Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BWI76_RS19345 BWI76_RS19345 D-arabinitol 4-dehydrogenase
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Koxy:BWI76_RS19345 Length = 455 Score = 229 bits (584), Expect = 2e-64 Identities = 134/399 (33%), Positives = 211/399 (52%), Gaps = 6/399 (1%) Query: 31 HIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGD 90 HIG+G FHRAHQA+Y L+ +G+ W I +R++ + LA Q + L + Sbjct: 9 HIGLGSFHRAHQAWYLHRLIASGDKR-WHIAAGNIRNDAEQVVQALAAQGGRYVLETVSP 67 Query: 91 TDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLP 150 + E I SI +L + Q LI++ A+P+ ++++ T+TEGGY ++ + + P Sbjct: 68 EGEREYEEITSIQKLLPWQAGLQPLINEGANPQTKVIAFTVTEGGYYLNTRH-QLETSNP 126 Query: 151 QIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALH 210 +Q DLA KT++G + L +R A T+++CDN+ HNG ++ F L Sbjct: 127 DLQADLA--GECKTIYGTLARILEKRMADNAGPLTLLNCDNVRHNGERFHDGMVEFLQLT 184 Query: 211 NAE-LHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDK 269 + + DW+ + + PN MVDRITP + ++ + GIDD PV+ E F+QWV+E+ Sbjct: 185 GKQAVIDWMAVNTTCPNTMVDRITPRPAADLPARIKAQTGIDDKAPVMGETFIQWVVENN 244 Query: 270 FVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVA 329 F + RP E VGV+ V PYEE KI +LN SH + + G L G +++HE+ A Sbjct: 245 FRDERPKLEAVGVEMVASVIPYEEAKIRILNASHSCIAWAGTLIGQQYIHESTLTDFIYA 304 Query: 330 YMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPT 389 Y+ DV P L GIDL Y+ ++ RF+N I D +RV +DG SK P PT Sbjct: 305 IADRYVTEDVIPCLGD-NGIDLPTYRDVVLKRFTNPYIQDTNQRVAADGFSKIPAMIAPT 363 Query: 390 INRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPD 428 + G E A++ A + ++++ + + Y D Sbjct: 364 LQECYQRGVRPEATAMLPALFFVFMEQWHKGTLPYQYQD 402 Lambda K H 0.321 0.137 0.414 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: 560 Number of extensions: 33 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: 493 Length of database: 455 Length adjustment: 33 Effective length of query: 460 Effective length of database: 422 Effective search space: 194120 Effective search space used: 194120 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 (21.8 bits) S2: 51 (24.3 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