Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__HerbieS:HSERO_RS04830 Length = 341 Score = 162 bits (409), Expect = 2e-44 Identities = 103/310 (33%), Positives = 154/310 (49%), Gaps = 13/310 (4%) Query: 48 GVCHSDHHMIHNNWGFT-TYPIVPGHEIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSC 106 GVCH+D H H +W T P +PGHE G V VG+ V+ VK GD VG+ L +C C Sbjct: 40 GVCHTDLHAAHGDWPVKPTPPFIPGHEGTGYVAAVGAGVKHVKEGDRVGVPWLHTACGCC 99 Query: 107 ESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLC 166 C E+ C +T G +G +++ +AD F+ P NL AP+LC Sbjct: 100 SPCRTGWETLCAEQQNT-------GYSVNGSFAEYGLADPKFVGHLPDNLDFGPAAPVLC 152 Query: 167 AGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEK 226 AG+T Y LK + +PG + + G+GGLGH+AV+ AKA G V DI E K A +K Sbjct: 153 AGVTVYKGLKETEV-RPGEWVVISGIGGLGHMAVQYAKAMGMHVVAADIHEDKLALA-KK 210 Query: 227 LGADSFLLNSDQE---QMKGARSSLDGIIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKP 283 LGAD + + +++ G + T + F L+ G + +VG P Sbjct: 211 LGADLTVDGRNHNAVAEVQRIIGGAHGALVTAVSPKAMEQAFGFLRARGTMALVGLPPGD 270 Query: 284 FELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKS 343 LPVF+ + R + G+I G ++ +E L FAA+ + A +D +N R+ + Sbjct: 271 ISLPVFNTVLKRITVRGSIVGTRQDLEESLVFAAEGKVAAHFTWDKLDNINAIFARMEEG 330 Query: 344 DVRYRFVIDI 353 + R V+D+ Sbjct: 331 KIDGRIVLDL 340 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: 284 Number of extensions: 17 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: 341 Length adjustment: 29 Effective length of query: 336 Effective length of database: 312 Effective search space: 104832 Effective search space used: 104832 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