Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate WP_037571613.1 BS73_RS11870 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >NCBI__GCF_000744815.1:WP_037571613.1 Length = 407 Score = 253 bits (645), Expect = 9e-72 Identities = 144/389 (37%), Positives = 230/389 (59%), Gaps = 17/389 (4%) Query: 3 LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGANL 62 LT+ Q I VRDF E+ P A + +P +G+ LG +G+ +PEEFGG Sbjct: 12 LTEVQRDILATVRDFVDKEIIPVATELEHRDEYPTKIVEGMKELGLFGLTIPEEFGGLGE 71 Query: 63 DYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGAFC 122 LT ALV+EEIA G S ++ T+ V ++ +G +QK +L +A GE+ GAF Sbjct: 72 SLLTYALVVEEIARGWMSVSGIVN-THFIVAHMINAHGTQEQKEYFLPRMAAGEVRGAFS 130 Query: 123 LTEPHVGSDASALRTTAVKQGD--EYVINGVKQFITSGKNGQVAIVIAVTDKG-----AG 175 ++EP +GSD +A+RT AV+ G+ ++V+NG K ++T+G + + ++A TD+G A Sbjct: 131 MSEPGLGSDVAAIRTKAVQDGEGGDWVVNGQKMWLTNGGSSTLVALLAHTDEGDPENTAA 190 Query: 176 KKGMSAFLVPTNN--------PGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIG-AE 226 + M+ FL+ PG V +K+G DT ++ + R+PA+ ++G A Sbjct: 191 HRNMTTFLIEKEPGFGENEKVPGLTVPGKIEKMGYKGVDTTELVLQDVRVPADRVLGGAS 250 Query: 227 GEGYKIALGALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADC 286 G G+ + +E GR+ +AA+ G+AR AF+ +AY+++RE+FG I HQA+ F+LA+ Sbjct: 251 GRGFYQMMDGVEVGRVNVAARGCGVARRAFELGIAYAQQRETFGKKIAQHQAIQFKLAEM 310 Query: 287 ATQIEAARQLIWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFP 346 AT++EAA Q++ AA +D+G+ EA MAK ASE + V A + GGYG ++ Sbjct: 311 ATKVEAAHQMMVMAARKKDSGERNDLEAGMAKYLASEYCKEVVEDAFRIHGGYGFSKEYE 370 Query: 347 VERIYRDVRVCQIYEGTSDVQKIIIQRAL 375 +ER+YR+ + I EGT+++QK+I+ R L Sbjct: 371 IERLYREAPMLLIGEGTAEIQKMIVGRRL 399 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: 402 Number of extensions: 17 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: 376 Length of database: 407 Length adjustment: 31 Effective length of query: 345 Effective length of database: 376 Effective search space: 129720 Effective search space used: 129720 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