Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_015818306.1 TERTU_RS10525 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000023025.1:WP_015818306.1 Length = 1286 Score = 157 bits (397), Expect = 2e-42 Identities = 112/361 (31%), Positives = 178/361 (49%), Gaps = 7/361 (1%) Query: 15 RDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGYLAYAMALEEI 74 R +A+ R+ +A D P + + A G GM VPEQ+ G +E++ Sbjct: 624 RQYAETRIN--SALIDERRCVPPYIVMDFASQGLLGMCVPEQYAGQAMTVSDSLRVIEQL 681 Query: 75 AAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALTEPQAGSDASG 134 AA D + ++SVH+ +G PILNYG+ K+ FL +A G +LGA A+TEP AGS+ Sbjct: 682 AAIDANLAAMVSVHHVLGTRPILNYGSQLTKDVFLPKIAEGRILGALAITEPGAGSNPHA 741 Query: 135 LKTRAR-LEGDHYVLNGCKQFITSGQNAGVVIVFA-VTDPSAGKRGISAFIVPTDSPGYK 192 + AR +++ G K +I +G +GV+ F V D +G++AF + G Sbjct: 742 ISATARPAPQGGWLITGEKCWIGNGSWSGVINTFVQVKDEQGNPKGLTAFAIEQGRSGMW 801 Query: 193 VARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGIASQSVGMA 252 + +G +I F+DV V ++ LG G+G IA + GR+ IA+ S+G Sbjct: 802 MGEEAPTMGMRGMVQNRIHFKDVHVTESDMLGRVGQGMEIAQDAMMHGRLVIAAMSLGGL 861 Query: 253 RAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGK--PA 310 + A + YA+ R+ + E RL++M IA + MV L D G P+ Sbjct: 862 KRAAQLMTRYAQRRDVASGKLFESSVSIQRLSEMHATIAAIQAMVRSLGELIDQGVEIPS 921 Query: 311 LVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTSDIQRMV 370 + A+ K A E K +Q LGG GY + V ++ RD+R+ +I+EG ++ + Sbjct: 922 EIYAA-CKTSAPEFLWKGVDQLMQMLGGRGYTENNAVPQLMRDLRLFRIFEGPTEALNVF 980 Query: 371 I 371 I Sbjct: 981 I 981 Lambda K H 0.320 0.135 0.394 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: 915 Number of extensions: 36 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: 1286 Length adjustment: 39 Effective length of query: 336 Effective length of database: 1247 Effective search space: 418992 Effective search space used: 418992 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: 54 (25.4 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