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= 0001.4642.p (411 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300314033|ref|YP_003778125.1| acyl-CoA dehydrogenase [Herbasp... 694 0.0 gi|300314032|ref|YP_003778124.1| acyl-CoA dehydrogenase [Herbasp... 419 e-118 gi|300310289|ref|YP_003774381.1| dibenzothiophene desulfurizatio... 384 e-107 gi|300311865|ref|YP_003775957.1| acyl-CoA dehydrogenase [Herbasp... 61 1e-10 gi|300313969|ref|YP_003778061.1| isovaleryl-CoA dehydrogenase [H... 58 2e-09 >gi|300314033|ref|YP_003778125.1| acyl-CoA dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 411 Score = 694 bits (1791), Expect = 0.0, Method: Compositional matrix adjust. Identities = 366/411 (89%), Positives = 381/411 (92%) Query: 1 MSAHILATPYRPGARSAQRITSQAQALQVAAELAAEFAQSAAQRDRERILPFQQIERFSH 60 MSAHI R G R AQRI+S++ ALQVAAELAAEFA SAAQRDRERILPF+QIERFS Sbjct: 1 MSAHIPEPIRRAGQRPAQRISSESHALQVAAELAAEFATSAAQRDRERILPFEQIERFSQ 60 Query: 61 SGLWAITVPRSHGGIGASWQTVAEVFRLISAADPSIGQIPQNHFGNLNLIANFASQAQQR 120 SGLWAITVPRSHGGIGASWQTVAEV RLISAADPSIGQIPQNHFGNLNLIA ASQ QQR Sbjct: 61 SGLWAITVPRSHGGIGASWQTVAEVIRLISAADPSIGQIPQNHFGNLNLIARLASQEQQR 120 Query: 121 FFFGEVLDGARLGNAGPERNGKNVLDVRTRATLDTEAGDGSYRLNGTRFYSTGALYAHWI 180 FF EVLDGARLGNAGPERNGKNVLDVRTRATLD AGDGSY LNGTRFYSTGALYAHWI Sbjct: 121 LFFAEVLDGARLGNAGPERNGKNVLDVRTRATLDRAAGDGSYLLNGTRFYSTGALYAHWI 180 Query: 181 PTRAIDDDGQPLVVYNRHDAAGLRVIDDWSSFGQRTTASGTVVFDNVRVPAEQVLPLKDT 240 P+RAIDDDGQPLVVY R DA G+RVIDDWSSFGQRTTASGTVVFDNVRVPA QVL LKD Sbjct: 181 PSRAIDDDGQPLVVYTRRDAPGVRVIDDWSSFGQRTTASGTVVFDNVRVPATQVLALKDA 240 Query: 241 LQRPNNIGPVSQLLQAAIDAGIAQAAVQDTIAFVTTRSRPYADSGLERAADDPYILRDIG 300 LQ+PNNIGPVSQL+QAAIDAGIA AAVQDTIAFVTTRSRPY DSGLERA+DDPYILRDIG Sbjct: 241 LQQPNNIGPVSQLIQAAIDAGIAHAAVQDTIAFVTTRSRPYVDSGLERASDDPYILRDIG 300 Query: 301 NLSLRLHAAEALLEDAAALLDALPAQISFEQMAQASVAVAEAKVLSTEVALQASEKLFEL 360 NLSLRLHAA+ALLEDAAALLD+LPAQ+SFEQMAQAS AVAEAKVLSTE+AL ASEKLFEL Sbjct: 301 NLSLRLHAADALLEDAAALLDSLPAQLSFEQMAQASAAVAEAKVLSTELALLASEKLFEL 360 Query: 361 SGSAATLATHNLDRHWRNARVHTLHDPVRWKYFAVGNYALNGTPPPRHNWS 411 SGSAATLA+HNLDRHWRNARVHTLHDPVRWKYFAVGNYALNGTPPPRH+WS Sbjct: 361 SGSAATLASHNLDRHWRNARVHTLHDPVRWKYFAVGNYALNGTPPPRHSWS 411 >gi|300314032|ref|YP_003778124.1| acyl-CoA dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 421 Score = 419 bits (1076), Expect = e-118, Method: Compositional matrix adjust. Identities = 224/396 (56%), Positives = 278/396 (70%), Gaps = 4/396 (1%) Query: 15 RSAQRITSQAQALQVAAELAAEFAQSAAQRDRERILPFQQIERFSHSGLWAITVPRSHGG 74 R RI A+A+ A +LA +F++ AA RDRER LP+ ++ER+ SGLW ITVP+ +GG Sbjct: 27 RLVARIRDDAEAIAAARKLAEDFSREAALRDRERKLPWDELERYVRSGLWGITVPKEYGG 86 Query: 75 IGASWQTVAEVFRLISAADPSIGQIPQNHFGNLNLIANFASQAQQRFFFGEVLDGARLGN 134 G S+ T+AEV ISAAD SIGQIPQNHF + LI S++Q+RFFF VL G R GN Sbjct: 87 AGVSYGTLAEVIATISAADGSIGQIPQNHFYAVELIRVNGSESQKRFFFERVLQGDRFGN 146 Query: 135 AGPERNGKNVLDVRTRATLDTEAGDGSYRLNGTRFYSTGALYAHWIPTRAIDDDG-QPLV 193 A E K D +TR L A YR++G +FY+TGALYA W+PT IDDDG Q L Sbjct: 147 ALAELGTKTSHDRKTR--LSRNAHGPGYRIDGRKFYATGALYADWVPTSVIDDDGVQQLA 204 Query: 194 VYNRHDAAGLRVIDDWSSFGQRTTASGTVVFDNVRVPAEQVLPLKDTLQRPNNIGPVSQL 253 + RH A GL +IDDWS FGQRTT SG+ VF+NV VPA+ V+ RP IGP++Q+ Sbjct: 205 IVPRH-APGLTIIDDWSGFGQRTTGSGSAVFENVHVPADAVIGFATAFSRPTQIGPMAQI 263 Query: 254 LQAAIDAGIAQAAVQDTIAFVTTRSRPYADSGLERAADDPYILRDIGNLSLRLHAAEALL 313 AAID GIA+AA D + FV TRSR + DSG+ERA DDP +R++G+L+++LHAAEALL Sbjct: 264 QHAAIDLGIARAAYADLLTFVRTRSRAWVDSGVERAVDDPLTIREVGDLTIQLHAAEALL 323 Query: 314 EDAAALLDALPAQISFEQMAQASVAVAEAKVLSTEVALQASEKLFELSGSAATLATHNLD 373 A +DA A + +A AS+AVAEA+VL+TEV+L A KLFEL+GS +TLA HNLD Sbjct: 324 RRAGRKVDAAAAAPDEDSVAAASIAVAEARVLTTEVSLAAGSKLFELAGSQSTLAEHNLD 383 Query: 374 RHWRNARVHTLHDPVRWKYFAVGNYALNGTPPPRHN 409 RHWRNAR HTLHDPVRWKY A+GNY LNG PPRH Sbjct: 384 RHWRNARTHTLHDPVRWKYHAIGNYVLNGKKPPRHG 419 >gi|300310289|ref|YP_003774381.1| dibenzothiophene desulfurization flavin reductase [Herbaspirillum seropedicae SmR1] Length = 419 Score = 384 bits (985), Expect = e-107, Method: Compositional matrix adjust. Identities = 201/395 (50%), Positives = 259/395 (65%), Gaps = 4/395 (1%) Query: 17 AQRITSQAQALQVAAELAAEFAQSAAQRDRERILPFQQIERFSHSGLWAITVPRSHGGIG 76 A I A+A+ VA LA AQ A++RD+ R P ++IE +S SGLWAI VPR+ GG Sbjct: 29 AHVIRDDAEAIAVAHALAPRLAQGASERDQLRRWPVEEIEAYSQSGLWAINVPRAFGGAE 88 Query: 77 ASWQTVAEVFRLISAADPSIGQIPQNHFGNLNLIANFASQAQQRFFFGEVLDGARLGNAG 136 S+ T+AEV +ISAADPS+GQI QNH G + + + QQR FF + L G R GNA Sbjct: 89 VSYATLAEVIAIISAADPSLGQITQNHLGFVAAVRTVSDPEQQRRFFADFLRGVRWGNAF 148 Query: 137 PERNGKNVLDVRTRATLDTEAGDGSYRLNGTRFYSTGALYAHWIPTRAIDDDGQPLVVYN 196 E K D TR +AGD + G +FYSTGAL AH++P A D++ + V Sbjct: 149 SESGSKRAADFETRFV---DAGDHVI-VTGKKFYSTGALLAHYVPIVANDEENRTWYVVA 204 Query: 197 RHDAAGLRVIDDWSSFGQRTTASGTVVFDNVRVPAEQVLPLKDTLQRPNNIGPVSQLLQA 256 +A GL VIDDWS+FGQRTT SGTV+ D V+VP ++P P+ G + Q++QA Sbjct: 205 ERNAPGLTVIDDWSAFGQRTTLSGTVIIDQVKVPKTHLIPAYKGYLEPSADGAIFQIIQA 264 Query: 257 AIDAGIAQAAVQDTIAFVTTRSRPYADSGLERAADDPYILRDIGNLSLRLHAAEALLEDA 316 A+D GIA+AA+ DT FV T+SRP+ DS + A +DPY ++ IG+L +RLHA+EALLE A Sbjct: 265 AVDVGIARAAIADTQDFVRTKSRPWIDSQRDHAWEDPYSIQAIGDLQIRLHASEALLERA 324 Query: 317 AALLDALPAQISFEQMAQASVAVAEAKVLSTEVALQASEKLFELSGSAATLATHNLDRHW 376 +DA A + +A A + AEAKVLSTE+A+ A+ KLFEL+G+ +TL +NLDRHW Sbjct: 325 GRAIDAAVAAPDAQSVAHAQILTAEAKVLSTEIAIHATNKLFELAGTRSTLGQYNLDRHW 384 Query: 377 RNARVHTLHDPVRWKYFAVGNYALNGTPPPRHNWS 411 RNAR HTLHDPVRWKY VGNY LNG PP H WS Sbjct: 385 RNARTHTLHDPVRWKYAIVGNYYLNGVKPPFHAWS 419 >gi|300311865|ref|YP_003775957.1| acyl-CoA dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 386 Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 91/380 (23%), Positives = 152/380 (40%), Gaps = 69/380 (18%) Query: 34 AAEFAQSAAQRDRERILPFQQIERFSHSGLWAITVPRSHGGIGASWQTVAEVFRLISAAD 93 A E A AA+ D E P I + G + P + GG+G S VF ++ A Sbjct: 21 AGEMAPFAAKWDEEAHFPLDVIAKAGELGFCGLYTPEADGGLGLSRLDATVVFEELARAC 80 Query: 94 PSIGQIPQNHFGNLNLIANFASQAQQRFFFGEVLDGARLGNAGPER--NGKNVLDVRTRA 151 S H +IA++ + + + ++ G ++G+ +G + ++T A Sbjct: 81 TSTAAYLTIHNMVSWMIASWGQPSLKAQWCEQLAAGRKIGSYCLTEPGSGSDAASLKTTA 140 Query: 152 TLDTEAGDGSYRLNGTRFYSTGALYAHWIPTRAIDDDGQPLVVYNRHDAAGLRVID---- 207 L+ DG Y LNG++ + +GA LVV R G R + Sbjct: 141 RLE----DGHYVLNGSKAFISGA------------GSTDVLVVMARTGGEGARGVSAIVV 184 Query: 208 ----DWSSFGQRTTASG-------TVVFDNVRVPAEQVL---------PLKDTLQRPNNI 247 S+G++ + G T+ FDNV+VPA+ +L +K NI Sbjct: 185 PGNAPGVSYGKKESKMGWNSQPTRTISFDNVKVPADHLLGQEGQGFIFAMKGLDGGRINI 244 Query: 248 GPVSQLLQAAIDAGIAQAAVQDTIAFVTTRS---RPYADSGLERAADDPYILRDIGNLSL 304 S G AQAA+ A++ R RP AD + + ++ Sbjct: 245 ATCS--------VGAAQAALDAAHAYMKERKQFGRPIADF--------QALQFKLADMQT 288 Query: 305 RLHAAEALLEDAAALLDALPAQISFEQMAQASVAVAEAKVLSTEVALQASEKLFELSGSA 364 L AA ++ AA LDA +A+ A AK L+T++ + + +L G Sbjct: 289 ELVAARQMVRLAATKLDA--------GSPEATTYCAMAKRLATDLGFRVCNEALQLHGGY 340 Query: 365 ATLATHNLDRHWRNARVHTL 384 + + L+R++R+ RVH + Sbjct: 341 GYIREYPLERYFRDVRVHQI 360 >gi|300313969|ref|YP_003778061.1| isovaleryl-CoA dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 394 Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 73/281 (25%), Positives = 108/281 (38%), Gaps = 56/281 (19%) Query: 29 VAAELAAEFAQSAAQRDRERILPFQQIERFSHSGLWAITVPRSHGGIGASWQTVAEVFRL 88 VAA +E A AA+ DR P ++ G+ ITV +GG G + Sbjct: 22 VAAFAHSEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVSEEYGGAGLGYLAHIIAMEE 81 Query: 89 ISAADPSIGQIPQNHFGNL--NLIANFASQAQQRFFFGEVLDGARLGN-AGPERN-GKNV 144 IS A S+G H NL N I ++ Q+R + ++ G +G A E N G +V Sbjct: 82 ISRASASVGLSYGAH-SNLCVNQIKRNGNEEQKRKYLPRLISGDFIGALAMSEPNAGSDV 140 Query: 145 LDVRTRATLDTEAGDGSYRLNGTRFYSTGALYAHWIPTRAIDDDGQPLVVYNRHDA---- 200 + ++ RA + GD Y LNG++ WI D LVVY + D Sbjct: 141 VSMKLRA---DKKGD-RYVLNGSKM---------WITN---GPDADVLVVYAKTDLEAGA 184 Query: 201 ------------AGLRVIDDWSSFGQRTTASGTVVFDNVRVPAEQVLPLKDTLQRPNNIG 248 G V G R + +G +VF + VP E VL +G Sbjct: 185 RGMTAFLVEKGYKGFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVL---------GGVG 235 Query: 249 PVSQLLQAAID----------AGIAQAAVQDTIAFVTTRSR 279 +L + +D GI QA + + +V R + Sbjct: 236 RGVNVLMSGLDFERSVLSGGPLGIMQACMDVVVPYVHDRKQ 276 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 0.318 0.131 0.387 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: 1,158,772 Number of extensions: 43965 Number of successful extensions: 147 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 145 Number of HSP's successfully gapped: 6 Length of query: 411 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 323 Effective length of database: 1,203,190 Effective search space: 388630370 Effective search space used: 388630370 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 (21.8 bits) S2: 132 (55.5 bits)