Align D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) (characterized)
to candidate SMa2313 SMa2313 Oxidoreductase
Query= BRENDA::D4GP30 (325 letters) >FitnessBrowser__Smeli:SMa2313 Length = 677 Score = 152 bits (384), Expect = 2e-41 Identities = 106/325 (32%), Positives = 158/325 (48%), Gaps = 18/325 (5%) Query: 3 FGILGTAGIGVKSVIPAVQASEHEAAAIASRDEARASAVADELGIPTAYGSYEALLADDS 62 +GILG I A+Q++ + AI +R+ A++ D G G Y+AL+ D Sbjct: 9 WGILGPGNIAKDFFAGALQSANGKVVAIGARNPAKSGLAEDFPGARIVDG-YDALIDDPG 67 Query: 63 LDAVYIPLPNGLHADWVRAAADRGLHVLCEKPLTASADETAAVFDYCEDAGVTLMEAFMY 122 +DAVYI + LHA+W AA++G HVLCEKP+ S E A+F+ AG + EA+MY Sbjct: 68 IDAVYIATVHPLHAEWAIKAAEKGKHVLCEKPMGLSTAEADAMFEAARKAGTFMAEAYMY 127 Query: 123 RFHPLTERAAELVASEL-GAVVSVTSNFSF-RLPDGADDIRIDPDLAGGSVMDVGCYAVS 180 R HPLT R ELV + + G V + S+F F +LP ++AGG ++DVG Y S Sbjct: 128 RLHPLTARIVELVKNGMVGDVRKIQSSFGFAKLPFDEGHRLFSNEMAGGGILDVGGYTTS 187 Query: 181 AARLF--LGTPDRVYATTTDTR-----DCGVDTRMSGVLEYDSGATARVESSFDTPETQY 233 ARL +GT V T GVD S +L + +G A + S + Sbjct: 188 MARLIAGIGTSSGVMEPAEVTALGHLGRTGVDEWTSALLSFPNGIIAELSCSVSLEQENV 247 Query: 234 YRVQTTDGRLEANPAF----NVDPTAAAELTYATDGRVVTETFDPTDSYRREVEAFARAV 289 R+ T GR+E + + T+ + +A + +P Y EVEA A+ Sbjct: 248 LRILGTKGRIEVDQFWFAGGKPGGTSIIRIVHADGRQEEVPLVEPRHLYSFEVEAAGDAI 307 Query: 290 ETGET----PRVDREESVSVMRTID 310 G T P + R +++ +R +D Sbjct: 308 RAGRTEFAYPGMSRADTLGNLRVMD 332 Lambda K H 0.316 0.131 0.371 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: 468 Number of extensions: 16 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: 325 Length of database: 677 Length adjustment: 33 Effective length of query: 292 Effective length of database: 644 Effective search space: 188048 Effective search space used: 188048 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: 51 (24.3 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