Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate H281DRAFT_02091 H281DRAFT_02091 hypothetical protein
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Burk376:H281DRAFT_02091 Length = 378 Score = 492 bits (1267), Expect = e-144 Identities = 249/377 (66%), Positives = 300/377 (79%), Gaps = 2/377 (0%) Query: 1 MLPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGC 60 M+ + L + DA R F +E + P+AA WDRE FPK+ ++AELG +G+LVPE +GG Sbjct: 1 MVLDQDHLMVRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGA 60 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGA 120 LA A+ LEEIAAGDG ST +SV+N C +L +GND QK +L PLA G MLGA Sbjct: 61 GMDALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLARGEMLGA 120 Query: 121 FALTEPQAGSDASSLKTRARLN--GDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRG 178 F LTEPQAGSDAS+L+T A + GD YVLNG KQFITSG+N V IV AVTD +AGKRG Sbjct: 121 FCLTEPQAGSDASALRTTATRDKDGDAYVLNGVKQFITSGKNGDVAIVMAVTDKAAGKRG 180 Query: 179 ISAFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLE 238 ISAFIVPTDS GY VARVEDKLGQH+SDT QI+FED +VP AN +G EGEGY+IAL+ LE Sbjct: 181 ISAFIVPTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLE 240 Query: 239 GGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVH 298 GGR+GIA+QSVGMARAA+EAA YA+ERESFG+P+ HQAV FRLADMATQ+ ARQ++ Sbjct: 241 GGRIGIAAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIW 300 Query: 299 YAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQ 358 +AA+L+D+G+P L EA+MAKLFASE AE++CS ALQ GGYGYLSDFP+ERIYRDVRVCQ Sbjct: 301 HAASLKDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQ 360 Query: 359 IYEGTSDIQRMVISRNL 375 IYEGTSDIQ+++I+R L Sbjct: 361 IYEGTSDIQKILIARGL 377 Lambda K H 0.319 0.134 0.389 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: 428 Number of extensions: 12 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: 378 Length adjustment: 30 Effective length of query: 345 Effective length of database: 348 Effective search space: 120060 Effective search space used: 120060 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