ref|YP_003774813.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 822 Score = 580 bits (1494), Expect = e-166, Method: Compositional matrix adjust. Identities = 284/396 (71%), Positives = 323/396 (81%), Gaps = 38/396 (9%) Query: 10 LSRQRGFLNPNIAKFLAFSVLGLAVIGALIIAYALIFINPRLPSLDVITDYRPKIPLRIY 69 L+RQRGFLNPNIAKF+ S+LGL V GAL++ YALIFINPRLPSL++ITDYRPK+PLRI+ Sbjct: 14 LTRQRGFLNPNIAKFIGLSILGLGVAGALLVVYALIFINPRLPSLELITDYRPKVPLRIW 73 Query: 70 SADNVLLGEFGEEKRSLVKLDDIPANMKNAVLAIEDNRFYQHGGIDYIGIARAIATDVVR 129 S D VLLGEFGEEKRSLVKLDDIPA+MKNAVLAIED RFY+HGGID+IGIARA+ TDV+R Sbjct: 74 SEDKVLLGEFGEEKRSLVKLDDIPADMKNAVLAIEDYRFYEHGGIDWIGIARALVTDVLR 133 Query: 130 GHASQGASTITMQVARNVFLTKEKTVSRKLYEVLLANKIEAALSKDQILE---------- 179 G ASQGASTITMQVARNVFLTKEKT SRKLYEVLLANKIE AL+KDQILE Sbjct: 134 GSASQGASTITMQVARNVFLTKEKTFSRKLYEVLLANKIEHALTKDQILEVYMNQIYLGQ 193 Query: 180 ----------------------------XPRPGAPSAYNPIVNPKRAHIRQQYILQRMLD 211 P APSAYNPIVNPKRAHIRQQYILQRMLD Sbjct: 194 RAFGFAAAARTYFGKDLKDVTLAEAAMLAGLPKAPSAYNPIVNPKRAHIRQQYILQRMLD 253 Query: 212 LDYITQKEYDAAVKEDIQVRAPGNQYNVHAEYVNEMVRQMVYAQYKEDTYTHGITVTTTI 271 + +IT+ +Y+ A KE+++VRAPG+QYN+HAEYVNEMVRQMVYAQYKEDTYT G V TT+ Sbjct: 254 VGFITKAQYEKAAKEELKVRAPGSQYNIHAEYVNEMVRQMVYAQYKEDTYTQGFNVYTTV 313 Query: 272 NAADQKAAYDAVRKGVMDYDRRHGYRGPEETIDLPSKDEDRAQAIDDAMDDYPDNDDILA 331 NAADQ+AAY AVRKGVMDYDRRHGYRGPEETI+LP+ EDRA AIDD MDD+PDNDDILA Sbjct: 314 NAADQQAAYLAVRKGVMDYDRRHGYRGPEETIELPANAEDRAAAIDDVMDDHPDNDDILA 373 Query: 332 AVVLSADPKQIQAVIRSGDKITLSGDTLKFVAXKIT 367 AVV++A PKQI AV+RSGDKI++ G+ L+FVA ++ Sbjct: 374 AVVVAASPKQIDAVLRSGDKISIKGEALRFVASALS 409 >gi|300313465|ref|YP_003777557.1| penicillin-binding 1 (peptidoglycan synthetase) transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 771 Score = 360 bits (924), Expect = e-100, Method: Compositional matrix adjust. Identities = 192/387 (49%), Positives = 251/387 (64%), Gaps = 52/387 (13%) Query: 25 LAFSVLGLAVIGALIIAYALIFINPRLPSLDVITDYRPKIPLRIYSADNVLLGEFGEEKR 84 L ++ GLAV+ L + + + P+LP LD +TDYRPKIPLRI+SAD VL+GEFGEE+R Sbjct: 11 LVGTIFGLAVMVLLGVTFIVALTYPKLPDLDTLTDYRPKIPLRIFSADGVLIGEFGEERR 70 Query: 85 SLVKLDDIPANMKNAVLAIEDNRFYQHGGIDYIGIARAIATDVVRGHASQGASTITMQVA 144 +LV DIP MK AVLAIED+RFY+HGG+DY GIARA +++ G GASTIT QVA Sbjct: 71 NLVHFKDIPEIMKKAVLAIEDDRFYEHGGVDYQGIARATFSNLSGGGG--GASTITQQVA 128 Query: 145 RNVFLTK------EKTVSRKLYEVLLANKIEAALSKDQILE------------------- 179 RN FLT +K + YE+ LA KIE L+KDQILE Sbjct: 129 RNFFLTSNEPTFLQKATRKFFYEIPLAWKIENNLTKDQILEVYMNQIYLGQRAYGFASAA 188 Query: 180 -------------------XPRPGAPSAYNPIVNPKRAHIRQQYILQRMLDLDYITQKEY 220 P APSAYNP+VNPKRAH RQQYIL RM L YIT +Y Sbjct: 189 QIYFGKQLKDLTIAEAAMLAGLPKAPSAYNPVVNPKRAHARQQYILLRMRQLGYITDAQY 248 Query: 221 DAAVKEDIQVRAPGNQYNVHAEYVNEMVRQMVYAQYKEDTYTHGITVTTTINAADQKAAY 280 AA E+++V+ + + +HAEYV EM RQ+VYAQYK++TYT G+ V TTI DQ AAY Sbjct: 249 QAAKDEELRVKGDSSAFGMHAEYVAEMARQLVYAQYKDETYTRGLNVFTTITKTDQDAAY 308 Query: 281 DAVRKGVMDYDRRHGYRGPEETIDLPSKDEDRAQAIDDAMD----DYPDNDDILAAVVLS 336 A+R+G++DY+RRHGYRGPE +DLP + A++DA++ D+PD+DD+++AVVL Sbjct: 309 IALRRGIIDYERRHGYRGPEGYMDLP--ENATKDAVEDAVEVELADHPDSDDMVSAVVLE 366 Query: 337 ADPKQIQAVIRSGDKITLSGDTLKFVA 363 A PK+I A++ +G++I++SG L F A Sbjct: 367 AKPKEITAMLSTGEEISISGAGLGFGA 393 >gi|300312242|ref|YP_003776334.1| penicillin-binding 2 protein [Herbaspirillum seropedicae SmR1] Length = 753 Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 38/104 (36%), Positives = 65/104 (62%), Gaps = 6/104 (5%) Query: 81 EEKRSLVKLDDIPANMKNAVLAIEDNRFYQHGGIDYIGIARAIATDVVRGHASQGASTIT 140 E K + V+L+D+ +++A++A ED RFYQH GID+ +A A A + ++GASTIT Sbjct: 61 ERKLAWVRLEDVSPALRHALIASEDRRFYQHSGIDWSAVA-ASAWGNLWNSKTRGASTIT 119 Query: 141 MQVARNVF-----LTKEKTVSRKLYEVLLANKIEAALSKDQILE 179 MQ+A ++ + +++++K+ + +A +E KDQILE Sbjct: 120 MQLAGLIYDDLRRKSGARSLTQKVSQAWIAQSLERNWRKDQILE 163 >gi|300309743|ref|YP_003773835.1| monofunctional biosynthetic peptidoglycan transglycosylase [Herbaspirillum seropedicae SmR1] Length = 235 Score = 65.9 bits (159), Expect = 7e-12, Method: Compositional matrix adjust. Identities = 32/88 (36%), Positives = 52/88 (59%) Query: 92 IPANMKNAVLAIEDNRFYQHGGIDYIGIARAIATDVVRGHASQGASTITMQVARNVFLTK 151 I N+K A++A ED+ F H G+D+ + +A + +G G STIT Q+A+N+FL+ Sbjct: 70 ISNNLKRAIIASEDSNFSSHDGVDWEALQKAYEKNEKKGKVVAGGSTITQQLAKNLFLSG 129 Query: 152 EKTVSRKLYEVLLANKIEAALSKDQILE 179 E++ RK E ++ +E L K +I E Sbjct: 130 ERSYLRKGQEFIITYMLEFLLDKQRIFE 157 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 0.320 0.136 0.389 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: 1,364,617 Number of extensions: 54943 Number of successful extensions: 164 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 158 Number of HSP's successfully gapped: 5 Length of query: 459 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 371 Effective length of database: 1,203,190 Effective search space: 446383490 Effective search space used: 446383490 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 (21.8 bits) S2: 132 (55.5 bits)