Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_011157858.1 TX73_RS11755 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000195775.1:WP_011157858.1 Length = 375 Score = 564 bits (1454), Expect = e-165 Identities = 280/375 (74%), Positives = 323/375 (86%) Query: 1 MIPNDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGC 60 MI N+ Q QIRD ARDFA ERL P AA D H FP+ + EM LGF GMLVPE +GG Sbjct: 1 MILNELQTQIRDTARDFAHERLAPTAAARDAAHAFPRAELTEMGQLGFLGMLVPEAYGGS 60 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGA 120 +TG +AY +ALEEIAAGDGACSTI+SVH+SV C+PIL +GT+EQK+RFL LASG +G Sbjct: 61 ETGMVAYTLALEEIAAGDGACSTIVSVHSSVACMPILKFGTEEQKQRFLPKLASGEWIGG 120 Query: 121 FALTEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180 FALTEPQAGSDAS L+T AR +GDHYV+NG KQFITSGQN ++I+FAVTDPSAGK+GI+ Sbjct: 121 FALTEPQAGSDASNLRTTARRDGDHYVINGAKQFITSGQNGQLIILFAVTDPSAGKKGIT 180 Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGG 240 AFIVPTD+PGY+V RVEDKLGQH+SDTCQ+ F D+++P RLG EGEG +IAL+NLEGG Sbjct: 181 AFIVPTDTPGYEVVRVEDKLGQHSSDTCQLAFNDMRIPADLRLGAEGEGLKIALSNLEGG 240 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+GIASQ+VGMARAAFEAARDYAR+R +FGKPIIEHQAVAFRLADMAT+IA ARQMV YA Sbjct: 241 RIGIASQAVGMARAAFEAARDYARDRVTFGKPIIEHQAVAFRLADMATRIAAARQMVLYA 300 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIY 360 A+LR++G P L EASMAKLFASE AE VCSSA+QTLGGYGYL DFPVERIYRDVRVCQIY Sbjct: 301 ASLREAGLPCLTEASMAKLFASETAEAVCSSAIQTLGGYGYLKDFPVERIYRDVRVCQIY 360 Query: 361 EGTSDIQRMVISRNL 375 EGTSD+QR+VI+RNL Sbjct: 361 EGTSDVQRIVIARNL 375 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: 467 Number of extensions: 11 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: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 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