Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate 6937588 Sama_1743 acyl-CoA dehydrogenase family protein (RefSeq)
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__SB2B:6937588 Length = 578 Score = 138 bits (347), Expect = 4e-37 Identities = 110/373 (29%), Positives = 169/373 (45%), Gaps = 43/373 (11%) Query: 39 ETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIY 98 E + G +G+ EYGG G + ++ E C + S T+ + I Sbjct: 82 EAYNAFVEGGWVGLSGDPEYGGMGMPKMLGVLVDEMGYSACNAFNLYGSL-TAGAALAIN 140 Query: 99 QYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQTTAVLDGD-EYILNGSKIFIT 157 +G EE K +L L SGE GA +TEP AG+D +T A D Y++ GSKIFIT Sbjct: 141 AHGTEELKSTYLPKLYSGEWAGAMDMTEPQAGSDLRHIRTRAEPQEDGSYLITGSKIFIT 200 Query: 158 NA----IAGDIYVVMAMTDKSKGNKGISAFIVEK----------GTPGFSFGVKEKKMGI 203 I++V+A K G+ +S F+V K G S G E KMG+ Sbjct: 201 GGDQDLTENVIHLVLA---KISGSNTLSLFLVPKIGVDDQGNLTEPNGVSVGSIEHKMGL 257 Query: 204 RGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGALDETVKY 263 +GSAT + F+ R L+G+E +G + ++ R+ I Q LG AQ A+ Y Sbjct: 258 KGSATCVMNFDSAR---GWLIGRENKGLACMFTMMNYERLAIGIQGLGSAQAAVQMASDY 314 Query: 264 VKERVQFGR--------PLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDL-------- 307 +ER+Q P+ + + L A R L DL Sbjct: 315 ARERLQGNAVGSTAAADPILVHGDVRRMLLTTRTLTDAGRALAVHTGKQLDLAKFADDDA 374 Query: 308 -----GKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYE 362 G+ G+ +AK F + +++T A Q+ GG+GY R+ +E+++RD +I +IYE Sbjct: 375 VKTKAGRYVGLLTPVAKAFLTDRGLDITIMAQQVFGGHGYIRETGIEQLVRDTRIAQIYE 434 Query: 363 GTSEVQRMVISGK 375 GT+ +Q + G+ Sbjct: 435 GTNGIQAIDFLGR 447 Lambda K H 0.315 0.133 0.373 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: 488 Number of extensions: 38 Number of successful extensions: 4 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: 378 Length of database: 578 Length adjustment: 33 Effective length of query: 345 Effective length of database: 545 Effective search space: 188025 Effective search space used: 188025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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