Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_041096890.1 SUTH_RS02660 acyl-CoA dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983 (375 letters) >NCBI__GCF_000828635.1:WP_041096890.1 Length = 379 Score = 535 bits (1379), Expect = e-157 Identities = 267/375 (71%), Positives = 312/375 (83%) Query: 1 MIPNDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGC 60 MI +Q+QIRDM RDFA+E+L P AAEWDR FP+E + + LG GM+VPEQWGG Sbjct: 1 MILTSEQEQIRDMLRDFAREQLAPKAAEWDRTSHFPREELRALGELGVCGMVVPEQWGGA 60 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGA 120 Y++ A+ALEEIAAGDGA STI+SV NSV C PI +GTD QKE++LK LASG LG Sbjct: 61 GLDYVSLALALEEIAAGDGATSTIISVQNSVVCGPINAFGTDAQKEKYLKKLASGEWLGC 120 Query: 121 FALTEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180 F LTEP GSDA+ ++TRA +GDH+VLNG KQFIT+G+NA V +VFAVTDP AGK+GIS Sbjct: 121 FCLTEPHVGSDAAAIRTRAVRDGDHWVLNGVKQFITTGKNAQVAVVFAVTDPGAGKKGIS 180 Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGG 240 AFIVP D+PGY VARVE+KLGQHASDT QILFE+ ++P N LG EG+GYRIAL+NLEGG Sbjct: 181 AFIVPADAPGYIVARVEEKLGQHASDTAQILFENCRIPAENLLGAEGQGYRIALSNLEGG 240 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+GI++Q+VGMARAAFEAA Y+ ER+SFGKPI EHQAV FRLADMATQI VARQMVH+A Sbjct: 241 RIGISAQAVGMARAAFEAALHYSHERQSFGKPIFEHQAVNFRLADMATQIEVARQMVHHA 300 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIY 360 AALRD+G+P L EASMAKLFASEMAEKVCS A+Q GGYGY++DFPVERIYRDVRVCQIY Sbjct: 301 AALRDAGRPCLKEASMAKLFASEMAEKVCSDAIQIHGGYGYVSDFPVERIYRDVRVCQIY 360 Query: 361 EGTSDIQRMVISRNL 375 EG SDIQR+VI R+L Sbjct: 361 EGASDIQRLVIGRSL 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: 475 Number of extensions: 18 Number of successful extensions: 1 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: 379 Length adjustment: 30 Effective length of query: 345 Effective length of database: 349 Effective search space: 120405 Effective search space used: 120405 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