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= 0001.1941.p (373 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 736 0.0 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 200 1e-52 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 155 4e-39 gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis... 150 1e-37 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 121 1e-28 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 736 bits (1901), Expect = 0.0, Method: Compositional matrix adjust. Identities = 354/373 (94%), Positives = 364/373 (97%) Query: 1 MSLPFLPFAKPTIDEATITAVGEVLRSGWITSGPKVQAFEKALSDYLGGRIVRTFNSGTC 60 MSLPFLPFAKPTIDE TI AVGEVLRSGWITSGPKVQAFEKALSDYLGGRIVRTFNSGTC Sbjct: 1 MSLPFLPFAKPTIDEPTIAAVGEVLRSGWITSGPKVQAFEKALSDYLGGRIVRTFNSGTC 60 Query: 61 TMEIALRIAGIGPGDEVITTPISWVATANVILETGATPVFADIDPVTRNIDLDQLEAAIT 120 TMEIALRIAG+GPGDEVITTPISWVATANVILETGATPVFADIDP+TRNIDLD+LEAAIT Sbjct: 61 TMEIALRIAGVGPGDEVITTPISWVATANVILETGATPVFADIDPITRNIDLDKLEAAIT 120 Query: 121 PHTKAVIPVYLSGLPVDMDRLYAIAAKHQLRVVEDAAQALGSTWNGKRIGAFGDFVSFSL 180 P TKAVIPVYLSGLPVDMDRLYAIAAKH+LRVVEDAAQALGSTWNGKRIGAFGDFVSFSL Sbjct: 121 PRTKAVIPVYLSGLPVDMDRLYAIAAKHKLRVVEDAAQALGSTWNGKRIGAFGDFVSFSL 180 Query: 181 QANKNITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFDGLEVDLLGGKFNMTDVAAAIG 240 QANKNITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFDGLEVD+LGGKFNMTDVAAAIG Sbjct: 181 QANKNITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFDGLEVDVLGGKFNMTDVAAAIG 240 Query: 241 LGQFAHVDAVTAHRKELARHYFACFGHDFEANYGAQLPVADFENSNWHMFQLVLPERITR 300 LGQFAH+DA+TAHRKELARHYFACFG DFE+ YGAQLPVADFENSNWHMFQLVLPERITR Sbjct: 241 LGQFAHIDAITAHRKELARHYFACFGSDFESRYGAQLPVADFENSNWHMFQLVLPERITR 300 Query: 301 AAFMEKMVEKQIGIGYHYPAIHLLKLYRERGFKEGMFPVAERVGQRIVSLPMFNAMRKED 360 AAFMEKM+EKQIGIGYHYPAIHLLKLYRERGF EGMFPVAERVGQRIVSLPMFN M K+D Sbjct: 301 AAFMEKMMEKQIGIGYHYPAIHLLKLYRERGFGEGMFPVAERVGQRIVSLPMFNTMSKDD 360 Query: 361 VERSVETVKSVLG 373 V RSVETVKSVLG Sbjct: 361 VVRSVETVKSVLG 373 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 200 bits (509), Expect = 1e-52, Method: Compositional matrix adjust. Identities = 132/385 (34%), Positives = 189/385 (49%), Gaps = 24/385 (6%) Query: 6 LPFAKPTIDEATITAVGEVLRSGWITSGPKVQAFEKALSDYLGGRIVRTFNSGTCTMEIA 65 +P A+ ++ EA I +V L +GW+ GPKV+ FE+ S + G R S T + ++ Sbjct: 3 VPIARTSLTEAEIQSVLAPLSNGWLVQGPKVREFEEKWSAFTGARHSIAVTSCTTALHLS 62 Query: 66 LRIAGIGPGDEVITTPISWVATANVILETGATPVFADIDPVTRNIDLDQLEAAITPHTKA 125 L G GPGDE I +W+ATANVI G VF DID T N+D+ L + IT TKA Sbjct: 63 LAALGFGPGDEAIVPAFTWIATANVIEHLGGKVVFCDIDLNTFNLDVAALRSKITSRTKA 122 Query: 126 VIPVYLSGLPVDMDRLYAIAAKHQLRVVEDAAQALGSTWNGKRIGAFGDFVSFSLQANKN 185 ++PV+L GL +MD++ +A +H L VVEDAA GS ++GK +G GD FS K Sbjct: 123 ILPVHLFGLAAEMDQINDVAKQHGLWVVEDAACGFGSRYHGKHVGVLGDTGCFSFHPRKA 182 Query: 186 ITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFD---GLEVDLL------GGKFNMTDVA 236 IT+ EGG + +N A + R G + G LL G MTD+ Sbjct: 183 ITTGEGGMITTDNDALAEKLRRLRDHGAAMTDLQRHLGARPYLLADHPDAGYNQRMTDIQ 242 Query: 237 AAIGLGQFAHVDAVTAHRKELARHYFACF---------GHDFEANYGAQLPVADFENSNW 287 AA+G Q D + A R+ LA Y A F H +G Q F+ Sbjct: 243 AALGAAQMERADDIIAERRRLAERYDAAFADLSWLRTPAHVDGLEHGYQSYPCLFQPEPV 302 Query: 288 HMFQLVLPERIT--RAAFMEKMVEKQIGIGYHYPAIHLLKLYRER-GFKEGMFPVAERVG 344 + + ERI R A+M+ + + I A+H+L YRE+ K FP A Sbjct: 303 NTDSI---ERINAARNAWMDSLQQAGISTRPATHAVHMLTFYREKYALKPADFPNAWAAN 359 Query: 345 QRIVSLPMFNAMRKEDVERSVETVK 369 +SLP+F+ M + + + +E V+ Sbjct: 360 DCSISLPLFHGMTQAEQDFVIEQVR 384 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 155 bits (393), Expect = 4e-39, Method: Compositional matrix adjust. Identities = 105/375 (28%), Positives = 179/375 (47%), Gaps = 12/375 (3%) Query: 1 MSLPFLPFAKPTIDEATITAVGEVLRSGWITSGPKVQAFEKALSDYLGGRIVRTFNSGTC 60 M ++ + P + + AV VL S +++GP V++FE + YLG SGT Sbjct: 1 MEQEWIKLSDPDVSTRELEAVTRVLVSSGLSAGPVVESFENEFASYLGRTYGVAAASGTV 60 Query: 61 TMEIALRIAGIGPGDEVITTPISWVATANVILETGATPVFADIDPVTRNIDLDQLEAAIT 120 + +ALR GI GDEVI + SW + I GATPVFADID + N+ ++ I+ Sbjct: 61 ALMLALRAMGIRAGDEVIASAYSWHQIVHAITLVGATPVFADIDYWSGNLAPHKVADKIS 120 Query: 121 PHTKAVIPVYLSGLPVDMDRLYAIAAKHQLRVVEDAAQALGSTWNGKRIGAFGDFVSFSL 180 T+A++ +G P +A H LR++ED+++A+GS + G+ +G FGD F Sbjct: 121 QRTRAIVVGNCNGHPAAWTEFRQLAQAHGLRLIEDSSEAIGSRYQGRVVGNFGDIAIFDF 180 Query: 181 QANKNITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFDGLEV-DLLGGKFNMTDVAAAI 239 + EG LV ++ E A +E + ++ S + V + + +M+D++AAI Sbjct: 181 SQPSALCCGEGAMLVTDDPELA--SELHYMRNRNLSDRQSIAVASRVPMQGSMSDLSAAI 238 Query: 240 GLGQFAHVDAVTAHRKELARHYFACFGHDFEANYGAQLPV--ADFENSNWHMFQLVLPER 297 G+ Q +D + RK++ +Y FE G + P D E W ++ + L R Sbjct: 239 GIAQLERLDEILMRRKQVEAYYLEHVQF-FE---GIKPPYIGPDVEEVYWMLYLVHLGTR 294 Query: 298 ITRA---AFMEKMVEKQIGIGYHYPAIHLLKLYRERGFKEGMFPVAERVGQRIVSLPMFN 354 TR +E + +++ +H Y K G + E++ R ++LP+ Sbjct: 295 FTRTMRNQIIEDLASQEVEAAAWCQPLHQQFYYSRFDCKRGDLLLTEKIADRCIALPLHG 354 Query: 355 AMRKEDVERSVETVK 369 + ++V V+ K Sbjct: 355 HLNTDEVHFIVQAAK 369 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 150 bits (380), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 117/368 (31%), Positives = 180/368 (48%), Gaps = 27/368 (7%) Query: 13 IDEATITAVGEVLRSGWITSGPKVQAFEKALSDYLGGRIVRTFNSGTCTMEIALRIAGIG 72 + +A + + +VL G GP+V+ E AL Y G + T SGT + I+L I Sbjct: 17 LKDAINSRIQKVLDHGQYIMGPEVRELEAALEAYTGAKHCITVASGTEALLISLMALDIK 76 Query: 73 PGDEVITTPISWVATANVILETGATPVFADIDPVTRNIDLDQLEAAITPHTKAVIPVYLS 132 PGDE+ITTP ++VATA V++ GA PVF D++P T NID+ +EA IT TKA++PV L Sbjct: 77 PGDEIITTPFTFVATAEVMVLLGAKPVFVDVEPDTGNIDVRLIEARITSKTKAIMPVSLY 136 Query: 133 GLPVDMDRLYAIAAKH-QLRVVEDAAQALGSTWNGKRIGAFGDFVSFSLQANKNI-TSSE 190 G DMD + AIAA+H L V+EDAAQ+ G+T+ G++ G S +K + + Sbjct: 137 GQAADMDEINAIAARHGNLPVIEDAAQSFGATYKGRKSGNLSSIGCTSFFPSKPLGCYGD 196 Query: 191 GGFLVLNNAEEARLAEKYRLQGV------TRSGFDGLEVDLLGGKFNMTDVAAAIGLGQF 244 GG + N+ A + R+ G TR G +GG+ M + AI L + Sbjct: 197 GGAIFTNDDAIALACRQIRVHGQSQRYVHTRVG--------VGGR--MDTLQCAIVLAKL 246 Query: 245 AHVDAVTAHRKELARHYFACFGHDFEANYGAQLPVADFENSNWHMFQLVLPERITRAAFM 304 D R L Y + +A A++ +S + + ++L R A Sbjct: 247 ERFDWEIEQRLALGSRYNSL----LDAAGIARIQQRPDRDSVFAQYTVLLD---NREAVQ 299 Query: 305 EKMVEKQIGIGYHYPA-IHLLKLYRERGFKEGMFPVAERVGQRIVSLPMFNAMRKEDVER 363 + I HYP ++ YR G + PVA+++ R++SLPM + + Sbjct: 300 AALQNAGIPTAVHYPVPLNRQPAYRHLGDPD-QTPVADQLAARVMSLPMSPDLEHTAQDS 358 Query: 364 SVETVKSV 371 V ++S+ Sbjct: 359 IVAALRSI 366 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 121 bits (303), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 94/326 (28%), Positives = 156/326 (47%), Gaps = 34/326 (10%) Query: 7 PFAKPTIDEATITAVGEVLRSG--WITSGPKVQAFEKALSDYLGGRIVRTFNSGTCTMEI 64 P + I + AV E LR +T+GP V+AFEK S++LG + NSG + Sbjct: 5 PLMRNNILREDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYSVFVNSGASANLL 64 Query: 65 ALRIAGIG--PGDEVITTPISWVATANVILETGATPVFADIDPVTRNIDLDQLEAAITPH 122 ++ + + G EVI P++W++ +++ G TPVFADIDP + + +Q+ A IT Sbjct: 65 SMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAKITER 124 Query: 123 TKAVIPVYLSGLPVDMDRLYAIAAKHQLRVVEDAAQALGSTWNGKRIGAFGDFVSFSLQA 182 T+AV ++ G D L A + + ++ED ++ G+T NG+R+G+FG +FS Sbjct: 125 TRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNFSFYY 184 Query: 183 NKNITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFDG------------LEVDLLGG-- 228 ++++ EGG + N+ E + R G+ R D L D + Sbjct: 185 AHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVREATDDDLKLGYRQDNPQLNPDFIFAFP 244 Query: 229 KFNM--TDVAAAIGLGQFAHVDAVTAHRK-ELARHYFACFGHDFEANYGAQLPVADF--E 283 +N+ T++ A +G Q +DA A R + R F +Q DF E Sbjct: 245 AYNVRNTEIGAIMGRSQLKRLDANCARRTANMMR---------FLDQIDSQRYRVDFKTE 295 Query: 284 NSNWHMFQLVLPERITRAAFMEKMVE 309 S+ + F LVL E F+E++++ Sbjct: 296 GSSNYAFNLVLRE--ADDVFVERLMQ 319 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 0.137 0.403 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: 1,216,513 Number of extensions: 53651 Number of successful extensions: 152 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 144 Number of HSP's successfully gapped: 5 Length of query: 373 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 286 Effective length of database: 1,207,925 Effective search space: 345466550 Effective search space used: 345466550 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: 131 (55.1 bits)