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= 0004.0067.p (399 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... 94 3e-20 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 86 8e-18 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 85 9e-18 gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 82 6e-17 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 63 5e-11 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 93.6 bits (231), Expect = 3e-20, Method: Compositional matrix adjust. Identities = 88/354 (24%), Positives = 157/354 (44%), Gaps = 22/354 (6%) Query: 18 LFEQIKSVSNLVRPDIESFLKYSRKFFDAQTSTGHGPVETLMERRLAEFHEARHCVSFCG 77 L Q +++ + + I+ L + + GP +E L + A+HC++ Sbjct: 10 LKSQYRALKDAINSRIQKVLDHGQYIM--------GPEVRELEAALEAYTGAKHCITVAS 61 Query: 78 GFWGLVLAMKCLALPGRTEVVMPSLTYRRLADIVAWAGLTPHFCEVDPDLLCITGETAAT 137 G L++++ L + E++ T+ A+++ G P F +V+PD I Sbjct: 62 GTEALLISLMALDIKPGDEIITTPFTFVATAEVMVLLGAKPVFVDVEPDTGNIDVRLIEA 121 Query: 138 CINENTALILGVHPIVNCCDIDGLEALSERTG-IPLLIDAVESVYESYKGRKIGSCARAE 196 I T I+ V D+D + A++ R G +P++ DA +S +YKGRK G+ + Sbjct: 122 RITSKTKAIMPVSLYGQAADMDEINAIAARHGNLPVIEDAAQSFGATYKGRKSGNLSSIG 181 Query: 197 CFSMQSSKLFNAF-EGGYVTTNDDVLAERLRTMRDFGVGADGIPDEVCALGVQQNEMHAS 255 C S SK + +GG + TNDD +A R +R G + V +G + + + + Sbjct: 182 CTSFFPSKPLGCYGDGGAIFTNDDAIALACRQIRVHGQSQRYVHTRV-GVGGRMDTLQCA 240 Query: 256 MALACLDDVDEQMAANLQRYRAYQRCLATVPGIKLREFDESERCGFKNILVELLDDWPLT 315 + LA L+ D ++ L Y L ++++ + + F V LLD+ Sbjct: 241 IVLAKLERFDWEIEQRLALGSRYNSLLDAAGIARIQQRPDRDSV-FAQYTV-LLDN---- 294 Query: 316 REATISLLNAENMLCRPYYSPPLHLKSTGYPMLWGDLAQT---ERLAKKFLLLP 366 REA + L + +Y PL+ + Y L GD QT ++LA + + LP Sbjct: 295 REAVQAALQNAGIPTAVHYPVPLN-RQPAYRHL-GDPDQTPVADQLAARVMSLP 346 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 85.5 bits (210), Expect = 8e-18, Method: Compositional matrix adjust. Identities = 77/329 (23%), Positives = 134/329 (40%), Gaps = 34/329 (10%) Query: 53 GPVETLMERRLAEFHEARHCVSFCGGFWGLVLAMKCLALPGRTEVVMPSLTYRRLADIVA 112 GP E + + F ARH ++ L L++ L E ++P+ T+ A+++ Sbjct: 30 GPKVREFEEKWSAFTGARHSIAVTSCTTALHLSLAALGFGPGDEAIVPAFTWIATANVIE 89 Query: 113 WAGLTPHFCEVDPDLLCITGETAATCINENTALILGVHPIVNCCDIDGLEALSERTGIPL 172 G FC++D + + + I T IL VH ++D + ++++ G+ + Sbjct: 90 HLGGKVVFCDIDLNTFNLDVAALRSKITSRTKAILPVHLFGLAAEMDQINDVAKQHGLWV 149 Query: 173 LIDAVESVYESYKGRKIGSCARAECFSMQSSKLFNAFEGGYVTTNDDVLAERLRTMRDFG 232 + DA Y G+ +G CFS K EGG +TT++D LAE+LR +RD G Sbjct: 150 VEDAACGFGSRYHGKHVGVLGDTGCFSFHPRKAITTGEGGMITTDNDALAEKLRRLRDHG 209 Query: 233 VGADGIPDEVCA----------LGVQQ--NEMHASMALACLDDVDEQMAAN---LQRYRA 277 + + A G Q ++ A++ A ++ D+ +A +RY A Sbjct: 210 AAMTDLQRHLGARPYLLADHPDAGYNQRMTDIQAALGAAQMERADDIIAERRRLAERYDA 269 Query: 278 ------YQRCLATVPGIKLREFDESERCGFK--NILVELLDDWPLTREATISLLNAENML 329 + R A V G L +S C F+ + + ++ R A + L + Sbjct: 270 AFADLSWLRTPAHVDG--LEHGYQSYPCLFQPEPVNTDSIERINAARNAWMDSLQQAGIS 327 Query: 330 CRP---------YYSPPLHLKSTGYPMLW 349 RP +Y LK +P W Sbjct: 328 TRPATHAVHMLTFYREKYALKPADFPNAW 356 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 85.1 bits (209), Expect = 9e-18, Method: Compositional matrix adjust. Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 10/229 (4%) Query: 26 SNLVRPDIESFLKYSRKFFDAQTSTGHGPVETLMERRLAEFHEARHCVSFCGGFWGLVLA 85 +N++R D+++ +++ R+ D T +GP E+ +E+ ++ V G +L+ Sbjct: 9 NNILREDLDAVIEHLRQ--DDPILT-NGPNVRAFEKEWSEWLGVKYSVFVNSGASANLLS 65 Query: 86 MKCLAL--PGRTEVVMPSLTYRRLADIVAWAGLTPHFCEVDPDLLCITGETAATCINENT 143 M L L P EV++P LT+ V G TP F ++DP L + E I E T Sbjct: 66 MAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAKITERT 125 Query: 144 ALILGVHPIVNCCD--IDGLEALSERTGIPLLIDAVESVYESYKGRKIGSCARAECFSMQ 201 + H V D D L A ER IPL+ D ES ++ G+++GS FS Sbjct: 126 RAVFLTH--VQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNFSFY 183 Query: 202 SSKLFNAFEGGYVTTNDDVLAERLRTMRDFGVGADGIPDEVCALGVQQN 250 + + EGG V TND + +++R +R G+ + D++ LG +Q+ Sbjct: 184 YAHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVREATDDDL-KLGYRQD 231 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 82.4 bits (202), Expect = 6e-17, Method: Compositional matrix adjust. Identities = 75/337 (22%), Positives = 150/337 (44%), Gaps = 21/337 (6%) Query: 53 GPVETLMERRLAEFHEARHCVSFCGGFWGLVLAMKCLALPGRTEVVMPSLTYRRLADIVA 112 GP E+ L+++ R +F G + +A++ + EV+ +++ A+++ Sbjct: 33 GPKVQAFEKALSDYLGGRIVRTFNSGTCTMEIALRIAGVGPGDEVITTPISWVATANVIL 92 Query: 113 WAGLTPHFCEVDPDLLCITGETAATCINENTALILGVHPIVNCCDIDGLEALSERTGIPL 172 G TP F ++DP I + I T ++ V+ D+D L A++ + + + Sbjct: 93 ETGATPVFADIDPITRNIDLDKLEAAITPRTKAVIPVYLSGLPVDMDRLYAIAAKHKLRV 152 Query: 173 LIDAVESVYESYKGRKIGSCARAECFSMQSSKLFNAFEGGYVTTND---DVLAERLRTMR 229 + DA +++ ++ G++IG+ FS+Q++K + EGG++ N+ LAE+ R Sbjct: 153 VEDAAQALGSTWNGKRIGAFGDFVSFSLQANKNITSSEGGFLVLNNAEEARLAEKYRLQG 212 Query: 230 DFGVGADGIPDEVCALGVQQNEMHASMALACLDDVDEQMAANLQRYRAYQRCLAT----- 284 G DG+ +V ++ A++ L +D A + R Y C + Sbjct: 213 VTRSGFDGLEVDVLGGKFNMTDVAAAIGLGQFAHIDAITAHRKELARHYFACFGSDFESR 272 Query: 285 -VPGIKLREFDESERCGFKNILVELLDDWPLTREATISLLNAENMLCRPYYSPPLHL--- 340 + + +F+ S F+ +L E +TR A + + E + Y+ P +HL Sbjct: 273 YGAQLPVADFENSNWHMFQLVLPER-----ITRAAFMEKM-MEKQIGIGYHYPAIHLLKL 326 Query: 341 -KSTGYPMLWGDLAQTERLAKKFLLLPCGYFVSEADV 376 + G+ G ER+ ++ + LP +S+ DV Sbjct: 327 YRERGFGE--GMFPVAERVGQRIVSLPMFNTMSKDDV 361 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 78/349 (22%), Positives = 143/349 (40%), Gaps = 21/349 (6%) Query: 53 GPVETLMERRLAEFHEARHCVSFCGGFWGLVLAMKCLALPGRTEVVMPSLTYRRLADIVA 112 GPV E A + + V+ G L+LA++ + + EV+ + ++ ++ + Sbjct: 33 GPVVESFENEFASYLGRTYGVAAASGTVALMLALRAMGIRAGDEVIASAYSWHQIVHAIT 92 Query: 113 WAGLTPHFCEVDPDLLCITGETAATCINENT-ALILGVHPIVNC----CDIDGLEALSER 167 G TP F ++D + A I++ T A+++G NC L++ Sbjct: 93 LVGATPVFADIDYWSGNLAPHKVADKISQRTRAIVVG-----NCNGHPAAWTEFRQLAQA 147 Query: 168 TGIPLLIDAVESVYESYKGRKIGSCARAECFSMQSSKLFNAFEGGYVTTNDDVLAERLRT 227 G+ L+ D+ E++ Y+GR +G+ F EG + T+D LA L Sbjct: 148 HGLRLIEDSSEAIGSRYQGRVVGNFGDIAIFDFSQPSALCCGEGAMLVTDDPELASELHY 207 Query: 228 MRDFGVG---ADGIPDEVCALGVQQNEMHASMALACLDDVDEQMAANLQRYRAYQRCLAT 284 MR+ + + + V G +++ A++ +A L+ +DE + Q Y + Sbjct: 208 MRNRNLSDRQSIAVASRVPMQG-SMSDLSAAIGIAQLERLDEILMRRKQVEAYYLEHVQF 266 Query: 285 VPGIKLREFD-ESERCGFKNILVELLDDWPLTREATISLLNAENMLCRPYYSPPLHLK-- 341 GIK + E + LV L + T I A + + PLH + Sbjct: 267 FEGIKPPYIGPDVEEVYWMLYLVHLGTRFTRTMRNQIIEDLASQEVEAAAWCQPLHQQFY 326 Query: 342 STGYPMLWGDLAQTERLAKKFLLLPCGYFVSEADVEQIAHFLAFIQKHA 390 + + GDL TE++A + + LP ++ +V HF+ K A Sbjct: 327 YSRFDCKRGDLLLTEKIADRCIALPLHGHLNTDEV----HFIVQAAKDA 371 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 0.138 0.425 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: 1,203,047 Number of extensions: 47712 Number of successful extensions: 123 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 118 Number of HSP's successfully gapped: 5 Length of query: 399 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 312 Effective length of database: 1,207,925 Effective search space: 376872600 Effective search space used: 376872600 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 (22.0 bits) S2: 131 (55.1 bits)