Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_26355 (375 letters) >NCBI__GCF_003253485.1:WP_111393848.1 Length = 401 Score = 226 bits (576), Expect = 8e-64 Identities = 133/375 (35%), Positives = 198/375 (52%), Gaps = 7/375 (1%) Query: 2 LPTEEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCD 61 L TEEQ IR R F ++ + P+ +W ++ FP E + + E+G FG +P ++G Sbjct: 26 LLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIVKKFGEVGAFGPQLPVEYGCGG 85 Query: 62 TGYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAF 121 Y++Y + ++EI GD + SV S+ PI KFG +EQ+ K+L LASG +LG F Sbjct: 86 LDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFGTEEQRLKYLPRLASGELLGCF 145 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISA 181 LTEP GS+ S + T + GDHY+LNG K +I++ A + +V+A + I Sbjct: 146 GLTEPDHGSNPSGMVTNFKDMGDHYLLNGAKMWISNSPKADIAVVWAKNEEGR----IQG 201 Query: 182 FIVPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRL-GEEGEGYKIALANLEGG 240 IV G+S +K AS T +++F+ VKVP N L G+ G G + L+ Sbjct: 202 LIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENLLPGKTGLG--APMMCLDSA 259 Query: 241 RVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R GIA A+G A +E+AR YA ER FGKPI Q +LA+M T+I A+ + Sbjct: 260 RFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKLAEMLTEITKAQLLAWKV 319 Query: 301 AALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIY 360 + + G+ V SMAK EMA + A Q GG G ++P+ R ++ Y Sbjct: 320 GKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITGEYPIMRHMMNLESVITY 379 Query: 361 EGTSDIQRMVISRNL 375 EGT DI +++ + Sbjct: 380 EGTHDIHLLILGNEI 394 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: 321 Number of extensions: 12 Number of successful extensions: 3 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: 401 Length adjustment: 30 Effective length of query: 345 Effective length of database: 371 Effective search space: 127995 Effective search space used: 127995 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