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= 0002.0149.p (289 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 147 8e-37 gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 117 1e-27 gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis... 106 2e-24 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 82 4e-17 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 61 1e-10 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 147 bits (372), Expect = 8e-37, Method: Compositional matrix adjust. Identities = 102/297 (34%), Positives = 147/297 (49%), Gaps = 36/297 (12%) Query: 2 TYNLSVDRLEEKLIRAEAAGRLPKVVIPVHLCGQPCDMQGIHALSKKYGFRIIEDASHAI 61 T+NL V L K+ K ++PVHL G +M I+ ++K++G ++EDA+ Sbjct: 104 TFNLDVAALRSKITSRT------KAILPVHLFGLAAEMDQINDVAKQHGLWVVEDAACGF 157 Query: 62 GGRYKEEPIGNCRYSDITVFSFHPVKIITTGEGGMAVTNHRQLAIHMARLRSHGITRDPA 121 G RY + +G D FSFHP K ITTGEGGM T++ LA + RLR HG A Sbjct: 158 GSRYHGKHVG--VLGDTGCFSFHPRKAITTGEGGMITTDNDALAEKLRRLRDHG-----A 210 Query: 122 EMT----HAPDGPWYY-QQIELGFNYRMTDIQAALGLSQMQRLNEFVAKRHELARTYDEL 176 MT H P+ + G+N RMTDIQAALG +QM+R ++ +A+R LA YD Sbjct: 211 AMTDLQRHLGARPYLLADHPDAGYNQRMTDIQAALGAAQMERADDIIAERRRLAERYDAA 270 Query: 177 LKDRPVTTPLQHEDGYS-GLHLY--------VIRLKLDAIHATHREVFERLRVSGIGVN- 226 D H DG G Y V ++ I+A + L+ +GI Sbjct: 271 FADLSWLRTPAHVDGLEHGYQSYPCLFQPEPVNTDSIERINAARNAWMDSLQQAGISTRP 330 Query: 227 ----LHYIPVYRQPYFEQQGFDPADFPEAEKYYAEAITLPMFPALTHAQQVEVVQRL 279 +H + YR+ Y PADFP A +I+LP+F +T A+Q V++++ Sbjct: 331 ATHAVHMLTFYREKY----ALKPADFPNAWAANDCSISLPLFHGMTQAEQDFVIEQV 383 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 117 bits (293), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 83/289 (28%), Positives = 135/289 (46%), Gaps = 26/289 (8%) Query: 1 VTYNLSVDRLEEKLIRAEAAGRLPKVVIPVHLCGQPCDMQGIHALSKKYGFRIIEDASHA 60 +T N+ +D+LE + K VIPV+L G P DM ++A++ K+ R++EDA+ A Sbjct: 106 ITRNIDLDKLEAAITPRT------KAVIPVYLSGLPVDMDRLYAIAAKHKLRVVEDAAQA 159 Query: 61 IGGRYKEEPIGNCRYSDITVFSFHPVKIITTGEGGMAVTNHRQLAIHMARLRSHGITRDP 120 +G + + IG + D FS K IT+ EGG V N+ + A + R G+TR Sbjct: 160 LGSTWNGKRIG--AFGDFVSFSLQANKNITSSEGGFLVLNNAEEARLAEKYRLQGVTR-- 215 Query: 121 AEMTHAPDGPWYYQQIELGFNYRMTDIQAALGLSQMQRLNEFVAKRHELARTY-----DE 175 DG + LG + MTD+ AA+GL Q ++ A R ELAR Y + Sbjct: 216 ----SGFDG---LEVDVLGGKFNMTDVAAAIGLGQFAHIDAITAHRKELARHYFACFGSD 268 Query: 176 LLKDRPVTTPLQHEDGYSGLHLYVIRLKLDAIHATHREVFERLRVSGIGVNLHYIPVYRQ 235 P+ + S H++ + L T E++ IG+ HY ++ Sbjct: 269 FESRYGAQLPVADFEN-SNWHMFQLVLPE---RITRAAFMEKMMEKQIGIGYHYPAIHLL 324 Query: 236 PYFEQQGFDPADFPEAEKYYAEAITLPMFPALTHAQQVEVVQRLTTPIG 284 + ++GF FP AE+ ++LPMF ++ V V+ + + +G Sbjct: 325 KLYRERGFGEGMFPVAERVGQRIVSLPMFNTMSKDDVVRSVETVKSVLG 373 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 106 bits (265), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 82/274 (29%), Positives = 130/274 (47%), Gaps = 28/274 (10%) Query: 10 LEEKLIRAEAAGRLPKVVIPVHLCGQPCDMQGIHALSKKYG-FRIIEDASHAIGGRYKEE 68 ++ +LI A + K ++PV L GQ DM I+A++ ++G +IEDA+ + G YK Sbjct: 114 IDVRLIEARITSKT-KAIMPVSLYGQAADMDEINAIAARHGNLPVIEDAAQSFGATYKGR 172 Query: 69 PIGNCRYSDITVFSFHPVKIITT-GEGGMAVTNHRQLAIHMARLRSHGITRDPAEMTHAP 127 GN S I SF P K + G+GG TN +A+ ++R HG ++ Sbjct: 173 KSGN--LSSIGCTSFFPSKPLGCYGDGGAIFTNDDAIALACRQIRVHGQSQ--------- 221 Query: 128 DGPWYYQQIELGFNYRMTDIQAALGLSQMQRLNEFVAKRHELARTYDELLKDRPVTTPLQ 187 Y +G RM +Q A+ L++++R + + +R L Y+ LL + Q Sbjct: 222 ----RYVHTRVGVGGRMDTLQCAIVLAKLERFDWEIEQRLALGSRYNSLLDAAGIARIQQ 277 Query: 188 HEDGYSGLHLYVIRLKLDAIHATHREVFER-LRVSGIGVNLHY-IPVYRQPYFEQQGFDP 245 D S Y + L +RE + L+ +GI +HY +P+ RQP + G DP Sbjct: 278 RPDRDSVFAQYTVLLD-------NREAVQAALQNAGIPTAVHYPVPLNRQPAYRHLG-DP 329 Query: 246 ADFPEAEKYYAEAITLPMFPALTHAQQVEVVQRL 279 P A++ A ++LPM P L H Q +V L Sbjct: 330 DQTPVADQLAARVMSLPMSPDLEHTAQDSIVAAL 363 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 82.4 bits (202), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 61/243 (25%), Positives = 110/243 (45%), Gaps = 18/243 (7%) Query: 25 KVVIPVHLCGQPCDMQGIHALSKKYGFRIIEDASHAIGGRYKEEPIGNCRYSDITVFSFH 84 + ++ + G P L++ +G R+IED+S AIG RY+ +GN + DI +F F Sbjct: 124 RAIVVGNCNGHPAAWTEFRQLAQAHGLRLIEDSSEAIGSRYQGRVVGN--FGDIAIFDFS 181 Query: 85 PVKIITTGEGGMAVTNHRQLAIHMARLRSHGITRDPAEMTHAPDGPWYYQQIELGFNYRM 144 + GEG M VT+ +LA + +R+ ++ D + A P M Sbjct: 182 QPSALCCGEGAMLVTDDPELASELHYMRNRNLS-DRQSIAVASRVP---------MQGSM 231 Query: 145 TDIQAALGLSQMQRLNEFVAKRHELARTYDELLK----DRPVTTPLQHEDGYSGLHLYVI 200 +D+ AA+G++Q++RL+E + +R ++ Y E ++ +P E+ Y LY++ Sbjct: 232 SDLSAAIGIAQLERLDEILMRRKQVEAYYLEHVQFFEGIKPPYIGPDVEEVY--WMLYLV 289 Query: 201 RLKLDAIHATHREVFERLRVSGIGVNLHYIPVYRQPYFEQQGFDPADFPEAEKYYAEAIT 260 L ++ E L + P+++Q Y+ + D EK I Sbjct: 290 HLGTRFTRTMRNQIIEDLASQEVEAAAWCQPLHQQFYYSRFDCKRGDLLLTEKIADRCIA 349 Query: 261 LPM 263 LP+ Sbjct: 350 LPL 352 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 65/249 (26%), Positives = 111/249 (44%), Gaps = 33/249 (13%) Query: 53 IIEDASHAIGGRYKEEPIGNCRYSDITVFSFHPVKIITTGEGGMAVTNHRQLAIHMARLR 112 +IED + G + + +G+ + ++ FSF+ ++T EGGM TN ++ + LR Sbjct: 154 LIEDVCESHGATHNGQRLGSFGW--MSNFSFYYAHHMSTIEGGMVCTNDPEVYQQVRMLR 211 Query: 113 SHGITR----DPAEMTHAPDGPWYYQQIELGF---NYRMTDIQAALGLSQMQRLNEFVAK 165 SHG+ R D ++ + D P F N R T+I A +G SQ++RL+ A+ Sbjct: 212 SHGMVREATDDDLKLGYRQDNPQLNPDFIFAFPAYNVRNTEIGAIMGRSQLKRLDANCAR 271 Query: 166 R-HELARTYDELLKDRPVTTPLQHEDGYSGLHLYVIRLKLDAIHATHREVFERLRVSGI- 223 R + R D++ R + E G S ++ + D + + + +R +GI Sbjct: 272 RTANMMRFLDQIDSQR-YRVDFKTE-GSSNYAFNLVLREADDVFV--ERLMQTMRSNGIE 327 Query: 224 -------GVNLHYIPVYRQPYFEQQGFDPAD----FPEAEKYYAEAITLPMFPALTHAQQ 272 G N RQPY +G PAD FP+ E + + FP L+ A+ Sbjct: 328 FRRGSAGGGNQ-----VRQPYL--KGIVPADHYLQFPQTEHIHFYGFYIGNFPDLSDAEV 380 Query: 273 VEVVQRLTT 281 ++ + L Sbjct: 381 DDICRILNA 389 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 0.323 0.139 0.421 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: 961,619 Number of extensions: 42165 Number of successful extensions: 112 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 101 Number of HSP's successfully gapped: 5 Length of query: 289 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 205 Effective length of database: 1,222,130 Effective search space: 250536650 Effective search space used: 250536650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 130 (54.7 bits)