Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_047215429.1 PATSB16_RS18075 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >NCBI__GCF_001931675.1:WP_047215429.1 Length = 327 Score = 428 bits (1101), Expect = e-125 Identities = 210/323 (65%), Positives = 251/323 (77%), Gaps = 3/323 (0%) Query: 16 IKGIDKSATRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEV 75 I GI +R+ LGTWAIGGWMWGG DD ASI TI AID GIN+IDTAP YG GHAEEV Sbjct: 8 IDGIATPVSRIGLGTWAIGGWMWGGADDTASIATIRNAIDQGINLIDTAPVYGFGHAEEV 67 Query: 76 VGKAIKGQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQV 135 VGKA++G+R+ +IATKV L+W D ++RNS+ +RI+ EIEDSLRRL TD IDLYQV Sbjct: 68 VGKALEGRREQAVIATKVALEWG---DDGIKRNSTPARIRTEIEDSLRRLRTDRIDLYQV 124 Query: 136 HWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFERE 195 HWPDP VP EETA LE LR+EGKI +IGVSN+S +QMD F + A LA Q PYNLFER Sbjct: 125 HWPDPRVPFEETAAELEKLRQEGKILAIGVSNFSPEQMDVFGRAARLAAVQPPYNLFERA 184 Query: 196 IDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAA 255 I+ D+LPYAK + L VL YGALCRGLLSGRM+A F GDDLR DPKFQ PRF YLAA Sbjct: 185 IEADVLPYAKSHGLTVLAYGALCRGLLSGRMSASTRFDGDDLRNHDPKFQPPRFAQYLAA 244 Query: 256 VEELKKLAKEHYNKSVLALAIRWMLEQGPTLALWGACKPEQIDGIDEVFGWQISDEDLKQ 315 V L +L+ + + KSVLALAIRW+L+QGPT+ALWGA +P+Q+ GID+ FGW++S DL Sbjct: 245 VGALAQLSHDRHGKSVLALAIRWILDQGPTIALWGARRPDQLRGIDDAFGWRLSPGDLAD 304 Query: 316 IDAILAKNIPNPIGAEFMAPPPR 338 IDA+LA++I +P+G EFMAPP R Sbjct: 305 IDALLARHITSPVGPEFMAPPLR 327 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: 406 Number of extensions: 13 Number of successful extensions: 2 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: 327 Length adjustment: 28 Effective length of query: 312 Effective length of database: 299 Effective search space: 93288 Effective search space used: 93288 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 24 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