Align D-xylose dehydrogenase; NADP-dependent D-xylose dehydrogenase; EC 1.1.1.179 (characterized)
to candidate AZOBR_RS11740 AZOBR_RS11740 oxidoreductase
Query= SwissProt::Q8GAK6 (388 letters) >FitnessBrowser__azobra:AZOBR_RS11740 Length = 383 Score = 461 bits (1187), Expect = e-134 Identities = 226/379 (59%), Positives = 272/379 (71%), Gaps = 4/379 (1%) Query: 9 VAMNGITGRMGYRQHLLRSILPIRDAGGFTLEDGTKVQIEPILVGRNEAKIRELAEKHKV 68 + M+G+TGRMG QHL+RSIL IR GG TL DG++V +PILVGRN KIRELA++H V Sbjct: 8 IIMHGVTGRMGMNQHLIRSILAIRAQGGVTLSDGSRVMPDPILVGRNAEKIRELAQRHGV 67 Query: 69 AEWSTDLDSVVNDPTVDIIFDASMTSLRAATLKKAMLAGKHIFTEKPTAETLEEAIELAR 128 W+ +LD+ + +P I FDA T +R L+ A+ AGKH++ EKP A LEEA+ + R Sbjct: 68 ERWTDNLDTALANPDDTIFFDAGTTQMRPTLLEAAIRAGKHVYCEKPIATNLEEALRVVR 127 Query: 129 IGKQAGVTAGVVHDKLYLPGLVKLRRLVDEGFFGRILSIRGEFGYWVFEGDVQAAQRPSW 188 + ++AGV G V DKL+LPGL KL+ L D GFFG+ILS+RGEFGYWVFEGD Q AQRPSW Sbjct: 128 LAEEAGVKNGTVQDKLFLPGLQKLKMLRDSGFFGKILSVRGEFGYWVFEGDWQPAQRPSW 187 Query: 189 NYRKEDGGGMTTDMFCHWNYVLEGIIGKVKSVNAKTATHIPTRWDEAGKEYKATADDASY 248 NYR+EDGGG+ DM CHW YVL+ + G+VKSV+ A HIP RWDE GK Y+ATADDA+Y Sbjct: 188 NYREEDGGGIILDMVCHWRYVLDNLFGQVKSVSCLGAIHIPERWDEQGKRYQATADDAAY 247 Query: 249 GIFELETPGGDDVIGQINSSWAVRVYRDELVEFQVDGTHGSAVAGLNKCVAQQRAHTPKP 308 FELE GG VI INSSWA RVYRD+LV FQVDGTHGSAVAGL+ CV Q R TP+P Sbjct: 248 ATFELE--GG--VIAHINSSWATRVYRDDLVTFQVDGTHGSAVAGLSDCVIQPRQGTPRP 303 Query: 309 VWNPDLPVTESFRDQWQEVPANAELDNGFKLQWEEFLRDVVAGREHRFGLLSAARGVQLA 368 VWNPD T F WQ VP N DNGFK QWE F+R VV GL+ A+GVQL Sbjct: 304 VWNPDQKQTMDFYATWQPVPDNQPTDNGFKTQWESFIRHVVEDAPFDHGLIEGAKGVQLV 363 Query: 369 ELGLQSNDERRTIDIPEIT 387 E L+S ERR +D+P +T Sbjct: 364 EAALKSWKERRWVDVPSLT 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: 534 Number of extensions: 21 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: 388 Length of database: 383 Length adjustment: 30 Effective length of query: 358 Effective length of database: 353 Effective search space: 126374 Effective search space used: 126374 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