Align Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial; SBCAD; 2-methyl branched chain acyl-CoA dehydrogenase; 2-MEBCAD; 2-methylbutyryl-coenzyme A dehydrogenase; 2-methylbutyryl-CoA dehydrogenase; EC 1.3.8.5 (characterized)
to candidate WP_013450481.1 CALNI_RS01740 acyl-CoA dehydrogenase
Query= SwissProt::P70584 (432 letters) >NCBI__GCF_000183405.1:WP_013450481.1 Length = 588 Score = 221 bits (562), Expect = 6e-62 Identities = 140/407 (34%), Positives = 216/407 (53%), Gaps = 35/407 (8%) Query: 39 EALLSVTNNALCFAPLQTFTDEDIMMQKAVKKFAQEQIAPLVSTMDENSKMEKSVIQGLF 98 E L+ F P + F+DE M + +KF E+ P + +D + V+Q + Sbjct: 6 EFLIKAEEADAVFTP-EDFSDEQKQMAETTEKFVTEKAIPFIDEIDAGNY--DKVVQLMK 62 Query: 99 QQGMMG---IEVEAKYGGTEASFLCSVLVIEELAKVDA-SVALLCDIQNTVINKLFRKHG 154 + G +G I+ +YGG S+LV E++A + SVA + ++ +G Sbjct: 63 EAGELGLLMIDGPEEYGGLNLDKATSMLVAEKVAPGGSFSVAYAAHTGIGTLPLVY--YG 120 Query: 155 TEEQKATYLPKLVT-EKLGSFCLSEAGAGSDSFALKTRADKS--GNYYVINGSKMWISNA 211 T+EQK YL KL+T E LG++CL+E G+GSD+ KT A S G YY++NG+K WI+NA Sbjct: 121 TKEQKEKYLEKLLTGEWLGAYCLTEPGSGSDALGAKTSAVLSDDGKYYILNGTKQWITNA 180 Query: 212 EHAELFLVFANVDPPSGYRGITCFLVDRDTEGFQIGRRENKMGIRASSTCQLTFENVKVP 271 A++F VFA VD + T FL++R+T G G E KMGI+ SST Q+ +NVKVP Sbjct: 181 GFADIFTVFAKVDK----QHFTAFLIERNTPGLSFGAEEKKMGIKGSSTRQVILDNVKVP 236 Query: 272 ETSVLGKIGHGYKYAIGSLNEGRIGIAAQMLGLAQGCFDYTIPYIKERMQFGKRIFDFQG 331 +VLG++G G+K A LN GR +AA + G A+ I Y R QF + I F Sbjct: 237 VENVLGEVGKGHKIAFNVLNVGRFKLAAAVTGAAKYALAEGIKYANVRKQFDRLISSFGA 296 Query: 332 LQHQVAHVATQLEAARLLTYNAARLVEAG-------------------RPFIKEASMAKY 372 +Q +++ + A+ L Y A L++ + E S++K Sbjct: 297 IQEKISDMTAYTYASESLIYRLAGLLDNALNKIDPSLPNYYEIYQKEIEEYAIECSISKV 356 Query: 373 YASEVAGLTTSKCIEWMGGVGYTKDYPVEKFFRDAKIGTIYEGTSNI 419 + S+V L + ++ GG G++++YP E+F+RD +I I+EGT+ I Sbjct: 357 FCSDVLALVVDETLQIFGGYGFSQEYPAERFYRDERINRIFEGTNEI 403 Lambda K H 0.319 0.134 0.389 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: 523 Number of extensions: 22 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: 432 Length of database: 588 Length adjustment: 34 Effective length of query: 398 Effective length of database: 554 Effective search space: 220492 Effective search space used: 220492 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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