Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate CA265_RS02820 CA265_RS02820 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__Pedo557:CA265_RS02820 Length = 384 Score = 350 bits (897), Expect = e-101 Identities = 172/370 (46%), Positives = 245/370 (66%) Query: 4 TQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGANLD 63 T+ Q+ ++ VRDFA+ + PH WD+ HFP + + L LG G+ VPEE+GG+ L Sbjct: 10 TETQQSVKAMVRDFAEKNIRPHIMEWDEAQHFPVELFKQLGELGLMGVLVPEEYGGSGLG 69 Query: 64 YLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGAFCL 123 Y V+ E+A G +++ N ++ + N +QK+ WL LA E +GA+ L Sbjct: 70 YQEYVDVIVEVARVCGSIGLSLAAHNSLCTGHILAFANPEQKQRWLPKLATAEWIGAWGL 129 Query: 124 TEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKGMSAFL 183 TE + GSDA + TTAV+ GD+Y+ING K +IT GK+G +A+V+ T + KG+SA + Sbjct: 130 TEANTGSDALRMMTTAVEDGDDYIINGAKNWITHGKSGDIAVVMVRTGEQGSSKGISAIV 189 Query: 184 VPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGGRIG 243 V PG+ + E+KLG +S+T ++ FDNCR+P NL+G GEG+K A+ L+GGRI Sbjct: 190 VERGTPGFTAGKKENKLGMRASETTEMIFDNCRVPKANLLGNVGEGFKQAMKVLDGGRIS 249 Query: 244 IAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIWHAAAL 303 IAA ++G+A+ AFDAA+AYSK+R+ FG I + QA+ F+LAD AT+IEAA LI AA L Sbjct: 250 IAALALGIAKGAFDAAVAYSKQRQQFGQPISSFQAISFKLADMATEIEAAELLIRQAADL 309 Query: 304 RDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQIYEGT 363 ++ P KE+AMAK FASE++ RV + A+Q GGYG DFPVE+ YRD ++C I EGT Sbjct: 310 KNRHLPMTKESAMAKYFASEVSVRVATDAVQIFGGYGYTKDFPVEKFYRDSKLCTIGEGT 369 Query: 364 SDVQKIIIQR 373 S++QKI+I R Sbjct: 370 SEIQKIVIAR 379 Lambda K H 0.319 0.134 0.396 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: 383 Number of extensions: 13 Number of successful extensions: 1 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: 376 Length of database: 384 Length adjustment: 30 Effective length of query: 346 Effective length of database: 354 Effective search space: 122484 Effective search space used: 122484 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 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