Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate GFF2696 PS417_13755 oxidoreductase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__WCS417:GFF2696 Length = 249 Score = 140 bits (354), Expect = 2e-38 Identities = 96/253 (37%), Positives = 132/253 (52%), Gaps = 18/253 (7%) Query: 4 RLAGKTALITAAGQGIGLATAELFAREGARVIATDIRID------GLAGKPVEARKLDVR 57 RL GK A++T GIGLATA FA EGA+V+ R D L G A + D+ Sbjct: 3 RLNGKIAVVTGGNSGIGLATAIRFATEGAQVVIVGRRQDELDKALALIGHEAIAIQGDIS 62 Query: 58 --DDAA--IKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAF 113 DD A + A+ G VDVLF AG I +EE +D F +NVK ++ Sbjct: 63 KLDDLARIFTQIKADKGRVDVLFANAGLGDFQPIGSITEESFDRTFGINVKGTLFTVQNA 122 Query: 114 LPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAIC 173 LP M GS + ++ + + G P YSA+KAA+ +S A D G+R N + Sbjct: 123 LPLM---HAGSSVILTGSTTGTMGTPAFSVYSATKAALRNFARSWALDLKGSGIRVNVLS 179 Query: 174 PGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSF 233 PG +++P L+ + Q + D A+ P+GRIGKPEE+AA AL+L SDESSF Sbjct: 180 PGPISTPGLDLALSGTGQKEAIIDD-----MTAQVPLGRIGKPEEVAAAALFLASDESSF 234 Query: 234 TTGHAHVIDGGWS 246 TG +DGG++ Sbjct: 235 MTGSEMFVDGGFA 247 Lambda K H 0.320 0.133 0.381 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: 162 Number of extensions: 7 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: 247 Length of database: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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