Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate WP_011781364.1 MVAN_RS21110 NAD(P)-dependent oxidoreductase
Query= CharProtDB::CH_091826 (259 letters) >NCBI__GCF_000015305.1:WP_011781364.1 Length = 252 Score = 113 bits (282), Expect = 4e-30 Identities = 81/255 (31%), Positives = 133/255 (52%), Gaps = 15/255 (5%) Query: 5 AVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDATD 64 A+V G +G+ + + LA AG V V D+++ A +A I+ GRA +D +D Sbjct: 12 ALVTGAAGGIGSAVAQALADAGAAVLVTDIDKDAAAVVAQRISD--SGGRAEAAALDVSD 69 Query: 65 EASVEALA-RAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSREF 123 S +A A +A T G ++V +AGV + A + F L ++++G F ++ Sbjct: 70 RDSADAAAAQAAALTGGALHIVVNNAGVTRPAMFDKTTPESFRLLFDIHVMGAFNVTQAA 129 Query: 124 SKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLM 183 + DG GRI+ + S +G G+ YSAAK G +G T+SLA +LA GITV++ Sbjct: 130 LPFIPIDGT-GRIVNVTSAAGLTGTLGQVNYSAAKAGIIGFTKSLARELATKGITVNA-- 186 Query: 184 LGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDKAA 243 L L +PM +++ T E+ ++++P+KR + ++ +F ASD A+ Sbjct: 187 LAPLAATPMTETIR---------TNEKFAANMMNRIPMKRWAEPSEIAGAFVFMASDAAS 237 Query: 244 YCTGQSINVTGGQVM 258 Y TGQ + V GG V+ Sbjct: 238 YVTGQVLPVDGGMVI 252 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: 188 Number of extensions: 12 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: 252 Length adjustment: 24 Effective length of query: 235 Effective length of database: 228 Effective search space: 53580 Effective search space used: 53580 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: 47 (22.7 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