Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate 7024806 Shewana3_1984 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= reanno::WCS417:GFF2713 (383 letters) >FitnessBrowser__ANA3:7024806 Length = 585 Score = 148 bits (373), Expect = 4e-40 Identities = 121/398 (30%), Positives = 182/398 (45%), Gaps = 54/398 (13%) Query: 8 EEQVMIRDMARDFARGEIAPYAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYVDY 67 E+ V+ +D G A Y Q + + GW+ + G +G+ M+ G VD Sbjct: 64 EQGVLHQDNRVITPDGYKAVYDQ-YSQGGWVGLCGEPEFGGMGMPKML------GVLVDE 116 Query: 68 VAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTESQKQTWLADLASGQAIGCFCLT 127 +AY+ G GA + I+ +G+E K+T+L L SG+ G +T Sbjct: 117 MAYSACNAFTLYGSLTAGAALCINA---------HGSEEIKETYLPKLYSGEWAGAMDMT 167 Query: 128 EPQAGSEAHNLRTRAELRD-GHWVITGAKQFVSNGKRAKLAIVFAITDPELGK-KGISAF 185 EPQAGS+ N+RTRA +D G + I+G+K F++ G V + +L + KGIS F Sbjct: 168 EPQAGSDLRNIRTRAIPQDDGSYAISGSKIFITGGDHDLTENVIHLVLAKLPESKGISLF 227 Query: 186 LVPTATP----------GFVVDRTEHKMGIRASDTCAVTLNQCTVPEANLLGERGKGLAI 235 LVP T G V EHKMG++ S TC + ++ + L+GE +GL Sbjct: 228 LVPKTTVNADGSLGQANGVSVGSIEHKMGLKGSATCVMNFDEA---KGYLIGEPNRGLVC 284 Query: 236 ALSNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKA-----------IIEHQSVAN 284 + + R+ I Q LG A+AA++ A YA++R Q A II H V Sbjct: 285 MFTMMNYERLAIGIQGLGSAQAAYQMAADYAKERNQGVAAGGSPTGSDSDPIIVHGDVRR 344 Query: 285 LLADMQTQLNAARLLILHAARLRSAGKPCLSEASQ------------AKLFASEMAEKVC 332 +L ++ A R L + + K E AK F ++ Sbjct: 345 MLLTIRAMTEAGRALSVFTGKQLDLAKYAEGEVKAKAARYVGLLTPVAKAFLTDRGLDAT 404 Query: 333 SSAMQIHGGYGYLEDYPVERYYRDARITQIYEGTSEIQ 370 A Q+ GG+GY+ + +E+ RD RI QIYEGT+ IQ Sbjct: 405 IMAQQVFGGHGYIRETGIEQLVRDTRIAQIYEGTNGIQ 442 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: 455 Number of extensions: 23 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: 585 Length adjustment: 33 Effective length of query: 350 Effective length of database: 552 Effective search space: 193200 Effective search space used: 193200 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