Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_012966422.1 FERP_RS09780 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000025505.1:WP_012966422.1 Length = 390 Score = 286 bits (733), Expect = 5e-82 Identities = 153/378 (40%), Positives = 243/378 (64%), Gaps = 7/378 (1%) Query: 4 TEEQTQIRDMARQFAEERLKP-FAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDT 62 TEEQ IR AR+FAE+ P A E DRE +FP E + A+LGF + +PE++GG Sbjct: 8 TEEQEDIRRAAREFAEKEFTPELARECDREEKFPFELWKKCAKLGFHAVAIPEEYGGGGY 67 Query: 63 GYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFA 122 G + + +EE +A + + + G +L G++EQK K++T +A G + A Sbjct: 68 GPIEQMIVMEEFSAVNPGLGLACLIP-TFGVEILLLHGSEEQKEKYVTKVAKGDAIMGMA 126 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVT-DPSAGK---RG 178 TEP AGSDA+S+KTRA +GD +VLNG KQFI++G A ++V A T +P + + +G Sbjct: 127 NTEPDAGSDAASIKTRAVRDGDEWVLNGTKQFISNGSIADFILVTARTSEPKSFEERHKG 186 Query: 179 ISAFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLE 238 IS FIV TD GY ++ K+G A+DT ++ +++VP N +GEEG+G+ + + Sbjct: 187 ISYFIVETDREGYKATKITGKMGIRATDTAEVSLNNVRVPAENLVGEEGKGFYYMMEFFD 246 Query: 239 GGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVH 298 RV +AAQAVG+AR A + DY ++R +FG P+ Q V F++A++AT+I AR + + Sbjct: 247 ITRVWVAAQAVGIARGALKLVVDYVKQRKAFGMPLAAFQYVQFKIAELATKIEAARTLTY 306 Query: 299 YAAALR-DSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVC 357 AAA++ ++G+P ++MAK +A E+A + C+ ALQ GGYGY++++P+ + YRD ++ Sbjct: 307 RAAAVQVETGKPDNTLSAMAKWYAGEVAVETCNWALQFHGGYGYIDEYPINQFYRDAKIT 366 Query: 358 QIYEGTSDIQRMVISRNL 375 +IYEG +I++++I+RN+ Sbjct: 367 EIYEGAKEIEKLIIARNI 384 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: 324 Number of extensions: 22 Number of successful extensions: 5 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: 390 Length adjustment: 30 Effective length of query: 345 Effective length of database: 360 Effective search space: 124200 Effective search space used: 124200 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