Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate H281DRAFT_01346 H281DRAFT_01346 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >FitnessBrowser__Burk376:H281DRAFT_01346 Length = 393 Score = 248 bits (634), Expect = 2e-70 Identities = 136/376 (36%), Positives = 216/376 (57%), Gaps = 5/376 (1%) Query: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 ++ + +RD FA + + P AAE DR +FP + + LG GM V E++GG + GY Sbjct: 13 EEIEMLRDSIAGFAAKEIAPRAAEIDRTDQFPMDLWRKFGDLGVLGMTVSEEYGGANMGY 72 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124 A+ +A+EEI+ + H+++ I GT+ QK+++L L SG +GA A++ Sbjct: 73 TAHMVAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEAQKQKYLPKLVSGEHVGALAMS 132 Query: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EP AGSD +K RA +GD YVLNG K +IT+G + ++V+A TD A RGI+AFIV Sbjct: 133 EPNAGSDVVSMKLRADRKGDRYVLNGTKMWITNGPDCDTLVVYAKTDVEANSRGITAFIV 192 Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244 G+ VA+ DKLG S T +++F+DV+VP N LG+ G ++ ++ L+ R + Sbjct: 193 EKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPEENILGQLNGGVKVLMSGLDYERAVL 252 Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 A G+ A +A Y +R+ FG+ I E Q + ++AD+ T + R ++ Sbjct: 253 AGGPTGIMVAVMDAVVPYIHDRKQFGQSIGEFQLIQGKVADLYTTLQACRAYLYAVGRQL 312 Query: 305 DSGKPALV-----EASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQI 359 D+ A V + + L+ +E A + A+Q LGG GY+N++PV R++RD ++ +I Sbjct: 313 DTLGTAHVRQVRKDCAGVILYTAEKATWMAGEAIQILGGNGYINEYPVGRLWRDAKLYEI 372 Query: 360 YEGTSDIQRMVISRNL 375 GTS+I+RM+I R L Sbjct: 373 GAGTSEIRRMLIGREL 388 Lambda K H 0.320 0.135 0.394 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: 318 Number of extensions: 11 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 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