Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate H281DRAFT_02091 H281DRAFT_02091 hypothetical protein
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__Burk376:H281DRAFT_02091 Length = 378 Score = 574 bits (1480), Expect = e-168 Identities = 284/377 (75%), Positives = 327/377 (86%), Gaps = 2/377 (0%) Query: 1 MLLTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGA 60 M+L QD M+RDA+R F + + P+AA WD+E FPKD H+ LA LGAYG+ VPE +GGA Sbjct: 1 MVLDQDHLMVRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGA 60 Query: 61 NLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGA 120 +D L LAL+LEEIAAGDGGTSTAISV NCPV +IL+ YGN QKR+WLTPLARGEMLGA Sbjct: 61 GMDALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLARGEMLGA 120 Query: 121 FCLTEPHVGSDASALRTTAV--KQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGKKG 178 FCLTEP GSDASALRTTA K GD YV+NGVKQFITSGKNG VAIV+AVTDK AGK+G Sbjct: 121 FCLTEPQAGSDASALRTTATRDKDGDAYVLNGVKQFITSGKNGDVAIVMAVTDKAAGKRG 180 Query: 179 MSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALE 238 +SAF+VPT++ GYVVAR+EDKLGQHSSDTAQI F++CR+PA NLIGAEGEGY+IAL LE Sbjct: 181 ISAFIVPTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLE 240 Query: 239 GGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQLIW 298 GGRIGIAAQSVGMAR+A++AAL Y+KERESFG +F+HQAV FRLAD ATQ+EAARQLIW Sbjct: 241 GGRIGIAAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIW 300 Query: 299 HAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRVCQ 358 HAA+L+DAG+PCL EAAMAKLFASE AER+CSAA+Q GGYG ++DFPVERIYRDVRVCQ Sbjct: 301 HAASLKDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQ 360 Query: 359 IYEGTSDVQKIIIQRAL 375 IYEGTSD+QKI+I R L Sbjct: 361 IYEGTSDIQKILIARGL 377 Lambda K H 0.319 0.134 0.396 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: 527 Number of extensions: 20 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: 376 Length of database: 378 Length adjustment: 30 Effective length of query: 346 Effective length of database: 348 Effective search space: 120408 Effective search space used: 120408 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