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= 0022.0093.p (390 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 815 0.0 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 132 4e-32 gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent a... 124 1e-29 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 112 6e-26 gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis... 105 7e-24 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 815 bits (2105), Expect = 0.0, Method: Compositional matrix adjust. Identities = 390/390 (100%), Positives = 390/390 (100%) Query: 1 MMKYPLMRNNILREDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYSVFVNSGAS 60 MMKYPLMRNNILREDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYSVFVNSGAS Sbjct: 1 MMKYPLMRNNILREDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYSVFVNSGAS 60 Query: 61 ANLLSMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAK 120 ANLLSMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAK Sbjct: 61 ANLLSMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAK 120 Query: 121 ITERTRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNF 180 ITERTRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNF Sbjct: 121 ITERTRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNF 180 Query: 181 SFYYAHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVREATDDDLKLGYRQDNPQLNPDFI 240 SFYYAHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVREATDDDLKLGYRQDNPQLNPDFI Sbjct: 181 SFYYAHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVREATDDDLKLGYRQDNPQLNPDFI 240 Query: 241 FAFPAYNVRNTEIGAIMGRSQLKRLDANCARRTANMMRFLDQIDSQRYRVDFKTEGSSNY 300 FAFPAYNVRNTEIGAIMGRSQLKRLDANCARRTANMMRFLDQIDSQRYRVDFKTEGSSNY Sbjct: 241 FAFPAYNVRNTEIGAIMGRSQLKRLDANCARRTANMMRFLDQIDSQRYRVDFKTEGSSNY 300 Query: 301 AFNLVLREADDVFVERLMQTMRSNGIEFRRGSAGGGNQVRQPYLKGIVPADHYLQFPQTE 360 AFNLVLREADDVFVERLMQTMRSNGIEFRRGSAGGGNQVRQPYLKGIVPADHYLQFPQTE Sbjct: 301 AFNLVLREADDVFVERLMQTMRSNGIEFRRGSAGGGNQVRQPYLKGIVPADHYLQFPQTE 360 Query: 361 HIHFYGFYIGNFPDLSDAEVDDICRILNAV 390 HIHFYGFYIGNFPDLSDAEVDDICRILNAV Sbjct: 361 HIHFYGFYIGNFPDLSDAEVDDICRILNAV 390 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 132 bits (333), Expect = 4e-32, Method: Compositional matrix adjust. Identities = 85/271 (31%), Positives = 138/271 (50%), Gaps = 11/271 (4%) Query: 2 MKYPLMRNNILREDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYSVFVNSGASA 61 M P+ R ++ ++ +V+ L + L GP VR FE++WS + G ++S+ V S +A Sbjct: 1 MNVPIARTSLTEAEIQSVLAPL--SNGWLVQGPKVREFEEKWSAFTGARHSIAVTSCTTA 58 Query: 62 NLLSMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAKI 121 LS+A L G E IVP TWI+ + G VF DID + + + +KI Sbjct: 59 LHLSLAALGF--GPGDEAIVPAFTWIATANVIEHLGGKVVFCDIDLNTFNLDVAALRSKI 116 Query: 122 TERTRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNFS 181 T RT+A+ H+ G D++ ++ + ++ED G+ ++G+ +G G FS Sbjct: 117 TSRTKAILPVHLFGLAAEMDQINDVAKQHGLWVVEDAACGFGSRYHGKHVGVLGDTGCFS 176 Query: 182 FYYAHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVREATDDDLKLGYRQDNPQLNPDFIF 241 F+ ++T EGGM+ T++ + +++R LR HG TD LG R +PD Sbjct: 177 FHPRKAITTGEGGMITTDNDALAEKLRRLRDHGAAM--TDLQRHLGARPYLLADHPD--- 231 Query: 242 AFPAYNVRNTEIGAIMGRSQLKRLDANCARR 272 YN R T+I A +G +Q++R D A R Sbjct: 232 --AGYNQRMTDIQAALGAAQMERADDIIAER 260 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 124 bits (312), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 108/405 (26%), Positives = 176/405 (43%), Gaps = 62/405 (15%) Query: 5 PLMRNNILREDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYSVFVNSGASANLL 64 P + I + AV E LR +T+GP V+AFEK S++LG + NSG + Sbjct: 7 PFAKPTIDEPTIAAVGEVLRSG--WITSGPKVQAFEKALSDYLGGRIVRTFNSGTCTMEI 64 Query: 65 SMAVLKLRHPEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAKITER 124 ++ + + G EVI P++W++ +++ G TPVFADIDP + + +++ A IT R Sbjct: 65 ALRIAGVG--PGDEVITTPISWVATANVILETGATPVFADIDPITRNIDLDKLEAAITPR 122 Query: 125 TRAVFLTHVQGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNFSFYY 184 T+AV ++ G D L A + + ++ED ++ G+T NG+R+G+FG +FS Sbjct: 123 TKAVIPVYLSGLPVDMDRLYAIAAKHKLRVVEDAAQALGSTWNGKRIGAFGDFVSFSLQA 182 Query: 185 AHHMSTIEGGMVCTNDPEVYQQVRMLRSHGMVREATDDDLKLGYRQDNPQLNPDFIFAFP 244 ++++ EGG + N+ E + R G+ R D L D + Sbjct: 183 NKNITSSEGGFLVLNNAEEARLAEKYRLQGVTRSGFDG------------LEVDVLGG-- 228 Query: 245 AYNVRNTEIGAIMGRSQLKRLDANCARRTANMMRFLDQIDS---QRYRVDFKT---EGSS 298 +N+ T++ A +G Q +DA A R + S RY E S+ Sbjct: 229 KFNM--TDVAAAIGLGQFAHIDAITAHRKELARHYFACFGSDFESRYGAQLPVADFENSN 286 Query: 299 NYAFNLVLRE--ADDVFVERLMQTMRSNGIEFRRGSAGGGNQVRQPYLKGIVPADHYLQ- 355 + F LVL E F+E++M+ G + PA H L+ Sbjct: 287 WHMFQLVLPERITRAAFMEKMMEKQIGIGYHY--------------------PAIHLLKL 326 Query: 356 ----------FPQTEHIHFYGFYIGNFPDLSDAEVDDICRILNAV 390 FP E + G I + P + DD+ R + V Sbjct: 327 YRERGFGEGMFPVAERV---GQRIVSLPMFNTMSKDDVVRSVETV 368 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 112 bits (279), Expect = 6e-26, Method: Compositional matrix adjust. Identities = 74/254 (29%), Positives = 123/254 (48%), Gaps = 19/254 (7%) Query: 30 LTNGPNVRAFEKEWSEWLGVKYSVFVNSGASANLLSMAVLKLRHPEGGEVIVPPLTWISD 89 L+ GP V +FE E++ +LG Y V SG A +L++ + +R G EVI +W Sbjct: 30 LSAGPVVESFENEFASYLGRTYGVAAASGTVALMLALRAMGIR--AGDEVIASAYSWHQI 87 Query: 90 VATVIQNGFTPVFADIDPRSLAMAPEQILAKITERTRAVFLTHVQGFDGLTDELLAELER 149 V + G TPVFADID S +AP ++ KI++RTRA+ + + G E + Sbjct: 88 VHAITLVGATPVFADIDYWSGNLAPHKVADKISQRTRAIVVGNCNGHPAAWTEFRQLAQA 147 Query: 150 RNIPLIEDVCESHGATHNGQRLGSFGWMSNFSFYYAHHMSTIEGGMVCTNDPEVYQQVRM 209 + LIED E+ G+ + G+ +G+FG ++ F F + EG M+ T+DPE+ ++ Sbjct: 148 HGLRLIEDSSEAIGSRYQGRVVGNFGDIAIFDFSQPSALCCGEGAMLVTDDPELASELHY 207 Query: 210 LRSHGMVREATDDDLKLGYRQDNPQLNPDFIFAFPAYNVRNTEIGAIMGRSQLKRLDANC 269 +R+ + D + P +++ A +G +QL+RLD Sbjct: 208 MRNRNL-----SDRQSIAVASRVPMQGS------------MSDLSAAIGIAQLERLDEIL 250 Query: 270 ARRTANMMRFLDQI 283 RR +L+ + Sbjct: 251 MRRKQVEAYYLEHV 264 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 105 bits (262), Expect = 7e-24, Method: Compositional matrix adjust. Identities = 62/204 (30%), Positives = 103/204 (50%), Gaps = 4/204 (1%) Query: 33 GPNVRAFEKEWSEWLGVKYSVFVNSGASANLLSMAVLKLRHPEGGEVIVPPLTWISDVAT 92 GP VR E + G K+ + V SG A L+S+ L ++ G E+I P T+++ Sbjct: 37 GPEVRELEAALEAYTGAKHCITVASGTEALLISLMALDIK--PGDEIITTPFTFVATAEV 94 Query: 93 VIQNGFTPVFADIDPRSLAMAPEQILAKITERTRAVFLTHVQGFDGLTDELLAELERR-N 151 ++ G PVF D++P + + I A+IT +T+A+ + G DE+ A R N Sbjct: 95 MVLLGAKPVFVDVEPDTGNIDVRLIEARITSKTKAIMPVSLYGQAADMDEINAIAARHGN 154 Query: 152 IPLIEDVCESHGATHNGQRLGSFGWMSNFSFYYAHHMSTI-EGGMVCTNDPEVYQQVRML 210 +P+IED +S GAT+ G++ G+ + SF+ + + +GG + TND + R + Sbjct: 155 LPVIEDAAQSFGATYKGRKSGNLSSIGCTSFFPSKPLGCYGDGGAIFTNDDAIALACRQI 214 Query: 211 RSHGMVREATDDDLKLGYRQDNPQ 234 R HG + + +G R D Q Sbjct: 215 RVHGQSQRYVHTRVGVGGRMDTLQ 238 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 0.322 0.138 0.417 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: 1,264,110 Number of extensions: 53434 Number of successful extensions: 131 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 124 Number of HSP's successfully gapped: 5 Length of query: 390 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 303 Effective length of database: 1,207,925 Effective search space: 366001275 Effective search space used: 366001275 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)