Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_068170917.1 HTA01S_RS11035 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_26355 (375 letters) >NCBI__GCF_001592305.1:WP_068170917.1 Length = 393 Score = 256 bits (653), Expect = 1e-72 Identities = 136/376 (36%), Positives = 220/376 (58%), Gaps = 5/376 (1%) Query: 5 EEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTGY 64 E+ +RD R+FAQ + P AAE D+ +FP + +M ELG G+ VPEQ+GG + GY Sbjct: 13 EDIDALRDAVREFAQAEIAPRAAEIDKSDQFPMDCWRKMGELGVLGITVPEQYGGANMGY 72 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124 LA+ + +EEI+ + H+++ I + GND QKAK+L L SG +GA A++ Sbjct: 73 LAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNDAQKAKYLPKLISGEHVGALAMS 132 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EP AGSD S+K +A +G +Y+LNG K +IT+G +A ++V+A ++P G RG++AF++ Sbjct: 133 EPGAGSDVISMKLKAEDKGGYYLLNGNKMWITNGPDADTLVVYAKSEPEMGARGVTAFLI 192 Query: 185 PTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVGI 244 PG+S+A+ DKLG S T +++F+ V+VP N LG G K+ ++ L+ R + Sbjct: 193 EKGMPGFSIAQKLDKLGMRGSHTGELVFQNVEVPAQNILGGLNMGAKVLMSGLDYERAVL 252 Query: 245 AAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 +G+ ++ + Y +R FG+ I E Q + ++ADM T + AR + A Sbjct: 253 TGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAARSFAYTVAKNL 312 Query: 305 D-----SGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQI 359 D + + + L+ +E A + +Q GG GY+N++PL R++RD ++ +I Sbjct: 313 DLLGTEHVRQVRKDCASVILWTAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLYEI 372 Query: 360 YEGTSDIQRMVISRNL 375 GTS+I+RM+I R L Sbjct: 373 GAGTSEIRRMLIGREL 388 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: 313 Number of extensions: 12 Number of successful extensions: 2 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: 393 Length adjustment: 30 Effective length of query: 345 Effective length of database: 363 Effective search space: 125235 Effective search space used: 125235 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