Align Altronate oxidoreductase; EC 1.1.1.58; Tagaturonate dehydrogenase; Tagaturonate reductase (uncharacterized)
to candidate BPHYT_RS27215 BPHYT_RS27215 D-mannonate oxidoreductase
Query= curated2:Q9KFI7 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS27215 Length = 386 Score = 125 bits (313), Expect = 4e-33 Identities = 114/373 (30%), Positives = 165/373 (44%), Gaps = 37/373 (9%) Query: 22 LPERVLQFGEGNFLRGFIDWMIQQMNKQNVFNGRVVAIQPT--PHGKVVPKLQEQDSLYT 79 + E +LQFG FL+ + + Q ++ G + +Q T P + Q + Y Sbjct: 1 MSEPILQFGTSRFLQAHVALFVSQALERGDAIGGICVVQTTDNPSSQARIAALAQAASYP 60 Query: 80 VWLRGIADGETVDHHEVITSISRGLNPYTNWQDVLEVAASPDISVVFSNTTEAGLTYLEE 139 V +RG G VD +I +W + AA D+ V+ SNT + G E Sbjct: 61 VKIRGREGGAIVDTVVDCRAIRAAWIANRDWATIRH-AAIHDVRVIVSNTGDMGYRLDER 119 Query: 140 GYD-----KEKAPLSFPGKLAACLWHRYETLGWGE--GSGLVIIPCELVEQNGKVLKELV 192 + +AP S+P KL L R W E SG+ I PCELV NG L++LV Sbjct: 120 DSPALLAREGQAPHSYPAKLLTLLHAR-----WRERPDSGISIFPCELVASNGDTLRDLV 174 Query: 193 CRYAKAWNFPQEFFTWLERENEFCHTLVDRIVPGFPSDTADECFERLGYEDILLTVAEPY 252 A+ W P F +L + + ++LVDRIV E E +G VAEPY Sbjct: 175 TGLARQWVLPTPFVAYLSQRCIWVNSLVDRIV--------SEPIEPVG------AVAEPY 220 Query: 253 HLFIIEGSERVRKLLPFNEAGLHVRWNHLEKHRNMKVRVLNGTHTFM---FALSYLSGVD 309 L+ IE R LP + V + L + +K+ LN HT++ + S + Sbjct: 221 ALWAIE--RRAGMELPCTHEHIVVT-DDLSSYEQLKLFFLNLGHTWLADQWLAQRRSATE 277 Query: 310 TVGEAMADEQLCSFIRKGLFEEIIPCVDAPEQEVTA--FAETVLERFENPFLQHRLTDIG 367 TV +AM D L I E++P A A + +V ERF NP+L HR+ DI Sbjct: 278 TVFDAMNDGPLRDGIEAVWDNEVLPVFSAMGLRARAVQYVASVRERFLNPYLDHRIADIA 337 Query: 368 LNAVNKFRTRLMP 380 + V K R R++P Sbjct: 338 NHHVEKVRRRILP 350 Lambda K H 0.321 0.138 0.419 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: 451 Number of extensions: 21 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: 512 Length of database: 386 Length adjustment: 32 Effective length of query: 480 Effective length of database: 354 Effective search space: 169920 Effective search space used: 169920 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: 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