Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate RR42_RS34260 RR42_RS34260 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Cup4G11:RR42_RS34260 Length = 342 Score = 176 bits (446), Expect = 8e-49 Identities = 110/331 (33%), Positives = 168/331 (50%), Gaps = 29/331 (8%) Query: 36 GEKDVRLKVLFCGVCHSDHHMIHNNWGFT-TYPIVPGHEIVGVVTEVGSKVEKVKVGDNV 94 G +++K+ GVCH+D H +W T P +PGHE VG V+ VG+ V +VK GD V Sbjct: 28 GRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLPFIPGHEGVGYVSAVGAGVSRVKEGDRV 87 Query: 95 GIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPK 154 G+ L +C CE C E+ CE +T G +GGY + +VAD +++ P Sbjct: 88 GVPWLYSACGYCEHCLQGWETLCEKQQNT-------GYSVNGGYGEYVVADPNYVGLLPD 140 Query: 155 NLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVID 214 ++ AP+LCAG+T Y LK +PG + + G+GGLGHVAV+ A+A G +V +D Sbjct: 141 SVGFVEIAPILCAGVTVYKGLKVTD-TRPGQWVVISGIGGLGHVAVQYARAMGLRVAAVD 199 Query: 215 ISESKRKEALEKLGAD-----------SFLLNSDQEQMKGARSSLDGIIDTVPVNHPLAP 263 I + K+ E KLGA+ +FL Q+++ GA G + T Sbjct: 200 I-DDKKLELARKLGAEVTVNARTTDPVAFL----QKEIGGAH----GALVTAVSPKAFGQ 250 Query: 264 LFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITA 323 +++ G + + G P F P+F ++ + G+I G + QE LDFAA + A Sbjct: 251 AIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSDLQESLDFAAHGAVKA 310 Query: 324 DVEVIPMDYVNTAMERLVKSDVRYRFVIDIA 354 V P++ +N R+ D+ R V+D A Sbjct: 311 TVSTAPLEKINEIFTRMRAGDIEGRVVMDFA 341 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: 270 Number of extensions: 16 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: 342 Length adjustment: 29 Effective length of query: 336 Effective length of database: 313 Effective search space: 105168 Effective search space used: 105168 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