Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_025274387.1 HALAL_RS0112855 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000527155.1:WP_025274387.1 Length = 410 Score = 220 bits (561), Expect = 5e-62 Identities = 143/396 (36%), Positives = 212/396 (53%), Gaps = 29/396 (7%) Query: 4 TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63 +EE IRD FA + ++P AAEWD P I E A++G +G+ Q+ DTG Sbjct: 10 SEEHEDIRDWVHGFAADVIRPAAAEWDEREETPWPIIQEAAKIGLYGLEALVQFWSDDTG 69 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNS-VGCVPILKFGNDEQKAKFLTPL---ASGAMLG 119 L + EE+ GD M++ S + I G EQ +++ + +G Sbjct: 70 -LQLQLVNEELFWGDAGIG--MAIFGSTLAAAGIYANGTPEQIVEWIPQCFGDENDPKVG 126 Query: 120 AFALTEPQAGSDASSLKTRARLE--GDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKR 177 AF +EP+AGSD ++++TRA+ D + L G K +IT+G A + +V AV DP G + Sbjct: 127 AFCSSEPEAGSDVAAMRTRAKYNEVDDTWTLRGQKAWITNGGIANIHVVMAVVDPELGTK 186 Query: 178 GISAFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLG------------- 224 G +AF++P +PG K G AS T + +++ VP LG Sbjct: 187 GHAAFVIPPGTPGLDSPSKVKKHGLRASHTADVFLDEVTVPGSCLLGGKEKLDERLARAH 246 Query: 225 ------EEGEGYKIALANLEGGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQA 278 + + +++ E R + AQA+G+ARAA+E + +YA ER FG+PII +QA Sbjct: 247 ERRRNPDAAKTKNPSMSTFEVSRPTVGAQALGIARAAYEHSLEYASERHQFGRPIISNQA 306 Query: 279 VAFRLADMATQIAVARQMVHYAAAL-RDSGQPALVEASMAKLFASEMAEKVCSMALQTLG 337 + F LADM T+I AR +V AA + R+ G E SMAKL ASE+A A+Q G Sbjct: 307 IGFTLADMKTEIDAARLLVWRAAWMARNGGGFTSGEGSMAKLKASEVAVWATERAIQIYG 366 Query: 338 GYGYLNDFPLERIYRDVRVCQIYEGTSDIQRMVISR 373 G GY + P+ER+ RD ++ I+EGTS+IQR+VI+R Sbjct: 367 GAGYSRENPVERLARDAKIYTIFEGTSEIQRLVIAR 402 Lambda K H 0.320 0.134 0.388 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: 356 Number of extensions: 15 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: 375 Length of database: 410 Length adjustment: 31 Effective length of query: 344 Effective length of database: 379 Effective search space: 130376 Effective search space used: 130376 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: 50 (23.9 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