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= 0001.2543.p (397 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311823|ref|YP_003775915.1| nitric oxide dioxygenase [Herba... 712 0.0 gi|300313415|ref|YP_003777507.1| phenylacetic acid degradation N... 88 1e-18 gi|300310642|ref|YP_003774734.1| electron transfer component of ... 70 4e-13 gi|300310671|ref|YP_003774763.1| flavodoxin reductases (ferredox... 68 1e-12 gi|300313278|ref|YP_003777370.1| vanillate O-demethylase (vanill... 63 4e-11 >gi|300311823|ref|YP_003775915.1| nitric oxide dioxygenase [Herbaspirillum seropedicae SmR1] Length = 397 Score = 712 bits (1837), Expect = 0.0, Method: Compositional matrix adjust. Identities = 349/396 (88%), Positives = 368/396 (92%) Query: 1 MLTDAQLAIVKSTVPLLESGGEALTTHFYKLLMRDYPQVHPLFNRAHQASGDQPRALANG 60 MLTDAQLAIVKSTVPLLESGGEALTTHFYK+LMRDYPQV PLFNRAHQASGDQPRALANG Sbjct: 1 MLTDAQLAIVKSTVPLLESGGEALTTHFYKMLMRDYPQVRPLFNRAHQASGDQPRALANG 60 Query: 61 VLMYARHIDRLEELGPLAAQIINKHVAVQVMPEHYPMVGDCLLRAIREVLGAEIATDAVI 120 VLMYARHIDRLEELGPLAAQIINKHVAVQV+PEHYPMVGDCLLRAIREVLGAEIATDAVI Sbjct: 61 VLMYARHIDRLEELGPLAAQIINKHVAVQVLPEHYPMVGDCLLRAIREVLGAEIATDAVI 120 Query: 121 DAWAAAYGQLADILIGAERQQYDAKAEAPGGWRGARNFVVTRKVAESEEITSFYFMPQDG 180 DAWAAAYGQLADILIGAERQQY+AKA+APGGW GARNF+V+RKVAESEEITSF+F+PQDG Sbjct: 121 DAWAAAYGQLADILIGAERQQYEAKAQAPGGWSGARNFIVSRKVAESEEITSFHFVPQDG 180 Query: 181 GALLDFEPGQYIGLRMVVDGLEQRRQYSLSAPLRQAGQPLQYRISVKREASGKVSRQLHD 240 G LLDF PGQYIGLRMVVDG EQRRQYSLSA LRQAGQP QYRISVKRE GKVSRQLHD Sbjct: 181 GELLDFAPGQYIGLRMVVDGEEQRRQYSLSALLRQAGQPPQYRISVKREPGGKVSRQLHD 240 Query: 241 HIHVGSVVELFPPAGDFTLTANAKPLALISGGVGITPMMTMLAAALPSGRPVHFIHAARH 300 IHVGSVVELFPPAG+FTL A+ KPLALISGGVGITPMM+MLAAALPSGRP+HFIHAARH Sbjct: 241 QIHVGSVVELFPPAGEFTLMASDKPLALISGGVGITPMMSMLAAALPSGRPIHFIHAARH 300 Query: 301 AGVHAFRRELEQLAAQHPQLQLHFCYEQARAGDPAAHANGFIDPARLQQWLPATRDIDAY 360 GVHAFRR+LE+LAA+HPQLQL FCYEQ R GD A HA G I+ + LQQWLP D+DAY Sbjct: 301 GGVHAFRRQLEELAARHPQLQLRFCYEQPRQGDAAPHATGLIERSLLQQWLPGNPDLDAY 360 Query: 361 FVGPKPFMKAIKHALAELGVPAAQSRYEFFGPAAAL 396 FVGPK FMKAIK LAELGVPAAQSRYEFFGPAA+L Sbjct: 361 FVGPKSFMKAIKRQLAELGVPAAQSRYEFFGPAASL 396 >gi|300313415|ref|YP_003777507.1| phenylacetic acid degradation NADH oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 88.2 bits (217), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 63/236 (26%), Positives = 112/236 (47%), Gaps = 14/236 (5%) Query: 168 EEITSFYFMPQDGGALLDFEPGQYIGLRMVVDGLEQRRQYSLSAPLRQAGQPLQYRISVK 227 + I + +P + ++ GQ++ LR ++G + RR YS+ + A Q Q R+++K Sbjct: 18 DTIVVSFAVPAELQDTFSYQQGQHLTLRSEINGEDLRRSYSICS----AVQERQLRVAIK 73 Query: 228 REASGKVSRQLHDHIHVGSVVELFPPAGDFTL---TANAKPLALISGGVGITPMMTMLAA 284 R G S ++ G +++ PP G F + N K + G GITPMM+++ Sbjct: 74 RAPGGLFSNWANESFVPGQRIDVMPPMGHFNVPLEAGNRKHYLAFAAGSGITPMMSIIKT 133 Query: 285 ALPSGRPVHF--IHAARHAGVHAFRRELEQLAAQHPQLQLHFCYEQARAGDPAAHANGFI 342 L S HF ++A R + F+ EL L + + + + Y +R NG I Sbjct: 134 TLLSEPHSHFTLVYANRASSSVIFKEELTDLKDAYLE-RFNVVYVMSREQQDVELFNGRI 192 Query: 343 DPARLQQWLPA---TRDIDAYFV-GPKPFMKAIKHALAELGVPAAQSRYEFFGPAA 394 D A+ + + +D+DA F+ GP+ ++A+ +L G+P Q + E F + Sbjct: 193 DRAKCDAFFASWIDLKDVDAAFLCGPEEMVQAVAASLQAHGLPKTQIKTELFAAST 248 >gi|300310642|ref|YP_003774734.1| electron transfer component of chlorobenzoate 1,2-dioxygenase [Herbaspirillum seropedicae SmR1] Length = 351 Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 61/213 (28%), Positives = 92/213 (43%), Gaps = 25/213 (11%) Query: 186 FEPGQYIGLRMVVDGLEQRRQYSLSAPLRQAGQPLQYRISVKREASGKVSRQLHDHIHVG 245 F PGQY+ + V G Q R YS S+P + + +K G +S L G Sbjct: 136 FLPGQYVNIG--VPGSGQHRSYSFSSPSGAS----RMSFLIKNVPGGLMSNWLAGASE-G 188 Query: 246 SVVELFPPAGDFTLTANAKPLALISGGVGITPMMTMLAAALPSG--RPVHFIHAARHAGV 303 + +EL P G F L +P+ +++GG G+ P ++ML G +PVH I+ Sbjct: 189 ATLELTGPLGSFYLRPVKRPVLMLAGGTGLAPFLSMLEELAQQGLDQPVHLIYGVTRDQD 248 Query: 304 HAFRRELEQLAAQHPQLQLHFCYEQARAGDPA-AHA-NGFIDPARLQQWLPAT----RDI 357 L+ LA + P C DPA HA G++ Q +PA ++ Sbjct: 249 LVLVERLQALADRLPGFSFTTC-----VADPATTHARQGYV-----TQHMPAAVLHDGNV 298 Query: 358 DAYFVGPKPFMKAIKHALAELGVPAAQSRYEFF 390 D Y GP P ++A++ G+ A YE F Sbjct: 299 DVYLCGPPPMVEAVQKHFQATGMQPASFYYEKF 331 >gi|300310671|ref|YP_003774763.1| flavodoxin reductases (ferredoxin-NADPH reductases) family 1 protein [Herbaspirillum seropedicae SmR1] Length = 318 Score = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 65/224 (29%), Positives = 97/224 (43%), Gaps = 35/224 (15%) Query: 157 NFVVTRKVAESEEITSFYFMPQDGGALLDFEPGQYIGLRMVVDGLEQRRQYSLSAPLRQA 216 +V E+ +I SF + DG L +EPG +I V RQYSL PL Sbjct: 2 KLIVDTLTDETGDIRSFRLVRADGAPLPAYEPGAHID---VTGPTGIMRQYSLCGPLEDR 58 Query: 217 GQPLQYRISVKREASGKV-SRQLHDHIHVGSVVELFPPAGDFTLTANAKPLALISGGVGI 275 Y I+VKRE++ + S LHD + G +E+ P F L A+A L G+G+ Sbjct: 59 ---CGYTIAVKRESASRGGSAALHDVVKAGMELEVGTPRNLFALDASAPEHLLFGAGIGV 115 Query: 276 TPMMTM---LAAALPSGRPVHFIHAARHAGVHAFRRELEQLAAQHPQLQLHFCYEQARAG 332 TP++ M L A +F+ A HA AF LE A ++ H+ Sbjct: 116 TPLLAMAYRLWAEEKRFTLHYFVRAREHA---AFADLLEN-APFAAHVRFHYA------- 164 Query: 333 DPAAHANGFIDPARLQQWLP-----ATRDIDAYFVGPKPFMKAI 371 + PA+++ +L +++ Y GP PFM A+ Sbjct: 165 ---------VMPAQMEHYLTVCLEAGSKEAHVYTCGPAPFMDAV 199 >gi|300313278|ref|YP_003777370.1| vanillate O-demethylase (vanillate degradation ferredoxin-like) oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 318 Score = 63.2 bits (152), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 69/236 (29%), Positives = 107/236 (45%), Gaps = 22/236 (9%) Query: 160 VTRKVAESEEITSFYFMPQDGGALLDFEPGQYIGLRMVVDGLEQRRQYSL-SAPLRQAGQ 218 V + E+ +I + + DG AL F G +I + + GL RQYSL +AP Q Sbjct: 8 VAARREEAHDIIALELVAVDGAALPAFTAGAHIDVHLP-GGLV--RQYSLCNAPHEQH-- 62 Query: 219 PLQYRISVKREASGKV-SRQLHDHIHVGSVVELFPPAGDFTLTANAKPLALISGGVGITP 277 +Y+I V R+ + + S +H+ + +G ++ + P F L L L++GG+G+TP Sbjct: 63 --RYQIGVLRDVNSRGGSVAVHEALKLGDILTISAPRNQFALVPAQHSL-LLAGGIGVTP 119 Query: 278 MMTMLAAALPSGRPVHFIHAARHAGVHAFRRELEQLAAQHPQLQLHFCYEQARAGDPAAH 337 ++ M A +G + AR AFR E++AA ++ Y+ A Sbjct: 120 ILCMAEALAAAGASFEMHYCARSPARQAFR---ERIAASGFAARVVHHYDDGEA------ 170 Query: 338 ANGFIDPARLQQWLPATRDIDAYFVGPKPFMKAIKHALAELGVPAAQSRYEFFGPA 393 A A L Q PAT Y GP F+ + G P AQ +E+FG A Sbjct: 171 AQKLDLDALLAQADPATH---LYVCGPAGFIAHVVDTARARGWPEAQVHFEYFGAA 223 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 0.136 0.408 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: 1,281,128 Number of extensions: 54094 Number of successful extensions: 183 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 177 Number of HSP's successfully gapped: 6 Length of query: 397 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 310 Effective length of database: 1,207,925 Effective search space: 374456750 Effective search space used: 374456750 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)