Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate CCNA_01747 CCNA_01747 3-oxoacyl-(acyl-carrier protein) reductase
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__Caulo:CCNA_01747 Length = 246 Score = 104 bits (260), Expect = 2e-27 Identities = 78/257 (30%), Positives = 128/257 (49%), Gaps = 19/257 (7%) Query: 3 QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDA 62 + A+V G +G + L G HV ++ ES L + R A + Sbjct: 7 KTALVTGATGGIGGAIARALHAQGAHVVLSGTRESALAELKAELGER-----ASTVVANL 61 Query: 63 TDEASVEALARAVDETFGRA-DLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSR 121 +D V+ L +E G D+++ +AGV + I + + D+D ++VNL GYF SR Sbjct: 62 SDAEQVDGLVAKAEEAAGAPLDIVIANAGVTRDGLIVRMKDEDWDTVIKVNLEGYFRLSR 121 Query: 122 EFSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHS 181 +K M++ GRII I S G G+ + Y+A+K G +G +++LA +LA G+TV+ Sbjct: 122 AAAKGMMKRRA-GRIIGITSIVGVTGNPGQTNYAASKAGMIGFSKALAQELASRGVTVNC 180 Query: 182 LMLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDK 241 + G + SPM +L Q +K GI + +P + + D+ ++ ASD+ Sbjct: 181 VAPG-FIASPMTDALNEQ--QKAGI---------LSTIPAGKLGEGADIAAACVYLASDQ 228 Query: 242 AAYCTGQSINVTGGQVM 258 A Y TGQ+++V GG M Sbjct: 229 AGYVTGQTLHVNGGMAM 245 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: 178 Number of extensions: 8 Number of successful extensions: 3 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: 246 Length adjustment: 24 Effective length of query: 235 Effective length of database: 222 Effective search space: 52170 Effective search space used: 52170 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