Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate CA265_RS17575 CA265_RS17575 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25670 (383 letters) >FitnessBrowser__Pedo557:CA265_RS17575 Length = 597 Score = 232 bits (592), Expect = 2e-65 Identities = 145/407 (35%), Positives = 225/407 (55%), Gaps = 34/407 (8%) Query: 5 ELTEEQVMIRDMARDFARGEIAPHAQAWEKAG--WIDDALVAKMGELGLLGMVVPEEWGG 62 E EEQ MI RDF E+ P+ +K + L+ K GELG+LG+ VPEE+GG Sbjct: 29 EFDEEQQMIAQTCRDFLAAEVYPNLDKIDKQEDPELMPTLLTKAGELGILGVSVPEEYGG 88 Query: 63 TYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIG 122 ++ L + + AG AL S H +G P+L YG E QK ++ L SG+ Sbjct: 89 FGKNFNTSMLVADVVGAGHSFAVAL-SAHTGIGTLPILYYGNEAQKAKYIPKLGSGEWKA 147 Query: 123 CFCLTEPQAGSEAHNLRTRAEL-RDGQ-WVINGAKQFVSNGRRAKLAIVFAVTDPDLGKK 180 +CLTEP +GS+A++ +T+A L DG+ ++I G K +++NG A + IVFA D D K Sbjct: 148 AYCLTEPNSGSDANSGKTKATLSEDGKHYIITGQKMWITNGGFADIFIVFAKIDDD---K 204 Query: 181 GLSAFLVPTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNL 240 L+AF+V D G ++ EHKMGI+ S T V N+C +P N+L +R G IA++ L Sbjct: 205 NLTAFIVEKDFGGITMNPEEHKMGIKGSSTRQVFFNDCPVPVENMLSDRENGFKIAVNIL 264 Query: 241 EGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLI 300 GRI ++A A+G ++A A+ Y+ +R+QF +PI ++ ++ +A++ ++L A Sbjct: 265 NIGRIKLSAAAIGASKATLNTAINYSNERIQFGRPISKYGAIRFKIAEIASKLYAVDAAN 324 Query: 301 LHA--------------------ARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHG 340 A ARL+S + + E + K++ SE + +QI+G Sbjct: 325 YRAGQNIDDTYDQLVAGGMESGKARLKSVEQFAV-ECAILKVWGSEALDYTVDEGVQIYG 383 Query: 341 GYGYLEDYPVERYYRDARITQIYEGSSEIQR-----MVIARELKNYL 382 G G+ D P++R YRDARI +I+EG++EI R M++ R +K L Sbjct: 384 GMGFSADAPMDRAYRDARINRIFEGTNEINRLLTVDMMLKRAMKGEL 430 Lambda K H 0.319 0.134 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 444 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 383 Length of database: 597 Length adjustment: 34 Effective length of query: 349 Effective length of database: 563 Effective search space: 196487 Effective search space used: 196487 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory