Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate BWI76_RS03140 BWI76_RS03140 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Koxy:BWI76_RS03140 Length = 339 Score = 227 bits (578), Expect = 4e-64 Identities = 117/339 (34%), Positives = 193/339 (56%), Gaps = 13/339 (3%) Query: 16 WAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEIV 75 +AA++ LS +++ +DV ++V +CG+CHSD MI N WG ++YP+V GHE++ Sbjct: 7 YAAKEAGADLSLWEYDAGDLKPEDVEVQVEYCGICHSDLSMIDNEWGMSSYPLVAGHEVI 66 Query: 76 GVVTEVGSKVEK--VKVGDNVGIGCLVGSCRSCESCCDNRESHC-ENTIDTYGSIYFDGT 132 G V +GS + +KVG VGIG SC C++C +C E ++ T Sbjct: 67 GRVAALGSAAQDKGLKVGQKVGIGWTARSCGHCDACISGNHVNCLEGSVPTI-------- 118 Query: 133 MTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGL 192 + GG++D + AD +++ P+N+ L+S P+LC GIT + PL + + +++GV+G+ Sbjct: 119 INRGGFADKLRADWQWVIPLPENVDLESAGPMLCGGITVFKPLLMHHVTA-NSRVGVIGI 177 Query: 193 GGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGII 252 GGLGH+A+K+ A GA+VT + +K +E L +GAD + + D E +K D II Sbjct: 178 GGLGHIAIKLLHAMGAEVTAFSSNPAKEQEVLA-MGADRVVNSRDPEALKALAGQFDLII 236 Query: 253 DTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEM 312 +TV V+ P F+ L G VGA KPF +P F+L+ G + + G+ G E +++ Sbjct: 237 NTVAVDLDWQPYFEALAYGGNFHTVGAVMKPFPVPAFTLIGGDRSISGSATGNPAELRKL 296 Query: 313 LDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVI 351 + FA + + E+ PM +N A++ + + RYR V+ Sbjct: 297 MKFAGRSKVAPTTELFPMSQINEALKHVREGKARYRVVL 335 Lambda K H 0.319 0.137 0.415 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: 283 Number of extensions: 18 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: 365 Length of database: 339 Length adjustment: 29 Effective length of query: 336 Effective length of database: 310 Effective search space: 104160 Effective search space used: 104160 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: 49 (23.5 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