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= 0001.3996.p (356 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313415|ref|YP_003777507.1| phenylacetic acid degradation N... 678 0.0 gi|300311823|ref|YP_003775915.1| nitric oxide dioxygenase [Herba... 86 5e-18 gi|300313278|ref|YP_003777370.1| vanillate O-demethylase (vanill... 83 4e-17 gi|300312623|ref|YP_003776715.1| chaperone activity ATPase [Herb... 60 4e-10 gi|300310642|ref|YP_003774734.1| electron transfer component of ... 57 3e-09 >gi|300313415|ref|YP_003777507.1| phenylacetic acid degradation NADH oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 678 bits (1750), Expect = 0.0, Method: Compositional matrix adjust. Identities = 320/356 (89%), Positives = 336/356 (94%) Query: 1 MSKFYPLTISGVKQETRDTIVVSFALPAELQDTFAYQQGQHLTLRSHINGEELRRSYSIC 60 MSKFYPLTIS VKQETRDTIVVSFA+PAELQDTF+YQQGQHLTLRS INGE+LRRSYSIC Sbjct: 1 MSKFYPLTISDVKQETRDTIVVSFAVPAELQDTFSYQQGQHLTLRSEINGEDLRRSYSIC 60 Query: 61 SARQDRQLRVAIKRVPGGLFSNWANESFVPGQSIEAMPPMGQFNVPLDAANRKHYLAFAA 120 SA Q+RQLRVAIKR PGGLFSNWANESFVPGQ I+ MPPMG FNVPL+A NRKHYLAFAA Sbjct: 61 SAVQERQLRVAIKRAPGGLFSNWANESFVPGQRIDVMPPMGHFNVPLEAGNRKHYLAFAA 120 Query: 121 GSGITPMLSIIKTTLLAEPHSQFTLVYANRASSSVIFKEELSDLKDAYLERFNVVYVMSR 180 GSGITPM+SIIKTTLL+EPHS FTLVYANRASSSVIFKEEL+DLKDAYLERFNVVYVMSR Sbjct: 121 GSGITPMMSIIKTTLLSEPHSHFTLVYANRASSSVIFKEELTDLKDAYLERFNVVYVMSR 180 Query: 181 EQQDVELFNGRIDRAKCDAFFASWIKLQDIDTAFLCGPQEMVQAVADSLQAHGMSKAQIK 240 EQQDVELFNGRIDRAKCDAFFASWI L+D+D AFLCGP+EMVQAVA SLQAHG+ K QIK Sbjct: 181 EQQDVELFNGRIDRAKCDAFFASWIDLKDVDAAFLCGPEEMVQAVAASLQAHGLPKTQIK 240 Query: 241 TELFSAGTSAREHAARPVVGKTECEVTVIVDGYHNVFTMDKERESVLDAGLKHGIDLRYS 300 TELF+A T R HAAR VVGK ECEVTVIVDGYHNVFTMDKE+ESVL+AGLKHGIDLRYS Sbjct: 241 TELFAASTPPRAHAARTVVGKQECEVTVIVDGYHNVFTMDKEKESVLEAGLKHGIDLRYS 300 Query: 301 CKGGVCATCRCKVVEGKVDMDANYALEDYEIARGFVLSCQSFPVSDKLLLDFDQDN 356 CKGGVCATCRCKVVEGKVDMDANYALEDYEIARGFVLSCQSFPVSDKLLLDFDQDN Sbjct: 301 CKGGVCATCRCKVVEGKVDMDANYALEDYEIARGFVLSCQSFPVSDKLLLDFDQDN 356 >gi|300311823|ref|YP_003775915.1| nitric oxide dioxygenase [Herbaspirillum seropedicae SmR1] Length = 397 Score = 85.9 bits (211), Expect = 5e-18, Method: Compositional matrix adjust. Identities = 61/229 (26%), Positives = 104/229 (45%), Gaps = 14/229 (6%) Query: 26 LPAELQDTFAYQQGQHLTLRSHINGEELRRSYSICS----ARQDRQLRVAIKRVPGGLFS 81 +P + + + GQ++ LR ++GEE RR YS+ + A Q Q R+++KR PGG S Sbjct: 176 VPQDGGELLDFAPGQYIGLRMVVDGEEQRRQYSLSALLRQAGQPPQYRISVKREPGGKVS 235 Query: 82 NWANESFVPGQSIEAMPPMGQFNVPLDAANRKHYLAFAAGSGITPMLSIIKTTLLAEPHS 141 ++ G +E PP G+F + A+ K + G GITPM+S++ L + Sbjct: 236 RQLHDQIHVGSVVELFPPAGEFTL---MASDKPLALISGGVGITPMMSMLAAALPSGRPI 292 Query: 142 QFTLVYANRASSSVIFKEELSDLKDAYLE-RFNVVYVMSREQQDVELFNGRIDRAKCDAF 200 F ++A R F+ +L +L + + + Y R+ G I+R + Sbjct: 293 HF--IHAARHGGVHAFRRQLEELAARHPQLQLRFCYEQPRQGDAAPHATGLIER----SL 346 Query: 201 FASWIKLQDIDTAFLCGPQEMVQAVADSLQAHGMSKAQIKTELFSAGTS 249 W+ A+ GP+ ++A+ L G+ AQ + E F S Sbjct: 347 LQQWLPGNPDLDAYFVGPKSFMKAIKRQLAELGVPAAQSRYEFFGPAAS 395 >gi|300313278|ref|YP_003777370.1| vanillate O-demethylase (vanillate degradation ferredoxin-like) oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 318 Score = 82.8 bits (203), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 89/354 (25%), Positives = 147/354 (41%), Gaps = 49/354 (13%) Query: 7 LTISGVKQETRDTIVVSF------ALPAELQDTFAYQQGQHLTLRSHINGEELRRSYSIC 60 + ++ ++E D I + ALPA + G H+ + H+ G L R YS+C Sbjct: 6 VKVAARREEAHDIIALELVAVDGAALPA-------FTAGAHIDV--HLPGG-LVRQYSLC 55 Query: 61 SA--RQDRQLRVAIKRVPGGLFSNWANESFVPGQSIEAMPPMGQFNVPLDAANRKHYLAF 118 +A Q R ++ V S +E+ G + P QF + +H L Sbjct: 56 NAPHEQHRYQIGVLRDVNSRGGSVAVHEALKLGDILTISAPRNQFAL----VPAQHSLLL 111 Query: 119 AAGSGITPMLSIIKTTLLAEPHSQFTLVYANRASSSVIFKEELSDLKDAYLERFNVVYVM 178 A G G+TP+L + + A + F + Y R+ + F+E ++ + R Y Sbjct: 112 AGGIGVTPILCMAEALAAAG--ASFEMHYCARSPARQAFRERIA--ASGFAARVVHHYDD 167 Query: 179 SREQQDVELFNGRIDRAKCDAFFASWIKLQDIDTAFLCGPQEMVQAVADSLQAHGMSKAQ 238 Q ++L DA A + ++CGP + V D+ +A G +AQ Sbjct: 168 GEAAQKLDL----------DALLAQADPATHL---YVCGPAGFIAHVVDTARARGWPEAQ 214 Query: 239 IKTELFSAGTSAREHAARPVVGKTECEVTVIVDGYHNVFTMDKERESVLDAGLKHGIDLR 298 + E F A + G EV + G V+T+ ER +V+ +HG+D+ Sbjct: 215 VHFEYFGAAPVKAD-------GNGAFEVKLASSG--QVYTIPPER-TVIQVLCEHGVDVP 264 Query: 299 YSCKGGVCATCRCKVVEGKVDMDANYALEDYEIARGFVLSCQSFPVSDKLLLDF 352 SC+ G+C TC +V+EG+ D Y ++ A C S S L+LD Sbjct: 265 VSCEQGICGTCLTRVLEGEPDHRDQYLTDEERAANDQFTPCCSRARSALLVLDL 318 >gi|300312623|ref|YP_003776715.1| chaperone activity ATPase [Herbaspirillum seropedicae SmR1] Length = 349 Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 48/187 (25%), Positives = 90/187 (48%), Gaps = 10/187 (5%) Query: 6 PLTISGVKQETRDTIVVSFALPAELQDTFAYQQGQHLTLRSHINGEELRRSYSICSA-RQ 64 P+ ++ + + D IV+S LPA D Y+ GQ++ + + RRSYS+ +A + Sbjct: 104 PVRVAKLDKVADDVIVLSLQLPA--NDRLQYKAGQYVEF---LLRDGKRRSYSMATAPHK 158 Query: 65 DRQLRVAIKRVPGGLFSNWANESFVPGQSIEAMPPMGQFNVPLDAANRKHYLAFAAGSGI 124 D + + I+ +PGGLF++ + + P+G F + D + K + A+G+G Sbjct: 159 DEHMSLHIRHLPGGLFTDQVFTTLKERDILRIEGPLGTFFLRED--SDKPIILLASGTGF 216 Query: 125 TPMLSIIKTTLLAEPHSQFTLVYANRASSSVIFKEELSDLKDAYLERFNVVYVMSREQQD 184 P+ +I++ A TL + R ++ + L + L F V V+S Q + Sbjct: 217 APIKAIVEQLEHAGSKRPVTLYWGGRRPQD-LYMDALCQQWEQTLPNFKYVPVVSNAQAE 275 Query: 185 VELFNGR 191 + ++GR Sbjct: 276 -DNWSGR 281 >gi|300310642|ref|YP_003774734.1| electron transfer component of chlorobenzoate 1,2-dioxygenase [Herbaspirillum seropedicae SmR1] Length = 351 Score = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 3/70 (4%) Query: 283 RESVLDAGLKHGIDLRYSCKGGVCATCRCKVVEGKVDMDANY---ALEDYEIARGFVLSC 339 +E VLDA ++ I+L C GVC TC+C+ G D+ +Y AL E G VL+C Sbjct: 23 KEKVLDAAFRNRINLPMDCSDGVCGTCKCRAESGLYDLGDDYIDDALSSDEAGAGMVLTC 82 Query: 340 QSFPVSDKLL 349 Q P SD ++ Sbjct: 83 QMVPQSDCVI 92 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 0.321 0.134 0.392 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: 1,050,923 Number of extensions: 40839 Number of successful extensions: 105 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 103 Number of HSP's successfully gapped: 5 Length of query: 356 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 270 Effective length of database: 1,212,660 Effective search space: 327418200 Effective search space used: 327418200 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)