Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate AZOBR_RS02275 AZOBR_RS02275 aldo-keto reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__azobra:AZOBR_RS02275 Length = 347 Score = 121 bits (303), Expect = 3e-32 Identities = 108/345 (31%), Positives = 159/345 (46%), Gaps = 49/345 (14%) Query: 24 TRVALGTWAIGGWMWGGTDDDASIKT-IHRAIDLGINIIDTAPAYG-------RGHAEEV 75 T +++ +G WG + +A + A+ G+N DTA Y G EEV Sbjct: 9 TGLSVSAIGLGTMTWGRQNSEAEGHAQMDYALGEGVNFWDTAEMYAIPPTADTYGRTEEV 68 Query: 76 VGKAIK--GQRDNLIIATKV------GLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGT 127 +G K G+RD +I+A+KV G W + + R + I +E SLRRL T Sbjct: 69 IGTWFKATGKRDQVILASKVVGASDGGFAWVRNGEAKLDR----ANIFAAVEASLRRLQT 124 Query: 128 DYIDLYQVHWPDPL-----------------VPIEETATILEALRKEGKIRSIGVSNYSV 170 DYIDLYQ+HWPD PIEET + L+ L GK+R IGVSN S Sbjct: 125 DYIDLYQLHWPDRATNRFGARNYVHRPEKDGTPIEETLSALDELVTSGKVRHIGVSNESP 184 Query: 171 QQMDEFKKYAE------LAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSG 224 + +F K AE +A Q+ YNL R ++ + + + D+ +L Y L G L+G Sbjct: 185 WGVMQFLKLAEDKGLPRIASIQNAYNLLNRTFEQGLAEVSLREDVGLLAYSPLAAGTLTG 244 Query: 225 RMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQGP 284 + D A R D + + + A E +A+ H S +AI + L+Q P Sbjct: 245 KY-LDGAVPAGTRRALDHRKSRYATVNADVATREYLDVARRH-GLSPTQMAIAFTLQQ-P 301 Query: 285 TLA--LWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAKNIPNP 327 +A L GA E + +SDE +K I+A+ A+ P+P Sbjct: 302 FVASSLIGATTMEDLKSNIAAVDVTLSDEVMKDIEAVNAR-YPDP 345 Lambda K H 0.317 0.136 0.407 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: 275 Number of extensions: 16 Number of successful extensions: 3 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: 340 Length of database: 347 Length adjustment: 29 Effective length of query: 311 Effective length of database: 318 Effective search space: 98898 Effective search space used: 98898 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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