Align tagaturonate reductase (EC 1.1.1.58) (characterized)
to candidate AZOBR_RS16160 AZOBR_RS16160 altronate oxidoreductase
Query= ecocyc::ALTRO-OXIDOREDUCT-MONOMER (483 letters) >FitnessBrowser__azobra:AZOBR_RS16160 Length = 489 Score = 389 bits (1000), Expect = e-113 Identities = 215/471 (45%), Positives = 298/471 (63%), Gaps = 5/471 (1%) Query: 1 MKTLNRRDFPGAQYPE--RIIQFGEGNFLRAFVDWQIDLLNEHTDLNSGVVVVRPIETSF 58 M+ LN G P RI+QFGEGNFLRAF DW++D LNE T + GV VVRPI F Sbjct: 1 MQRLNASFLNGRPRPTTTRIVQFGEGNFLRAFFDWKVDRLNEATGGDWGVTVVRPIPGGF 60 Query: 59 PPSLSTQDGLYTTIIRGLNEKGEAVSDARLIRSVNREISVYSEYDEFLKLAHNPEMRFVF 118 P +L+ Q+G+YT + RG++E G VS ARLI V EI+ + E+ L+LA +P + V Sbjct: 61 PQTLNEQEGVYTVLSRGVDEAGRKVSQARLIGCVRNEIAAHGEWASVLELARDPNVTVVV 120 Query: 119 SNTTEAGISYHAGDKFDDAPAVSYPAKLTRLLFERFSHFNGALDKGWIIIPCELIDYNGD 178 SNTT+AGI+Y + D P VS+P K+TR L ER+ F+GA + G ++ CELID+NG+ Sbjct: 121 SNTTDAGIAYVPSVAYADEPPVSFPGKMTRFLHERWKAFDGAPEAGLQMLACELIDHNGE 180 Query: 179 ALRELVLRYAQEWALPEAFIQWLDQANSFCSTLVDRIVTGYPRDEVAKLEEELGYHDGFL 238 L+ +VL +A++WAL AFI W++ AN+F +TLVDRIV G+PR E L ELGY D F+ Sbjct: 181 ELKRIVLLHARDWALEPAFIAWIETANAFYNTLVDRIVPGFPRAEADDLRRELGYDDSFM 240 Query: 239 DTAEHFYLFVIQGPKSL-ATELRLDKYPLNVLIVDDIKPYKERKVAILNGAHTALVPVAF 297 AE F+LFVI+ + A L L ++ ++ D+ PYK RKVAILNGAHT L +A Sbjct: 241 AAAELFHLFVIERKEGTPALRLPLGEHDEGTVVTADVTPYKARKVAILNGAHTGLCALAL 300 Query: 298 QAGLDTVGEAMNDAEICAFVEKAIYEEIIPVLDLPRDELESFASAVTGRFRNPYIKHQLL 357 AG++TVGEA++D F+++ + EE+IP L LP+ ELE FA+AV RFRNPYI+H Sbjct: 301 LAGVETVGEAVSDPAGARFLDRLLNEEVIPFLTLPKPELEDFAAAVLRRFRNPYIRHLWH 360 Query: 358 SIALNGMTKFRTRILPQLLAGQKANGTLPARLTFALAALIAFYRGERNG-ETYPVQDDAH 416 I+LNG+ K++TR L +LLA ++ GT ++ +LAA +AFY G G T P +D A Sbjct: 361 DISLNGLVKYQTRNLDRLLAYRERFGTPAPLMSLSLAAWLAFYLGRFPGAATLPPRDSAE 420 Query: 417 WLERYQQLWSQHRDRVIGTQELVAIVLAEKDHWEQDLTQVPGLVEQVANDL 467 +ER + + + G + +VA L E W + + L QV D+ Sbjct: 421 IVERVRAIGALDDGTPAGLEAMVAAYLGETAFWGRSIDD-RSLRAQVMEDI 470 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: 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: 489 Length adjustment: 34 Effective length of query: 449 Effective length of database: 455 Effective search space: 204295 Effective search space used: 204295 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