Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate 351334 BT1806 acyl-CoA dehydrogenase (NCBI ptt file)
Query= reanno::WCS417:GFF2713 (383 letters) >FitnessBrowser__Btheta:351334 Length = 568 Score = 178 bits (451), Expect = 4e-49 Identities = 115/358 (32%), Positives = 181/358 (50%), Gaps = 33/358 (9%) Query: 46 MGELGLLGMVVPEEWGGTYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTE 105 M + GL GM +P +GG Y + E ++A D G + S+ + + + +G Sbjct: 98 MVKAGLNGMTMPRRFGGLNFPITPYTMCAEIVAAADAGFGNIWSLQDCIET--LYEFGNA 155 Query: 106 SQKQTWLADLASGQAIGCFCLTEPQAGSEAHNLRTRAEL--RDGHWVITGAKQFVSNGKR 163 Q ++ + G+ + LTEP AGS+ + +A +DG W++ G K+F++NG Sbjct: 156 DQHSRFIPRVCQGETMS-MDLTEPDAGSDLQAVMLKATYSEKDGCWLLNGVKRFITNGDA 214 Query: 164 AKLAIVFAITDPELGKKGISAFLVPTATPGFVVDRTEHKMGIRASDTCAVTLNQCTVPEA 223 ++ + +G+S F+ G V R EHK+GI S TC + +A Sbjct: 215 DIHLVLARSEEGTRDGRGLSMFIYDKRQGGVDVRRIEHKLGIHGSPTCELVYKNA---KA 271 Query: 224 NLLGERGKGLA-IALSNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKAIIEHQSV 282 L G+R GL ++ + G R+GIAAQ++G+++AA+ LAYA+DR QF KAII+ +V Sbjct: 272 ELCGDRKLGLIKYVMALMNGARLGIAAQSVGLSQAAYNEGLAYAKDRKQFGKAIIDFPAV 331 Query: 283 ANLLADMQTQLNAARLLILHAARLRSAGKPC--------------LSEASQAKL------ 322 ++LA M+ +L+A R L+ AR K L + AKL Sbjct: 332 YDMLAIMKGKLDAGRALLYQTARYVDIYKALDDISRERKLTPEERLEQKKYAKLADSFTP 391 Query: 323 ----FASEMAEKVCSSAMQIHGGYGYLEDYPVERYYRDARITQIYEGTSEIQRMVIAR 376 SE A + +QIHGG G++ +Y +R YRDARIT IYEGT+++Q + R Sbjct: 392 LAKGMNSEYANQNAYDCIQIHGGSGFMMEYACQRIYRDARITSIYEGTTQLQTVAAIR 449 Lambda K H 0.319 0.133 0.390 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: 399 Number of extensions: 14 Number of successful extensions: 5 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: 568 Length adjustment: 33 Effective length of query: 350 Effective length of database: 535 Effective search space: 187250 Effective search space used: 187250 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