Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF1011 PGA1_c10280 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_26355 (375 letters) >FitnessBrowser__Phaeo:GFF1011 Length = 386 Score = 289 bits (739), Expect = 1e-82 Identities = 154/372 (41%), Positives = 230/372 (61%), Gaps = 2/372 (0%) Query: 5 EEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTGY 64 E+ +RDM ++AQER++P A E D+++ FP E EM ELG G+ VPE++GG Y Sbjct: 12 EDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFGGAGMSY 71 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKF-GNDEQKAKFLTPLASGAMLGAFAL 123 LA+ + +EEIA + S H+++ CV +K GN EQKAK+L L SG +GA A+ Sbjct: 72 LAHTVAVEEIARASASVSLSYGAHSNL-CVNQIKLNGNAEQKAKYLPRLVSGEHVGALAM 130 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 +E AGSD S+ RA DHY LNG K +IT+G +A ++V+A TDP AG +G++AF+ Sbjct: 131 SEAGAGSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDAGSKGMTAFL 190 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVG 243 + + G+S ++ DKLG S+T +++FE+V+VP N LGEEG+G ++ ++ L+ RV Sbjct: 191 IEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLDYERVV 250 Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 +A G+ A + Y +ER FG+PI Q + ++ADM T + AR V+ A Sbjct: 251 LAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVYEVAKA 310 Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363 D G +A+ L+ASE+A A+Q GG GYL+D P+ RI+RD ++ +I GT Sbjct: 311 CDKGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLMEIGAGT 370 Query: 364 SDIQRMVISRNL 375 S+I+RM+I R L Sbjct: 371 SEIRRMLIGREL 382 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: 325 Number of extensions: 16 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: 386 Length adjustment: 30 Effective length of query: 345 Effective length of database: 356 Effective search space: 122820 Effective search space used: 122820 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