Align D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) (characterized)
to candidate H281DRAFT_02753 H281DRAFT_02753 Predicted dehydrogenase
Query= BRENDA::Q5UY95 (360 letters) >FitnessBrowser__Burk376:H281DRAFT_02753 Length = 444 Score = 171 bits (432), Expect = 4e-47 Identities = 118/349 (33%), Positives = 174/349 (49%), Gaps = 21/349 (6%) Query: 22 DNPVRFAMIGVGWWTTEQAMPAVDAGDLCETTVLVSSDREKAADVAADSETVEHAI-TYE 80 D V +A++G+G + +Q +PA+ + LVS DR KA VA E I Y+ Sbjct: 89 DERVGYAIVGLGRLSLDQILPALAQCKYSKVVALVSGDRAKALRVARQYGVREADIYDYQ 148 Query: 81 EFHDGAASDAYDAVYIVTPNALHLPYVETAAELDKAILCEKPMEATIERAERMVEVCDEH 140 F A + VYIV PN +H + +A + K +LCEKPM + E MV Sbjct: 149 NFERLADNPRVQVVYIVLPNGMHKEFTLRSANIGKHVLCEKPMANSAADCEAMVRAMKRA 208 Query: 141 DATLMIAYRMHTEPAVRRAKDLIDEGYIGEPL--FVHGNMTEPILELVPDPDQWRLDGEL 198 + LMIAYR EP R ++ E +G PL FV GN + V DP QWRL L Sbjct: 209 NRKLMIAYRSQYEPMDRMIAKMVKEKQLG-PLREFVAGNS-----QNVGDPGQWRLKKSL 262 Query: 199 SGGCAVMDIGIYPLNTSRFLLDADPVAVRGTVASVQEE--FADVPDEHGAFQLDFPGHVY 256 +GG A+ DIG+Y LN +RFL +P+ V +V + + F +V +E F L FP Sbjct: 263 AGGGAMPDIGLYCLNAARFLSGEEPLEVVASVHRPENDPRFVEV-EESVHFILRFPSGFT 321 Query: 257 AVCTASQNAHLDSHISVLGTEGKVRVEPAFYPWDDRALQLSH------EGTTVEIDFEQI 310 A C +S +H + G++G V ++PAF L+L H + T E+ + Sbjct: 322 ATCMSSYASHESRFFRLQGSKGWVEMDPAF---GYNGLRLRHGMLVEGKSATTELQIDPQ 378 Query: 311 DQMEEEFEYFAHCLLTDTEPYADGEHGLVDINTIKSVYEASETESTVRL 359 +Q E ++ + C+ D +P+ GE GL D I ++YE++ T V+L Sbjct: 379 NQFAREIDHMSVCVKDDIQPHTPGEEGLQDQRIIDAIYESARTGRAVKL 427 Lambda K H 0.317 0.134 0.400 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: 386 Number of extensions: 24 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: 360 Length of database: 444 Length adjustment: 31 Effective length of query: 329 Effective length of database: 413 Effective search space: 135877 Effective search space used: 135877 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: 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