Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate GFF2840 HP15_2784 3-ketoacyl-(acyl-carrier-protein) reductase
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__Marino:GFF2840 Length = 247 Score = 110 bits (274), Expect = 4e-29 Identities = 81/257 (31%), Positives = 130/257 (50%), Gaps = 17/257 (6%) Query: 3 QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLN-ESNANRLADTINSRYGAGRAYGFKVD 61 +VA+V G + +G + LAQ G VA+ + +S +A I + RA FK D Sbjct: 7 KVALVTGASRGIGRHIALQLAQRGADVAINYRSRQSEGEEVAKEIEAT--GVRALSFKAD 64 Query: 62 ATDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSR 121 + +L R V E +GR D+LV +AG+ K + + D++ L NL + Sbjct: 65 LSKMPEARSLVRQVQEQWGRIDILVNNAGITKDKSMKKLTDDDWNDVLDTNLGSVYATCS 124 Query: 122 EFSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHS 181 E K+M+ D GRII I S G+ G+ + Y+A+K G + T++LAL++A+Y ITV++ Sbjct: 125 EVLKIMM-DQKYGRIINITSFVGQAGNFGQANYAASKGGIIAFTKTLALEMAKYNITVNA 183 Query: 182 LMLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDK 241 + +P F E L PE + + +VP+ R +++ ++F A++ Sbjct: 184 I-------APGFTE-----TEMLAQVPENIREQIIARVPMGRFGKPEEIARAVVFLAAE- 230 Query: 242 AAYCTGQSINVTGGQVM 258 Y TGQ INV GG M Sbjct: 231 GDYITGQQINVNGGVYM 247 Lambda K H 0.319 0.136 0.387 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: 181 Number of extensions: 15 Number of successful extensions: 5 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: 259 Length of database: 247 Length adjustment: 24 Effective length of query: 235 Effective length of database: 223 Effective search space: 52405 Effective search space used: 52405 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 (21.7 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