Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate HSERO_RS22235 HSERO_RS22235 short-chain dehydrogenase
Query= CharProtDB::CH_091827 (259 letters) >FitnessBrowser__HerbieS:HSERO_RS22235 Length = 690 Score = 121 bits (303), Expect = 4e-32 Identities = 86/256 (33%), Positives = 131/256 (51%), Gaps = 4/256 (1%) Query: 3 QVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYGF-GAD 61 ++A+V GGG +G + L AEG V + DI A + AQ+ ++G A G AD Sbjct: 429 RIALVTGGGGGIGQAVARQLLAEGACVMLTDIDQS-ALDSAQQSLLKHGGPDAIGVVRAD 487 Query: 62 ATSEQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFLCAR 121 TSE V + V FG +DLLV +AGIA A+ + D L + R+L V GYFL +R Sbjct: 488 ITSEADVTTILNSVALRFGGIDLLVSNAGIASASPLQDTSLEVWQRNLSVLATGYFLVSR 547 Query: 122 EFSRLMIRDGIQGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHS 181 M+ G+ G I+ + SK+G V S S Y AK + L + +AL+ A +GI V+ Sbjct: 548 AAFSSMLTQGLGGSIVYVASKNGLVASAGASAYCTAKAAEIHLARCIALEGAPHGIRVNV 607 Query: 182 LMLGNLLKSPMF--QSLLPQYATKLGIKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYAS 239 + +++ + A I+ D VE++Y + LKR +D+ + F+AS Sbjct: 608 VNPDAVIRGSRIWDGKWKEERAASNKIEADDVEEFYRQRSMLKRSVLPEDIAEAVYFFAS 667 Query: 240 PKASYCTGQSINVTGG 255 K++ TG +NV G Sbjct: 668 EKSAKSTGNILNVDAG 683 Lambda K H 0.320 0.137 0.391 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: 387 Number of extensions: 17 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: 259 Length of database: 690 Length adjustment: 32 Effective length of query: 227 Effective length of database: 658 Effective search space: 149366 Effective search space used: 149366 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 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