Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate GFF2883 HP15_2827 oxidoreductase, aldo/keto reductase family
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Marino:GFF2883 Length = 329 Score = 386 bits (991), Expect = e-112 Identities = 190/329 (57%), Positives = 240/329 (72%), Gaps = 3/329 (0%) Query: 12 DKISIKGIDKSATRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGH 71 DK + D T V LGTWAIGGWMWGGTD+ SI TIHRAID GI ++DTAP YG G Sbjct: 2 DKRTFGNTDIQVTPVGLGTWAIGGWMWGGTDEAQSIDTIHRAIDKGIGLVDTAPVYGFGR 61 Query: 72 AEEVVGKAIK-GQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYI 130 +EE+VGKA+ G+RD + +ATKV L+W D+ + R++SASRI++E+EDSL+RL TD I Sbjct: 62 SEEIVGKALSDGRRDQVALATKVALNWNDDHDK-VWRDASASRIEREVEDSLKRLQTDRI 120 Query: 131 DLYQVHWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYN 190 D+YQVHWPDP P+EETA LE L + GKIR+IGVSN++ QMDE +K L Q PYN Sbjct: 121 DIYQVHWPDPKTPMEETARALEKLYQAGKIRAIGVSNFTPSQMDELQKSVPLHSLQPPYN 180 Query: 191 LFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFE 250 LFEREI++DILPY ++N + + YG LCRG L+G+M D FTGDDLRK DPKFQ R+ Sbjct: 181 LFEREIEQDILPYCRENGIATITYGGLCRGFLTGKMREDTQFTGDDLRKNDPKFQGDRYR 240 Query: 251 HYLAAVEELKKLAKEHYNKSVLALAIRWMLEQ-GPTLALWGACKPEQIDGIDEVFGWQIS 309 YL AV EL A+E Y KSVLALA+RW+++Q G T ALWGA +PEQ+D +DE+ GW + Sbjct: 241 QYLNAVAELDAFARERYQKSVLALALRWLVDQPGVTTALWGARRPEQLDPVDEIDGWSLD 300 Query: 310 DEDLKQIDAILAKNIPNPIGAEFMAPPPR 338 + +ID IL + I +P+G EFMAPP R Sbjct: 301 KNAMAEIDGILDRCITDPVGPEFMAPPTR 329 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: 412 Number of extensions: 13 Number of successful extensions: 4 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: 329 Length adjustment: 28 Effective length of query: 312 Effective length of database: 301 Effective search space: 93912 Effective search space used: 93912 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