Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_015948065.1 G491_RS0119515 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_000429905.1:WP_015948065.1 Length = 384 Score = 277 bits (708), Expect = 4e-79 Identities = 155/383 (40%), Positives = 227/383 (59%), Gaps = 9/383 (2%) Query: 1 MDFNFNEDQRQFADLARQFAADEL-APFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESE 59 MDF+ N++Q AR+FA E A + D +H +P + +KAGELGF L+ PE Sbjct: 1 MDFSLNKEQLDLQKAAREFAKGEFDMELARELDAKHEYPTKIWKKAGELGFIGLHFPEKY 60 Query: 60 GGMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQML 119 GMG L+ ++ EEL +G ++ A + + A+ +V +G+D ++ W + + L Sbjct: 61 SGMGYGVLENILVAEELCRGDSSIGACMVLAGFASEIVLHFGSDAQKEKWLPQVAEAKTL 120 Query: 120 ASYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTG-QAGP-- 176 ++ TEPG GSD + T AV +GDE+V++G+K+FI+ +C+T A P Sbjct: 121 SAGAFTEPGHGSDITGMDTTAVLDGDEWVINGTKIFITNGNLAGFFCTLCQTDPDAKPAY 180 Query: 177 KGISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKG 236 +G+S I + AD EG+ DK+G T V F +VRVP NL+G EG+GF ++ Sbjct: 181 RGLSMILVEADREGVSTTSVGDKLGIRMMDTAEVVFKDVRVPKENLIGVEGKGFYQVLEF 240 Query: 237 LDGGRINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQM 296 D RI IA ++GTAQ AL+RA +Y+ +R+QFGK LA FQ Q KLADMAT++ AR M Sbjct: 241 FDESRILIAAQALGTAQGALDRAVEYVKQREQFGKKLAQFQITQHKLADMATKVELARLM 300 Query: 297 VRLAAFKLDSG--DPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRD 354 AA+ D G DP+ T +MAK FA +V D A+Q+ GGYGY+REY +ER +RD Sbjct: 301 TYKAAWNYDQGKIDPKLT---SMAKMFAARTAVEVADEAIQLLGGYGYMREYDVERFYRD 357 Query: 355 VRVHQILEGTNEIMRLIIARRLL 377 ++ +I EGT EI + IA ++ Sbjct: 358 AKITEIYEGTKEIQKNTIASSVI 380 Lambda K H 0.320 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: 342 Number of extensions: 20 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: 385 Length of database: 384 Length adjustment: 30 Effective length of query: 355 Effective length of database: 354 Effective search space: 125670 Effective search space used: 125670 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