Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF2427 Psest_2475 Acyl-CoA dehydrogenases
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >FitnessBrowser__psRCH2:GFF2427 Length = 392 Score = 256 bits (655), Expect = 6e-73 Identities = 138/372 (37%), Positives = 213/372 (57%), Gaps = 1/372 (0%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64 ++QT +D R+F ++ + P +W+ +H+ PR + E G G+ +PEQ GGC G Sbjct: 16 DDQTLFQDSVRRFLQQEVAPHYEQWEADHQLPRALWHRLGEAGLLGVDLPEQLGGCAAGV 75 Query: 65 LAYAMTLEEIAA-GDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 M EEI+ G G ++ ++H ++ I GN Q+A +L +A+G +LGA A+ Sbjct: 76 ETCLMICEEISRQGFGGLASGYNIHANIVMPYIHHLGNPAQQACWLPRMAAGEVLGAIAM 135 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP AGSD ++++ A+ + LNG K FIT+G A +VIV A TDP+A RG+S F+ Sbjct: 136 TEPGAGSDLAAMRASAQKVPGGWKLNGSKVFITNGLLADMVIVCAKTDPNARARGVSLFL 195 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243 V T PG+S + K+GQHASDT ++ F+DL VP LG+ G+G+ + L R+G Sbjct: 196 VDTTLPGFSRGKAIRKIGQHASDTAELFFDDLIVPEDALLGDAGKGFAYLMQELPRERLG 255 Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 +AAQA+G A + DY ++R +FG+ I + Q F LA++ + + R Sbjct: 256 VAAQAIGAIDGALQLTLDYVQQRRAFGQRIADFQNTRFTLAEVRAHLEMGRAYFEKCLQR 315 Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363 G+ + +A+ KL SEM + LQ GGYGY ++P+ R Y D R+ IY GT Sbjct: 316 YARGEMSSTDAAALKLMLSEMQCRCVDQCLQLFGGYGYTLEYPISRFYVDARIQTIYAGT 375 Query: 364 SDIQRMVISRNL 375 S+I + VI+R++ Sbjct: 376 SEIMKEVIARDM 387 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: 337 Number of extensions: 14 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: 392 Length adjustment: 30 Effective length of query: 345 Effective length of database: 362 Effective search space: 124890 Effective search space used: 124890 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