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= 0004.0066.p (381 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis... 91 1e-19 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 78 1e-15 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 77 2e-15 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 75 9e-15 gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 63 3e-11 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 91.3 bits (225), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 85/321 (26%), Positives = 139/321 (43%), Gaps = 18/321 (5%) Query: 35 GPLAQRLEARLAEYLSVAHAMCIT----NEAIALCLAAQALRLHGKVLVPGISDIFTAQS 90 GP + LEA L Y H CIT EA+ + L A ++ +++ + + TA+ Sbjct: 37 GPEVRELEAALEAYTGAKH--CITVASGTEALLISLMALDIKPGDEIITTPFTFVATAEV 94 Query: 91 LAWADAEPVFCDVDADTGMLSAEAAKIHLEKGGINAILAVNAWGGAADASALQELADRY- 149 + A+PVF DV+ DTG + + + AI+ V+ +G AAD + +A R+ Sbjct: 95 MVLLGAKPVFVDVEPDTGNIDVRLIEARI-TSKTKAIMPVSLYGQAADMDEINAIAARHG 153 Query: 150 DIPLYFDSSQAFGSSTDGVSLGGRGRLEVFSLQSAHVLSC-GEGAFIATNDDDLAAHVRN 208 ++P+ D++Q+FG++ G G + S + L C G+G I TNDD +A R Sbjct: 154 NLPVIEDAAQSFGATYKGRKSGNLSSIGCTSFFPSKPLGCYGDGGAIFTNDDAIALACRQ 213 Query: 209 IRSNYGMGRPVPVVKTSNGRFSEAQAAIALMSFDDLEIHIANNGLLAARYAASLSGIPGV 268 IR + R V GR Q AI L + + I L +RY + L Sbjct: 214 IRVHGQSQRYVHTRVGVGGRMDTLQCAIVLAKLERFDWEIEQRLALGSRYNSLLDAAGIA 273 Query: 269 TIRKAVGVDRSNQQCLMLAIDEVQFGLSAQALRKVLRAENIESSSRLASGWYRHGT--HA 326 I++ D Q +L + +A++ L+ I ++ R H Sbjct: 274 RIQQRPDRDSVFAQYTVLLDNR-------EAVQAALQNAGIPTAVHYPVPLNRQPAYRHL 326 Query: 327 VSVGALPIADSLCASLLELPI 347 P+AD L A ++ LP+ Sbjct: 327 GDPDQTPVADQLAARVMSLPM 347 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 64/246 (26%), Positives = 112/246 (45%), Gaps = 16/246 (6%) Query: 35 GPLAQRLEARLAEYLSVAHAMCITN--EAIALCLAAQALRLHGKVLVPGISDIFTAQSLA 92 GP + E + + + H++ +T+ A+ L LAA + +VP + I TA + Sbjct: 30 GPKVREFEEKWSAFTGARHSIAVTSCTTALHLSLAALGFGPGDEAIVPAFTWIATANVIE 89 Query: 93 WADAEPVFCDVDADTGMLSAEAAKIHLEKGGINAILAVNAWGGAADASALQELADRYDIP 152 + VFCD+D +T L A + + AIL V+ +G AA+ + ++A ++ + Sbjct: 90 HLGGKVVFCDIDLNTFNLDVAALRSKI-TSRTKAILPVHLFGLAAEMDQINDVAKQHGLW 148 Query: 153 LYFDSSQAFGSSTDGVSLGGRGRLEVFSLQSAHVLSCGEGAFIATNDDDLAAHVRNIRSN 212 + D++ FGS G +G G FS ++ GEG I T++D LA +R +R + Sbjct: 149 VVEDAACGFGSRYHGKHVGVLGDTGCFSFHPRKAITTGEGGMITTDNDALAEKLRRLRDH 208 Query: 213 ---------YGMGRPVPVVKTS----NGRFSEAQAAIALMSFDDLEIHIANNGLLAARYA 259 + RP + N R ++ QAA+ + + IA LA RY Sbjct: 209 GAAMTDLQRHLGARPYLLADHPDAGYNQRMTDIQAALGAAQMERADDIIAERRRLAERYD 268 Query: 260 ASLSGI 265 A+ + + Sbjct: 269 AAFADL 274 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 77.0 bits (188), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 78/344 (22%), Positives = 138/344 (40%), Gaps = 17/344 (4%) Query: 35 GPLAQRLEARLAEYLSVAHAMCITNEAIALCLAAQAL--RLHGKVLVPGISDIFTAQSLA 92 GP+ + E A YL + + + +AL LA +A+ R +V+ S ++ Sbjct: 33 GPVVESFENEFASYLGRTYGVAAASGTVALMLALRAMGIRAGDEVIASAYSWHQIVHAIT 92 Query: 93 WADAEPVFCDVDADTGMLSAEAAKIHLEKGGINAILAVNAWGGAADASALQELADRYDIP 152 A PVF D+D +G L+ + + AI+ N G A + ++LA + + Sbjct: 93 LVGATPVFADIDYWSGNLAPHKVADKISQR-TRAIVVGNCNGHPAAWTEFRQLAQAHGLR 151 Query: 153 LYFDSSQAFGSSTDGVSLGGRGRLEVFSLQSAHVLSCGEGAFIATNDDDLAAHVRNIRSN 212 L DSS+A GS G +G G + +F L CGEGA + T+D +LA+ + +R+ Sbjct: 152 LIEDSSEAIGSRYQGRVVGNFGDIAIFDFSQPSALCCGEGAMLVTDDPELASELHYMRNR 211 Query: 213 YGMGRPVPVVKTS---NGRFSEAQAAIALMSFDDLEIHIANNGLLAARYAASLSGIPGVT 269 R V + G S+ AAI + + L+ + + A Y + G+ Sbjct: 212 NLSDRQSIAVASRVPMQGSMSDLSAAIGIAQLERLDEILMRRKQVEAYYLEHVQFFEGIK 271 Query: 270 IRKAVGVDRSNQQCLMLAIDEVQFGLSAQALRKVLRAENIESSSRLASGW-------YRH 322 +G D ++ V G + E++ S A+ W + + Sbjct: 272 -PPYIGPDVEEVYWMLYL---VHLGTRFTRTMRNQIIEDLASQEVEAAAWCQPLHQQFYY 327 Query: 323 GTHAVSVGALPIADSLCASLLELPIGAKTDADKVALIADIIRQA 366 G L + + + + LP+ + D+V I + A Sbjct: 328 SRFDCKRGDLLLTEKIADRCIALPLHGHLNTDEVHFIVQAAKDA 371 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 75.1 bits (183), Expect = 9e-15, Method: Compositional matrix adjust. Identities = 59/190 (31%), Positives = 97/190 (51%), Gaps = 10/190 (5%) Query: 34 HGPLAQRLEARLAEYLSVAHAMCITNEAIALCLAAQALRLH----GKVLVPGISDIFTAQ 89 +GP + E +E+L V +++ + + A A L+ L+L G+V+VP ++ I Sbjct: 32 NGPNVRAFEKEWSEWLGVKYSVFVNSGASANLLSMAVLKLRHPEGGEVIVPPLTWISDVA 91 Query: 90 SLAWADAEPVFCDVDADTGMLSAEA--AKIHLEKGGINAILAVNAWGGAADASALQELAD 147 ++ PVF D+D + ++ E AKI E+ + V + G D L EL + Sbjct: 92 TVIQNGFTPVFADIDPRSLAMAPEQILAKI-TERTRAVFLTHVQGFDGLTD-ELLAEL-E 148 Query: 148 RYDIPLYFDSSQAFGSSTDGVSLGGRGRLEVFSLQSAHVLSCGEGAFIATNDDDLAAHVR 207 R +IPL D ++ G++ +G LG G + FS AH +S EG + TND ++ VR Sbjct: 149 RRNIPLIEDVCESHGATHNGQRLGSFGWMSNFSFYYAHHMSTIEGGMVCTNDPEVYQQVR 208 Query: 208 NIRSNYGMGR 217 +RS +GM R Sbjct: 209 MLRS-HGMVR 217 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 63.2 bits (152), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 85/367 (23%), Positives = 145/367 (39%), Gaps = 53/367 (14%) Query: 28 RQYYTNHGPLAQRLEARLAEYLSVAHAMCITNEAIALCLAAQALRLHG-----KVLVPGI 82 R + GP Q E L++YL + C ALR+ G +V+ I Sbjct: 26 RSGWITSGPKVQAFEKALSDYLG---GRIVRTFNSGTCTMEIALRIAGVGPGDEVITTPI 82 Query: 83 SDIFTAQSLAWADAEPVFCDVDADTGMLSAEAAKIHLEKGGINAILAVNAWGGAADASAL 142 S + TA + A PVF D+D T + + + + A++ V G D L Sbjct: 83 SWVATANVILETGATPVFADIDPITRNIDLDKLEAAITPR-TKAVIPVYLSGLPVDMDRL 141 Query: 143 QELADRYDIPLYFDSSQAFGSSTDGVSLGGRGRLEVFSLQSAHVLSCGEGAFIATNDDD- 201 +A ++ + + D++QA GS+ +G +G G FSLQ+ ++ EG F+ N+ + Sbjct: 142 YAIAAKHKLRVVEDAAQALGSTWNGKRIGAFGDFVSFSLQANKNITSSEGGFLVLNNAEE 201 Query: 202 --LAAHVR---NIRSNYGMGRPVPVVKTSNGRF--SEAQAAIALMSFDDLEIHIANNGLL 254 LA R RS + G V V+ G+F ++ AAI L F ++ A+ L Sbjct: 202 ARLAEKYRLQGVTRSGFD-GLEVDVL---GGKFNMTDVAAAIGLGQFAHIDAITAHRKEL 257 Query: 255 AARYAASLSGIPGVTIRKAVG-------VDRSNQQCLMLAIDEVQFGLSAQALRKVLRAE 307 A Y A G G + SN L + E ++ RA Sbjct: 258 ARHYFACF----GSDFESRYGAQLPVADFENSNWHMFQLVLPE-----------RITRAA 302 Query: 308 NIES--SSRLASGWYRHGTHAVSV--------GALPIADSLCASLLELPIGAKTDADKVA 357 +E ++ G++ H + + G P+A+ + ++ LP+ D V Sbjct: 303 FMEKMMEKQIGIGYHYPAIHLLKLYRERGFGEGMFPVAERVGQRIVSLPMFNTMSKDDVV 362 Query: 358 LIADIIR 364 + ++ Sbjct: 363 RSVETVK 369 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 0.134 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: 1,176,884 Number of extensions: 48266 Number of successful extensions: 188 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 178 Number of HSP's successfully gapped: 5 Length of query: 381 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 294 Effective length of database: 1,207,925 Effective search space: 355129950 Effective search space used: 355129950 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: 131 (55.1 bits)