Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF2 HP15_2 acyl-CoA dehydrogenase domain protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >FitnessBrowser__Marino:GFF2 Length = 389 Score = 282 bits (722), Expect = 1e-80 Identities = 148/372 (39%), Positives = 228/372 (61%), Gaps = 1/372 (0%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64 E +R+ FA + P A E DR + FP + +M ++G G+ V E++GG D GY Sbjct: 14 ETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITVSEEYGGSDMGY 73 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124 LA+ + +EEI+ + H+++ I + G +EQK K+L L SG +GA A++ Sbjct: 74 LAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLVSGEHIGALAMS 133 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EP AGSD S+K A+ EGDHY+LNG K +IT+G +A +++A TD SAG RG++AFIV Sbjct: 134 EPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTSAGSRGVTAFIV 193 Query: 185 PTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVGI 244 D+PG+S + DKLG S+TC+++F+D KVP N LG G G K+ ++ L+ R+ + Sbjct: 194 ERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVLMSGLDYERLVL 253 Query: 245 AAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 + +G+ +AA + Y RER FG+ I E + V ++ADM T + A+ V+ A Sbjct: 254 SGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTAKSYVYMVAMSA 313 Query: 305 DSG-QPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363 D G + +A+ A L+++EMA K+ A+Q LGG GY+N++P R+ RD ++ +I GT Sbjct: 314 DRGAETTRKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLRDAKLYEIGAGT 373 Query: 364 SDIQRMVISRNL 375 S+I+RM+I R L Sbjct: 374 SEIRRMLIGREL 385 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: 339 Number of extensions: 15 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: 389 Length adjustment: 30 Effective length of query: 345 Effective length of database: 359 Effective search space: 123855 Effective search space used: 123855 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 17 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