Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate AZOBR_RS13230 AZOBR_RS13230 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__azobra:AZOBR_RS13230 Length = 340 Score = 169 bits (427), Expect = 1e-46 Identities = 103/320 (32%), Positives = 157/320 (49%), Gaps = 13/320 (4%) Query: 36 GEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYP-IVPGHEIVGVVTEVGSKVEKVKVGDNV 94 G + +K+ GVCH+D H +W P +PGHE VG V VG+ V VK GD V Sbjct: 28 GPGQILVKIEASGVCHTDLHAADGDWPVKPNPPFIPGHEGVGTVAAVGTGVTAVKEGDRV 87 Query: 95 GIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPK 154 G+ L +C C C E+ C+ +T G +GG+++ +AD +++ P Sbjct: 88 GVPWLHTACGHCRQCLAGWETLCDLQQNT-------GYSVNGGFAEYTLADPNYVGHLPD 140 Query: 155 NLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVID 214 L + AP+LCAG+T Y LK KPG + + G+GGLGH+AV+ AKA G V +D Sbjct: 141 RLDWEMAAPILCAGVTVYKGLKETDT-KPGDTVVISGIGGLGHIAVQYAKAMGLDVIAVD 199 Query: 215 ISESKRKEALEKLGADSFLLNSDQE---QMKGARSSLDGIIDTVPVNHPLAPLFDLLKPN 271 IS+ K A +GAD+ + + ++K G++ T H +L Sbjct: 200 ISDEKLALA-RAMGADAAINAKTTDPVAEVKALCGGAQGVLVTAVSRHAFNQALGMLAKR 258 Query: 272 GKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVIPMD 331 G + +VG P FEL +FS + RK + G+I G + E L FA + V +D Sbjct: 259 GTMALVGLPPGSFELDIFSTVLMRKTIRGSIVGTRLDLAECLQFAGDGKVKVHYSVEHLD 318 Query: 332 YVNTAMERLVKSDVRYRFVI 351 +N R+ +++ R V+ Sbjct: 319 NINNVFSRMRNNEIDGRVVM 338 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: 258 Number of extensions: 11 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: 340 Length adjustment: 29 Effective length of query: 336 Effective length of database: 311 Effective search space: 104496 Effective search space used: 104496 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 Apr 09 2024. 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