Align tagaturonate reductase (EC 1.1.1.58) (characterized)
to candidate BWI76_RS03945 BWI76_RS03945 altronate oxidoreductase
Query= ecocyc::ALTRO-OXIDOREDUCT-MONOMER (483 letters) >FitnessBrowser__Koxy:BWI76_RS03945 Length = 481 Score = 686 bits (1770), Expect = 0.0 Identities = 338/483 (69%), Positives = 398/483 (82%), Gaps = 3/483 (0%) Query: 1 MKTLNRRDFPGAQYPERIIQFGEGNFLRAFVDWQIDLLNEHTDLNSGVVVVRPIETSFPP 60 MK+LNR+DFPG QYP R IQFGEGNFLRAF+DWQ+DLLNE TDL +GV +VRPI T FPP Sbjct: 1 MKSLNRQDFPGPQYPTRAIQFGEGNFLRAFIDWQLDLLNEKTDLAAGVTIVRPINTEFPP 60 Query: 61 SLSTQDGLYTTIIRGLNEKGEAVSDARLIRSVNREISVYSEYDEFLKLAHNPEMRFVFSN 120 SL+TQDGLYTT+IRGL+E+GEAVS+AR+IRSVN EI+ + ++ +L LA NP + FVFSN Sbjct: 61 SLNTQDGLYTTVIRGLDERGEAVSEARIIRSVNNEINPWQDFAGYLALARNPAIAFVFSN 120 Query: 121 TTEAGISYHAGDKFDDAPAVSYPAKLTRLLFERFSHFNGALDKGWIIIPCELIDYNGDAL 180 TTEAGISYHAGD+ DD P VS+PAKL +LL ERF HFNGA DKGW IIPCELIDYNG+AL Sbjct: 121 TTEAGISYHAGDRPDDKPPVSFPAKLAQLLLERFRHFNGAADKGWTIIPCELIDYNGEAL 180 Query: 181 RELVLRYAQEWALPEAFIQWLDQANSFCSTLVDRIVTGYPRDEVAKLEEELGYHDGFLDT 240 + LVLRYA+EW LP AF W++ AN+FCSTLVDRIVTGYPRDE KLE ELGYHD FLDT Sbjct: 181 KALVLRYAEEWQLPAAFRDWVETANTFCSTLVDRIVTGYPRDEAEKLEAELGYHDAFLDT 240 Query: 241 AEHFYLFVIQGPKSLATELRLDKYPLNVLIVDDIKPYKERKVAILNGAHTALVPVAFQAG 300 AE+F+LFVIQGP++LA +LRLD+ PLN+ IV+DI+PYKERKVAILNGAHTALVPVA+ G Sbjct: 241 AEYFWLFVIQGPRALAEKLRLDRCPLNIHIVEDIRPYKERKVAILNGAHTALVPVAWLCG 300 Query: 301 LDTVGEAMNDAEICAFVEKAIYEEIIPVLDLPRDELESFASAVTGRFRNPYIKHQLLSIA 360 +DTVGEAM D I +V++ I EEIIP LDLP DEL FA AVTGRF NP+I+HQLLSIA Sbjct: 301 VDTVGEAMRDEAIRHYVQQTIDEEIIPALDLPADELRQFADAVTGRFLNPFIRHQLLSIA 360 Query: 361 LNGMTKFRTRILPQLLAGQKANGTLPARLTFALAALIAFYRGERNGETYPVQDDAHWLER 420 LNGMTKFRTRILPQLLA + +G +P RLTFALAALIAFYRG+R+G+TYP+QDD WL R Sbjct: 361 LNGMTKFRTRILPQLLANTRQHGVIPPRLTFALAALIAFYRGQRDGQTYPLQDDDVWLTR 420 Query: 421 YQQLWSQ-HRDRVIGTQELVAIVLAEKDHWEQDLTQVPGLVEQVANDLDAILEKGMREAV 479 + + W+Q + R +G ELV VL + HW +DLT +PGL EQV L+ IL GMREA+ Sbjct: 421 FAEGWAQVAQGRPLG--ELVTEVLQDTAHWGEDLTAIPGLAEQVTRYLEVILSAGMREAL 478 Query: 480 RPL 482 L Sbjct: 479 SRL 481 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: 838 Number of extensions: 33 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: 483 Length of database: 481 Length adjustment: 34 Effective length of query: 449 Effective length of database: 447 Effective search space: 200703 Effective search space used: 200703 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