Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_058929012.1 AU252_RS00305 acyl-CoA dehydrogenase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_001484605.1:WP_058929012.1 Length = 400 Score = 225 bits (574), Expect = 1e-63 Identities = 136/378 (35%), Positives = 211/378 (55%), Gaps = 12/378 (3%) Query: 4 TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCD-T 62 T E+ IRD R FAE+R+ P E+ + FP + +AELG G ++ Q GC Sbjct: 22 TPEEIGIRDKVRAFAEQRVLPVINEYWEKAEFPTVLLPPLAELGIIGTII--QGYGCPGM 79 Query: 63 GYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFA 122 A M E+A DG+ +T + +H+++ + G+DEQK ++L LA GAFA Sbjct: 80 SRKAAGMVAREMARADGSLNTFLGIHSNLCMGALNILGSDEQKERWLPALARIEKTGAFA 139 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAF 182 LTEP GSD+ +L+T AR +GDH+VLNG K++I +G A V+++FA ++AF Sbjct: 140 LTEPDHGSDSVALETSARRDGDHWVLNGHKRWIGNGHVADVIVLFARNTEDGN---VNAF 196 Query: 183 IVPTDSPG-----YSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANL 237 ++ D G YS + K+G+ A I+ E++++P NRL E ++ L Sbjct: 197 VIEKDDDGRYPAGYSPTVITGKVGKRAILQADIVIEEMRLPAANRL-EGCHSFRDVSRVL 255 Query: 238 EGGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMV 297 + R G A +AVG A AAFE A DYA+ R FGKPI +Q V RLA+M +++ + + Sbjct: 256 QATRGGAAWEAVGHAMAAFEIASDYAQTRIQFGKPIASYQLVQSRLANMLSELTTMQLLC 315 Query: 298 HYAAALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVC 357 + A L D GQ + +ASM K+ ++ + +C+ A + LGG G L + + R D+ V Sbjct: 316 NRMAELADRGQLTVAQASMVKMATAQKGKWICNEARELLGGNGLLLENHVIRHMTDMEVV 375 Query: 358 QIYEGTSDIQRMVISRNL 375 YEGT +Q +++ R++ Sbjct: 376 STYEGTDSMQALIVGRDI 393 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: 334 Number of extensions: 11 Number of successful extensions: 4 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: 400 Length adjustment: 30 Effective length of query: 345 Effective length of database: 370 Effective search space: 127650 Effective search space used: 127650 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 Apr 09 2024. 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