Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_231851071.1 SUTH_RS00430 acyl-CoA dehydrogenase family protein
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_000828635.1:WP_231851071.1 Length = 392 Score = 260 bits (665), Expect = 4e-74 Identities = 146/376 (38%), Positives = 224/376 (59%), Gaps = 8/376 (2%) Query: 5 FNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGL 64 F ED F D R+F E+AP A+W+E+ H +D+ KAG G PE GG+G+ Sbjct: 21 FEEDHEAFRDTVRRFMEQEVAPHHARWEEQSHVDRDIWNKAGAAGLLCATMPEEYGGVGV 80 Query: 65 SRLDASIIFEELSKGCTATTAMLTIHN--MATWMVTTWGTDTLRQAWSEPLTTGQMLASY 122 + + I+ EE ++ AT +H+ +A +++ +G++ L+Q + + +G+M+ + Sbjct: 81 DKRFSVIVMEEAAR-INATGLGWGLHSEIVAPYLLH-YGSEHLKQKYLPKMASGEMVGAI 138 Query: 123 CLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQA-GPKGISA 181 +TEP AGSD ++T AV++GD Y+V+GSK+FI+ +L++V+ +T A G KG S Sbjct: 139 AMTEPAAGSDLQGVRTTAVKDGDHYIVNGSKIFITNGYLCDLVIVVAKTDPAKGAKGTSL 198 Query: 182 IAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGR 241 + + G K K G AQ T + FDNVRVP NLLGEEG GF + M+ L R Sbjct: 199 LVVDTSMPGFTKAKPLHKAGMKAQDTCELFFDNVRVPAENLLGEEGNGFVYLMQELPWER 258 Query: 242 INIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMV-RLA 300 + IA ++ +A+AA++ Y ER+ FG+ + FQ +FKLA++ TE+ R V R Sbjct: 259 LQIAVIAMASAEAAIDWTVAYTRERKAFGQEIMKFQNTRFKLAELKTEVQIGRVFVDRCV 318 Query: 301 AFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQI 360 L++ ATA +MAK + TD+ F+V D +Q+HGGYGY+ EYP+ R + D RV +I Sbjct: 319 ELLLNNKLDPATA--SMAKYWCTDLQFKVMDECVQLHGGYGYMWEYPITRAWADARVQRI 376 Query: 361 LEGTNEIMRLIIARRL 376 GTNEIM+ +I+R L Sbjct: 377 YGGTNEIMKELISRSL 392 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: 321 Number of extensions: 15 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: 392 Length adjustment: 30 Effective length of query: 355 Effective length of database: 362 Effective search space: 128510 Effective search space used: 128510 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 Apr 09 2024. 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