Align D-xylose dehydrogenase; NADP-dependent D-xylose dehydrogenase; EC 1.1.1.179 (characterized)
to candidate SMc04133 SMc04133 oxidoreductase
Query= SwissProt::Q8GAK6 (388 letters) >FitnessBrowser__Smeli:SMc04133 Length = 382 Score = 450 bits (1157), Expect = e-131 Identities = 221/381 (58%), Positives = 275/381 (72%), Gaps = 5/381 (1%) Query: 9 VAMNGITGRMGYRQHLLRSILPIRDAGGFTLEDGTKVQIEPILVGRNEAKIRELAEKHKV 68 + ++G+TGRMGY QHL+RSIL IRD GG TL+ G +++I+PI+VGRN K+ +LA++H + Sbjct: 6 IILHGVTGRMGYNQHLVRSILAIRDRGGITLQSGERLEIDPIIVGRNRDKMEQLAKRHDI 65 Query: 69 AEWSTDLDSVVNDPTVDIIFDASMTSLRAATLKKAMLAGKHIFTEKPTAETLEEAIELAR 128 A WSTDLD+ + DP I FDA T +RA + +A+ AGKH++ EKP ++ L A++LAR Sbjct: 66 ARWSTDLDAALADPNDQIFFDAGTTLMRAELIGRALDAGKHVYCEKPISDDLRTAVKLAR 125 Query: 129 IGKQAGVTAGVVHDKLYLPGLVKLRRLVDEGFFGRILSIRGEFGYWVFEGDVQA-AQRPS 187 + +G+ GVV DKL+LPGL KL L D GFFG+ILS+RGEFGYWVFEGD AQRPS Sbjct: 126 KARASGLKHGVVQDKLFLPGLRKLALLRDSGFFGKILSVRGEFGYWVFEGDWGVPAQRPS 185 Query: 188 WNYRKEDGGGMTTDMFCHWNYVLEGIIGKVKSVNAKTATHIPTRWDEAGKEYKATADDAS 247 WNYRK+DGGG+ DM CHW YVL+ + G+VK+V+ ATHIP+R DE G+ Y DDA+ Sbjct: 186 WNYRKKDGGGIILDMLCHWRYVLDNLFGEVKAVSCLGATHIPSRIDEQGRAYDCDTDDAA 245 Query: 248 YGIFELETPGGDDVIGQINSSWAVRVYRDELVEFQVDGTHGSAVAGLNKCVAQQRAHTPK 307 Y FELE GG ++ INSSWAVRV RD+LV FQVDGTHGSAVAGL KC Q R +TPK Sbjct: 246 YATFELE--GG--IVAHINSSWAVRVRRDDLVTFQVDGTHGSAVAGLTKCWTQHRVNTPK 301 Query: 308 PVWNPDLPVTESFRDQWQEVPANAELDNGFKLQWEEFLRDVVAGREHRFGLLSAARGVQL 367 PVWNPD P T F W EVP DNGFK QWE FLR V GL + A+GVQL Sbjct: 302 PVWNPDQPQTIDFYRTWDEVPDTQAFDNGFKAQWEMFLRHVAEDGPWPHGLEAGAKGVQL 361 Query: 368 AELGLQSNDERRTIDIPEITL 388 AELGL+S ERR +D+PE+ L Sbjct: 362 AELGLKSWAERRWLDVPELEL 382 Lambda K H 0.318 0.136 0.406 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: 561 Number of extensions: 20 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: 388 Length of database: 382 Length adjustment: 30 Effective length of query: 358 Effective length of database: 352 Effective search space: 126016 Effective search space used: 126016 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 (21.7 bits) S2: 50 (23.9 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