Align tagaturonate reductase (EC 1.1.1.58) (characterized)
to candidate AZOBR_RS31275 AZOBR_RS31275 altronate oxidoreductase
Query= ecocyc::ALTRO-OXIDOREDUCT-MONOMER (483 letters) >FitnessBrowser__azobra:AZOBR_RS31275 Length = 501 Score = 378 bits (970), Expect = e-109 Identities = 202/478 (42%), Positives = 290/478 (60%), Gaps = 14/478 (2%) Query: 15 PERIIQFGEGNFLRAFVDWQIDLLNEHTDLNSGVVVVRPIETSFPPSLSTQDGLYTTIIR 74 P I+Q G+GNFLR FVDW +D+ N +++GV + +P++ L+ Q+GLYT ++R Sbjct: 26 PVTILQIGDGNFLRGFVDWMVDVANGAGLMSAGVAIAQPLDQGVAGLLNAQEGLYTVLLR 85 Query: 75 GLNEKGEAVSDARLIRSVNREISVYSEYDEFLKLAHNPEMRFVFSNTTEAGISYHAGDKF 134 G+ E+G+ V R++ V+ ++ Y+E+D L LA +P +RF+ SNTTEAGI+ A Sbjct: 86 GI-EQGKEVESRRVVSCVSDALNPYAEWDRMLALATSPALRFLVSNTTEAGIADVAEPYT 144 Query: 135 DDAPAVSYPAKLTRLLFERFSHFNGALDKGWIIIPCELIDYNGDALRELVLRYAQEWALP 194 A S+PAK+ LL RF+ G D G +++PCELI+ NG L+ +VL +A+ W L Sbjct: 145 PGACQQSFPAKVAALLHARFTALGGTPDSGLVLLPCELIEANGAKLKRIVLAHAKRWGLE 204 Query: 195 EAFIQWLDQANSFCSTLVDRIVTGYPRDEVAKLEEELGYHDGFLDTAEHFYLFVIQGPKS 254 F W++ N F +TLVDRIV GYPRDE L GY D T E F+++VI+GP + Sbjct: 205 SGFAAWVEAHNHFLNTLVDRIVPGYPRDEAEALAATWGYEDPLAVTGEPFHVWVIEGPAA 264 Query: 255 LATELRLDKYPLNVLIVDDIKPYKERKVAILNGAHTALVPVAFQAGLDTVGEAMNDAEIC 314 LA E L K LNV+ DD+KPY+ RKV ILNGAHTA AF AG+DTV M+DA + Sbjct: 265 LAEEFPLHKAGLNVVWTDDLKPYRTRKVRILNGAHTASALAAFVAGVDTVKGMMDDATLS 324 Query: 315 AFVEKAIYEEIIPVLDLPRDELESFASAVTGRFRNPYIKHQLLSIALNGMTKFRTRILPQ 374 A++ ++ EI+P + LP E + +A + RF NPYI+H+L++IALN ++K++ R+LP Sbjct: 325 AYLNTVMFGEIVPFVPLPDAERQDYARTIMERFGNPYIRHELIAIALNSVSKWQVRVLPS 384 Query: 375 LLAGQKANGTLPARLTFALAALIAFYR----------GERNGETYPVQDDAHWLERYQQL 424 L A+G P L+F+LAAL+ FY+ G R+ YP++DDA L Sbjct: 385 LKDYAAAHGEAPDGLSFSLAALLRFYKGTLAADGACTGTRDAGPYPIRDDAAVLTALSGA 444 Query: 425 WSQHRDRVIGTQELVAIVLAEKDHWEQDLTQVPGLVEQVANDLDAILEKGMREAVRPL 482 W+ H LV VL+ W +DLT++PGL + A L I E+GMR A+ L Sbjct: 445 WAAHGG---DPAALVDAVLSNAALWGEDLTRIPGLAHRTAVHLAVIEERGMRGALEAL 499 Lambda K H 0.321 0.138 0.413 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: 684 Number of extensions: 19 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: 483 Length of database: 501 Length adjustment: 34 Effective length of query: 449 Effective length of database: 467 Effective search space: 209683 Effective search space used: 209683 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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