Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_011840847.1 RSPH17029_RS05935 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_26355 (375 letters) >NCBI__GCF_000015985.1:WP_011840847.1 Length = 385 Score = 279 bits (714), Expect = 8e-80 Identities = 148/371 (39%), Positives = 224/371 (60%) Query: 5 EEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTGY 64 EE +R+ +AQER+KP AA DRE+ FP E EM ELG G+ VPE++GG D GY Sbjct: 12 EEIAALRETVHAWAQERVKPMAARIDRENVFPAELWREMGELGLLGITVPEEFGGSDMGY 71 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124 LA+ + +EE+A + S H+++ I G+ EQKA++L L SG +GA A++ Sbjct: 72 LAHTVAVEEVARASASVSLSYGAHSNLCVNQIRLNGSPEQKARYLPKLVSGEHVGALAMS 131 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 E AGSD S+K +A +YVLNG K +IT+G +A V++V+A TDP AG +GI+AF++ Sbjct: 132 EAGAGSDVVSMKLKAEKRNGYYVLNGTKYWITNGPDADVLVVYAKTDPEAGAKGITAFLI 191 Query: 185 PTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVGI 244 G+S + DK+G S+T +++FE +VP N LG++G+G ++ ++ L+ RV + Sbjct: 192 EKSMTGFSTSPHFDKVGMRGSNTGELIFENCEVPFENVLGQDGKGVRVLMSGLDYERVVL 251 Query: 245 AAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 + G+ A + Y + R FG+PI Q + +LADM + AR V+ A Sbjct: 252 SGIGTGIMAACLDEVVPYCQSRQQFGQPIGNFQLMQGKLADMYVALNTARAYVYETARAC 311 Query: 305 DSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGTS 364 D+G+ +A+ L+ASE A A+Q LGG GYLND + R++RD ++ +I GTS Sbjct: 312 DAGRVTRADAAGCVLYASEQAMVQAHQAVQALGGAGYLNDSVVSRLFRDAKLMEIGAGTS 371 Query: 365 DIQRMVISRNL 375 +I+RM+I R L Sbjct: 372 EIRRMLIGREL 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: 352 Number of extensions: 14 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: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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