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= 0004.0060.p (365 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... 168 7e-43 gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis... 161 9e-41 gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent a... 146 3e-36 gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotrans... 137 1e-33 gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-... 107 2e-24 >gi|300311404|ref|YP_003775496.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 373 Score = 168 bits (425), Expect = 7e-43, Method: Compositional matrix adjust. Identities = 123/371 (33%), Positives = 188/371 (50%), Gaps = 19/371 (5%) Query: 6 PFLPPL--EEFVAYLQQIWANKHITNNGPFHQQLEAALADYLGVKYVCLFSNGTLALITA 63 PF P E +A + ++ + IT+ GP Q E AL+DYLG + V F++GT + A Sbjct: 7 PFAKPTIDEPTIAAVGEVLRSGWITS-GPKVQAFEKALSDYLGGRIVRTFNSGTCTMEIA 65 Query: 64 LQALGIT--GEAITSPYSFVATSHALIWNGIKPVFADIDKDTLLLDPAKIEAAITEHTTA 121 L+ G+ E IT+P S+VAT++ ++ G PVFADID T +D K+EAAIT T A Sbjct: 66 LRIAGVGPGDEVITTPISWVATANVILETGATPVFADIDPITRNIDLDKLEAAITPRTKA 125 Query: 122 IVPVHCYGYPCKVEAIQKIADKYKLKVIYDAAHAFGVQYKSSSVLTYGDLSILSFHATKV 181 ++PV+ G P ++ + IA K+KL+V+ DAA A G + + +GD S A K Sbjct: 126 VIPVYLSGLPVDMDRLYAIAAKHKLRVVEDAAQALGSTWNGKRIGAFGDFVSFSLQANKN 185 Query: 182 FNTFEGGAIICHNAE-----MKLRIDQLKNFGTVDEVTVVAAGINGKMSEVNAAMGLLQL 236 + EGG ++ +NAE K R+ + G D + V G M++V AA+GL Q Sbjct: 186 ITSSEGGFLVLNNAEEARLAEKYRLQGVTRSG-FDGLEVDVLGGKFNMTDVAAAIGLGQF 244 Query: 237 QYMDEILTQRKAIDAQYRSLLSA--VKHIDCLQPPEHTSAWNYSYFPILVRPGYPISRDA 294 ++D I RK + Y + + P N+ F LV P I+R A Sbjct: 245 AHIDAITAHRKELARHYFACFGSDFESRYGAQLPVADFENSNWHMFQ-LVLP-ERITRAA 302 Query: 295 LYTKMREQNIFPRRYFYPLISEFPMYRNLASSVPENL-PVATEITQQILCLPIYPGLNID 353 KM E+ I Y YP I +YR E + PVA + Q+I+ LP++ ++ D Sbjct: 303 FMEKMMEKQI-GIGYHYPAIHLLKLYRE--RGFGEGMFPVAERVGQRIVSLPMFNTMSKD 359 Query: 354 HIRQVADIIQS 364 + + + ++S Sbjct: 360 DVVRSVETVKS 370 >gi|300313482|ref|YP_003777574.1| lipopolysaccharide biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 366 Score = 161 bits (407), Expect = 9e-41, Method: Compositional matrix adjust. Identities = 107/326 (32%), Positives = 170/326 (52%), Gaps = 15/326 (4%) Query: 31 GPFHQQLEAALADYLGVKYVCLFSNGTLALITALQALGIT--GEAITSPYSFVATSHALI 88 GP ++LEAAL Y G K+ ++GT AL+ +L AL I E IT+P++FVAT+ ++ Sbjct: 37 GPEVRELEAALEAYTGAKHCITVASGTEALLISLMALDIKPGDEIITTPFTFVATAEVMV 96 Query: 89 WNGIKPVFADIDKDTLLLDPAKIEAAITEHTTAIVPVHCYGYPCKVEAIQKIADKY-KLK 147 G KPVF D++ DT +D IEA IT T AI+PV YG ++ I IA ++ L Sbjct: 97 LLGAKPVFVDVEPDTGNIDVRLIEARITSKTKAIMPVSLYGQAADMDEINAIAARHGNLP 156 Query: 148 VIYDAAHAFGVQYKSSSVLTYGDLSILSFHATKVFNTF-EGGAIICHNAEMKLRIDQLKN 206 VI DAA +FG YK + SF +K + +GGAI ++ + L Q++ Sbjct: 157 VIEDAAQSFGATYKGRKSGNLSSIGCTSFFPSKPLGCYGDGGAIFTNDDAIALACRQIRV 216 Query: 207 FGTVDEVTVVAAGINGKMSEVNAAMGLLQLQYMDEILTQRKAIDAQYRSLLSAVKHIDCL 266 G G+ G+M + A+ L +L+ D + QR A+ ++Y SLL A Sbjct: 217 HGQSQRYVHTRVGVGGRMDTLQCAIVLAKLERFDWEIEQRLALGSRYNSLLDAAGIARIQ 276 Query: 267 QPPEHTSAWNYSYFPILVRPGYPISRDALYTKMREQNIFPRRYFYPL-ISEFPMYRNLAS 325 Q P+ S ++ + +L+ +R+A+ ++ I P YP+ ++ P YR+L Sbjct: 277 QRPDRDSV--FAQYTVLLD-----NREAVQAALQNAGI-PTAVHYPVPLNRQPAYRHLGD 328 Query: 326 SVPENLPVATEITQQILCLPIYPGLN 351 P+ PVA ++ +++ LP+ P L Sbjct: 329 --PDQTPVADQLAARVMSLPMSPDLE 352 >gi|300312168|ref|YP_003776260.1| pyridoxal phosphate-dependent aminotransferase [Herbaspirillum seropedicae SmR1] Length = 382 Score = 146 bits (368), Expect = 3e-36, Method: Compositional matrix adjust. Identities = 98/334 (29%), Positives = 168/334 (50%), Gaps = 14/334 (4%) Query: 31 GPFHQQLEAALADYLGVKYVCLFSNGTLALITALQALGITG--EAITSPYSFVATSHALI 88 GP + E A YLG Y ++GT+AL+ AL+A+GI E I S YS+ HA+ Sbjct: 33 GPVVESFENEFASYLGRTYGVAAASGTVALMLALRAMGIRAGDEVIASAYSWHQIVHAIT 92 Query: 89 WNGIKPVFADIDKDTLLLDPAKIEAAITEHTTAIVPVHCYGYPCKVEAIQKIADKYKLKV 148 G PVFADID + L P K+ I++ T AIV +C G+P +++A + L++ Sbjct: 93 LVGATPVFADIDYWSGNLAPHKVADKISQRTRAIVVGNCNGHPAAWTEFRQLAQAHGLRL 152 Query: 149 IYDAAHAFGVQYKSSSVLTYGDLSILSFHATKVFNTFEGGAIICHNAEMKLRIDQLKNFG 208 I D++ A G +Y+ V +GD++I F EG ++ + E+ + ++N Sbjct: 153 IEDSSEAIGSRYQGRVVGNFGDIAIFDFSQPSALCCGEGAMLVTDDPELASELHYMRNRN 212 Query: 209 TVDEVTVVAAG---INGKMSEVNAAMGLLQLQYMDEILTQRKAIDAQYRSLLSAVKHIDC 265 D ++ A + G MS+++AA+G+ QL+ +DEIL +RK ++A Y L V+ + Sbjct: 213 LSDRQSIAVASRVPMQGSMSDLSAAIGIAQLERLDEILMRRKQVEAYY---LEHVQFFEG 269 Query: 266 LQPPEHTSAWNYSYFPI-LVRPGYPIS---RDALYTKMREQNIFPRRYFYPLISEFPMYR 321 ++PP Y+ + LV G + R+ + + Q + + PL +F Y Sbjct: 270 IKPPYIGPDVEEVYWMLYLVHLGTRFTRTMRNQIIEDLASQEVEAAAWCQPLHQQF--YY 327 Query: 322 NLASSVPENLPVATEITQQILCLPIYPGLNIDHI 355 + +L + +I + + LP++ LN D + Sbjct: 328 SRFDCKRGDLLLTEKIADRCIALPLHGHLNTDEV 361 >gi|300313484|ref|YP_003777576.1| DegT/DnrJ/EryC1/StrS aminotransferase family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 137 bits (346), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 96/348 (27%), Positives = 164/348 (47%), Gaps = 34/348 (9%) Query: 31 GPFHQQLEAALADYLGVKYVCLFSNGTLALITALQALGIT--GEAITSPYSFVATSHALI 88 GP ++ E + + G ++ ++ T AL +L ALG EAI ++++AT++ + Sbjct: 30 GPKVREFEEKWSAFTGARHSIAVTSCTTALHLSLAALGFGPGDEAIVPAFTWIATANVIE 89 Query: 89 WNGIKPVFADIDKDTLLLDPAKIEAAITEHTTAIVPVHCYGYPCKVEAIQKIADKYKLKV 148 G K VF DID +T LD A + + IT T AI+PVH +G +++ I +A ++ L V Sbjct: 90 HLGGKVVFCDIDLNTFNLDVAALRSKITSRTKAILPVHLFGLAAEMDQINDVAKQHGLWV 149 Query: 149 IYDAAHAFGVQYKSSSVLTYGDLSILSFHATKVFNTFEGGAIICHNAEMKLRIDQLKNFG 208 + DAA FG +Y V GD SFH K T EGG I N + ++ +L++ G Sbjct: 150 VEDAACGFGSRYHGKHVGVLGDTGCFSFHPRKAITTGEGGMITTDNDALAEKLRRLRDHG 209 Query: 209 TVDEVTVVA---------------AGINGKMSEVNAAMGLLQLQYMDEILTQRKAIDAQY 253 +T + AG N +M+++ AA+G Q++ D+I+ +R+ + +Y Sbjct: 210 AA--MTDLQRHLGARPYLLADHPDAGYNQRMTDIQAALGAAQMERADDIIAERRRLAERY 267 Query: 254 RSLLSAVKHIDCLQPPEHTSAWNYSY--FPILVRPGYPISRDALYTKMREQNIFPRRYFY 311 +A + L+ P H + Y +P L +P P++ D++ +N + Sbjct: 268 D---AAFADLSWLRTPAHVDGLEHGYQSYPCLFQP-EPVNTDSIERINAARNAWMDSLQQ 323 Query: 312 PLISEFP---------MYRNLASSVPENLPVATEITQQILCLPIYPGL 350 IS P YR + P + P A + LP++ G+ Sbjct: 324 AGISTRPATHAVHMLTFYREKYALKPADFPNAWAANDCSISLPLFHGM 371 >gi|300313698|ref|YP_003777790.1| CDP-4-keto-6-deoxy-D-glucose-3-dehydrase [Herbaspirillum seropedicae SmR1] Length = 390 Score = 107 bits (266), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 81/326 (24%), Positives = 146/326 (44%), Gaps = 38/326 (11%) Query: 12 EEFVAYLQQIWANKHITNNGPFHQQLEAALADYLGVKYVCLFSNGTLALITALQALGIT- 70 E+ A ++ + + I NGP + E +++LGVKY ++G A + ++ L + Sbjct: 14 EDLDAVIEHLRQDDPILTNGPNVRAFEKEWSEWLGVKYSVFVNSGASANLLSMAVLKLRH 73 Query: 71 ---GEAITSPYSFVATSHALIWNGIKPVFADIDKDTLLLDPAKIEAAITEHTTAIVPVHC 127 GE I P ++++ +I NG PVFADID +L + P +I A ITE T A+ H Sbjct: 74 PEGGEVIVPPLTWISDVATVIQNGFTPVFADIDPRSLAMAPEQILAKITERTRAVFLTHV 133 Query: 128 YGYPCKVEAIQKIADKYKLKVIYDAAHAFGVQYKSSSVLTYGDLSILSFHATKVFNTFEG 187 G+ + + ++ + +I D + G + + ++G +S SF+ +T EG Sbjct: 134 QGFDGLTDELLAELERRNIPLIEDVCESHGATHNGQRLGSFGWMSNFSFYYAHHMSTIEG 193 Query: 188 GAIICHNAEMKLRIDQLKNFGTVDEVT--------------------VVAAGINGKMSEV 227 G + ++ E+ ++ L++ G V E T N + +E+ Sbjct: 194 GMVCTNDPEVYQQVRMLRSHGMVREATDDDLKLGYRQDNPQLNPDFIFAFPAYNVRNTEI 253 Query: 228 NAAMGLLQLQYMDEILTQRKAIDAQYRSLLSAVKHIDCLQ-----PPEHTSAWNYSYFPI 282 A MG QL+ +D +R A +++ + ID + E +S NY+ F + Sbjct: 254 GAIMGRSQLKRLDANCARRTA------NMMRFLDQIDSQRYRVDFKTEGSS--NYA-FNL 304 Query: 283 LVRPGYPISRDALYTKMREQNIFPRR 308 ++R + + L MR I RR Sbjct: 305 VLREADDVFVERLMQTMRSNGIEFRR 330 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 0.137 0.410 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: 1,107,134 Number of extensions: 43684 Number of successful extensions: 140 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 129 Number of HSP's successfully gapped: 5 Length of query: 365 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 279 Effective length of database: 1,212,660 Effective search space: 338332140 Effective search space used: 338332140 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)