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= 0001.0303.p (592 letters) Database: BlastDatabases/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134095977|ref|YP_001101052.1| division-specific transpeptidas... 758 0.0 gi|134093460|ref|YP_001098535.1| putative penicillin-binding pro... 115 7e-27 >gi|134095977|ref|YP_001101052.1| division-specific transpeptidase, penicillin-binding protein 3 [Herminiimonas arsenicoxydans] Length = 471 Score = 758 bits (1958), Expect = 0.0, Method: Compositional matrix adjust. Identities = 359/471 (76%), Positives = 418/471 (88%), Gaps = 1/471 (0%) Query: 123 LAKLLEMSDAELRKKLDSDRSFVYLKRQVEQDTADKIVKLGIPGIETRKEYKRFYPEGEV 182 +AKLL+MS+ +LR+KLDSDR FVYLKRQVE DT DKI+KLGI GI+TRKEYKR+YPEGEV Sbjct: 1 MAKLLDMSERDLRRKLDSDRGFVYLKRQVELDTVDKILKLGIAGIDTRKEYKRYYPEGEV 60 Query: 183 MAHVVGFTNIEDAGQDGMELAAQKTLAGVTGSRRVIKDRLGRVVEDIESIREPHDGRDLT 242 MAH+VGFTN+ED GQ+GMELA QKTL GVTG+RRVIKDRLGR+VEDIES+REPHDG+DLT Sbjct: 61 MAHIVGFTNVEDKGQEGMELAFQKTLVGVTGNRRVIKDRLGRIVEDIESVREPHDGKDLT 120 Query: 243 LSIDSKIQYIAFTQLKEAVEKYKAKAGGIIVVDAKTGEVLALANMPTYNPNDRSELTGAQ 302 LSIDSKIQYIAF+ LKEAVE +KAKAGGI+V+DAKTGEVLALAN+PTYNPN+RS LTGAQ Sbjct: 121 LSIDSKIQYIAFSALKEAVELHKAKAGGIVVLDAKTGEVLALANLPTYNPNNRSVLTGAQ 180 Query: 303 LRNRVVTDTFEPGSTLKPFTVALALDTHRVTPSTVFQTAPGKMTIGTATIGDSHAHGALT 362 LRNRV+TDTFEPGSTLKPFT+ALAL+ +TP+T+ QTAPGK+TIG ATIGD+HA G L+ Sbjct: 181 LRNRVLTDTFEPGSTLKPFTIALALENKHITPNTMIQTAPGKLTIGKATIGDAHAGGLLS 240 Query: 363 VAQIIEKSSNIGTAKIALGMPAEEMWEMFTTVGFGQQPKFGFPGAVAGRVRPYKSWRPIE 422 V+Q+IEKSSN+GTAKIAL M +EMW+MFT+VGFGQQPK GFPGAVAGRVRPYKSWRPIE Sbjct: 241 VSQVIEKSSNVGTAKIALEMEPQEMWDMFTSVGFGQQPKVGFPGAVAGRVRPYKSWRPIE 300 Query: 423 QATMSYGHGISVSLIQLAHAYLIFARNGDIIPLSFTKVTDSPIGQRVISADTALQMRRML 482 QATMSYGHGIS SL+Q+AHAY+IFAR+G++IPL+F + +D PI QRVIS A R ML Sbjct: 301 QATMSYGHGISTSLLQIAHAYMIFARDGEMIPLTFQRSSDQPISQRVISEKNARLTRGML 360 Query: 483 ETVVAPGGTAPQAQVPGYRVGGKTGTAYKIENGKYVRKYVASFSGIAPMSDPRLIISVMI 542 E P GTAP+AQVPGYRV GKTGTAYK+E G+YVRKYVASF G AP+SDPR+I++VMI Sbjct: 361 EMAAGPTGTAPRAQVPGYRVAGKTGTAYKLEKGQYVRKYVASFVGFAPVSDPRIIVAVMI 420 Query: 543 DEPQ-GQHYGGPVAGPVFANVAANALRALNVPPDSSVTNIIIPKEPLEESM 592 DEP G+HYGG VA PVF+ V ANALR++NV PDSSVTNIIIP + +E+M Sbjct: 421 DEPAVGRHYGGQVAAPVFSVVTANALRSMNVAPDSSVTNIIIPVDAAQENM 471 >gi|134093460|ref|YP_001098535.1| putative penicillin-binding protein 2 (PBP-2) (MrdA) [Herminiimonas arsenicoxydans] Length = 635 Score = 115 bits (287), Expect = 7e-27, Method: Compositional matrix adjust. Identities = 143/582 (24%), Positives = 233/582 (40%), Gaps = 93/582 (15%) Query: 41 VLFVLFAAFVALVLRALWLQGVSTDFLQKQGASRYARTLEMPATRGKITDRNGQVLASSV 100 ++F+LFA A R +WLQ + Q + + RG I DRNG +LA + Sbjct: 24 LVFILFACLFA---RFIWLQVYKHNDYVAQAEDNRISIVPVVPNRGLIFDRNGVLLARNY 80 Query: 101 PVKAIWAIPEDVQAAPKDKLVQLAKLLEMS--DAELRKKLDSDR-----SFVYLKRQVEQ 153 + + + + +LA L+++ D + KKL + S + ++ E+ Sbjct: 81 SAYTLEITASKINGDLETLIDELATLVDIQPKDRKRFKKLQEESRNLASSPIRVRLTDEE 140 Query: 154 DTADKIVKLGIPGIETRKEYKRFYPEGEVMAHVVGF------------------TNI--- 192 + PG+E + R YP G V +HV+G+ TN Sbjct: 141 VARFSAQRYRFPGVEIQARLFRQYPLGSVASHVIGYIGRINTREAKEIDESDDATNYRGS 200 Query: 193 EDAGQDGMELAAQKTLAGVTGSRRVIKDRLGRVVEDIESIREPHDGRDLTLSIDSKIQYI 252 E G++G+E + L G TG V GR + + S G +L LSID ++Q Sbjct: 201 EHIGKEGLEKNYEDRLHGRTGYEEVEVSAGGRPIRTL-SRTAATPGDNLILSIDIELQ-- 257 Query: 253 AFTQLKEAVEKYKAKAGGIIVVDAKTGEVLALANMPTYNPNDRSELTGAQ---------- 302 K + + + G +I ++ TG+VLA +MPT++PN E Q Sbjct: 258 -----KVVEQAFGNRRGALIAIEPSTGDVLAYVSMPTFDPNLFVEGIDQQNWDALNNSPD 312 Query: 303 --LRNRVVTDTFEPGSTLKPFTVALALDTHRVTPSTVFQTAPGKMTIGTATIGDSH--AH 358 L NR ++ + PGST KPF AL+ + PS PG G D H Sbjct: 313 HPLLNRPLSGAYPPGSTYKPFMALAALELGKRKPSDAI-ADPGYFWFGNHKFRDDKEGGH 371 Query: 359 GALTVAQIIEKSSNIGTAKIALGMPAEEMWEMFTTVGFGQQPKFGFPGAVAGRVRPYKSW 418 G + + + I +S + +A + + + + GFGQ+ G V P +W Sbjct: 372 GMVDMYKSIVQSCDTYYYLLANDLGVDAIHDFMKPFGFGQKTGIDLRFERTG-VLPSTAW 430 Query: 419 RPI-----EQATMSYGHGISVSL---------IQLAHAYLIFARNGDII-PLSFTKVTDS 463 + EQ G IS+ + +QLAHA A NG ++ P ++ + Sbjct: 431 KAAAYKKPEQKRWYAGETISIGIGQGYNTFTPLQLAHATATLANNGVVMKPHLVREIENG 490 Query: 464 PIGQRVISA----------DTALQMRRMLETVVAPGGTAPQAQVPG-YRVGGKTGTAYKI 512 QR ++ + + + V GT +A Y GGKTGT+ I Sbjct: 491 VTRQRTLTVPKESYRIPLKQENIDIIKHAMVGVNKEGTGARAFARAEYVSGGKTGTSQVI 550 Query: 513 ENGKYVRKYVAS-----------FSGIAPMSDPRLIISVMID 543 K KY AS ++ AP PR+ ++++++ Sbjct: 551 AIKK-GEKYDASKISDRHHDHALYTAFAPADKPRIALALIVE 591 Database: BlastDatabases/690/690 Posted date: Apr 9, 2011 4:48 AM Number of letters in database: 1,000,347 Number of sequences in database: 3295 Lambda K H 0.318 0.134 0.382 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 3295 Number of Hits to DB: 1,052,567 Number of extensions: 41518 Number of successful extensions: 143 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 139 Number of HSP's successfully gapped: 2 Length of query: 592 Length of database: 1,000,347 Length adjustment: 87 Effective length of query: 505 Effective length of database: 713,682 Effective search space: 360409410 Effective search space used: 360409410 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: 131 (55.1 bits)