Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_036257156.1 DL86_RS00105 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000746085.1:WP_036257156.1 Length = 387 Score = 282 bits (721), Expect = 1e-80 Identities = 147/370 (39%), Positives = 223/370 (60%) Query: 6 DQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGYL 65 D +RDM R FA + + P AAE DR FP++ +M LG G+ V E +GG GYL Sbjct: 14 DLDIMRDMVRAFASDNIAPRAAEIDRTDAFPQDLWPQMGALGLLGITVEEDYGGAGLGYL 73 Query: 66 AYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALTE 125 A+ +A+EEI+ + H+++ I GTD QK R+L L SG +GA A++E Sbjct: 74 AHCVAMEEISRASASVGLSYGAHSNLCVNQIRRNGTDAQKRRYLPKLLSGEHVGALAMSE 133 Query: 126 PQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVP 185 +GSD ++ RA +GD YVLNG K +IT+G A ++V+A TDP+AG G++AF++ Sbjct: 134 ANSGSDVLSMRLRADRKGDRYVLNGAKLWITNGHYASTLVVYAKTDPAAGGHGVTAFLIE 193 Query: 186 TDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGIA 245 G++ A+ DKLG S T +++FED +VP N LG+ +G + ++ L+ R +A Sbjct: 194 KGFKGFRPAQKLDKLGMRGSPTSELVFEDCEVPEENVLGKVNQGVGVLMSGLDYERAVLA 253 Query: 246 SQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRD 305 + +G+ +A + Y RER+ FG+PI E + V +LADM +++ R V+ A D Sbjct: 254 AGPIGIMQACLDICLPYTRERKQFGRPIGEFELVQGKLADMYARLSACRAYVYAVAGACD 313 Query: 306 SGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTSD 365 G+PA +A+ A LFA+E A + A+Q LGG GY+ND+P R+ RD ++ +I GTS+ Sbjct: 314 RGQPARKDAAGALLFAAESATQAALDAIQLLGGNGYINDYPAGRLLRDAKLYEIGAGTSE 373 Query: 366 IQRMVISRNL 375 I+RM+I R L Sbjct: 374 IRRMLIGREL 383 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: 365 Number of extensions: 13 Number of successful extensions: 1 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: 387 Length adjustment: 30 Effective length of query: 345 Effective length of database: 357 Effective search space: 123165 Effective search space used: 123165 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