Align tagaturonate reductase (EC 1.1.1.58) (characterized)
to candidate WP_053935922.1 WG78_RS01025 tagaturonate reductase
Query= ecocyc::ALTRO-OXIDOREDUCT-MONOMER (483 letters) >NCBI__GCF_001294205.1:WP_053935922.1 Length = 477 Score = 488 bits (1255), Expect = e-142 Identities = 255/468 (54%), Positives = 320/468 (68%), Gaps = 4/468 (0%) Query: 15 PERIIQFGEGNFLRAFVDWQIDLLNEHTDLNSGVVVVRPIETSFPPSLSTQDGLYTTIIR 74 P R +QFGEGNFLRAF+DWQIDLLNE L++ VV+VRPI P L+TQ G+YTT+IR Sbjct: 13 PIRFVQFGEGNFLRAFIDWQIDLLNERVGLDASVVIVRPIARPDMPLLNTQGGVYTTLIR 72 Query: 75 GLNEKGEAVSDARLIRSVNREISVYSEYDEFLKLAHNPEMRFVFSNTTEAGISYHAGDKF 134 GLNE G V + R I+ V E+ + +++ L LAH P +RFV SNTTEAGI + D F Sbjct: 73 GLNEDGVPVKEYRQIQCVKGEVDATARWNDVLALAHVPSLRFVVSNTTEAGICINNTDGF 132 Query: 135 DDAPAVSYPAKLTRLLFERFSHFNGALDKGWIIIPCELIDYNGDALRELVLRYAQEWALP 194 +D P S+PAKLTR LFER+ HF GA DKG +++PCELID+NGDAL++ V+ +A W L Sbjct: 133 EDFPPSSFPAKLTRFLFERYRHFEGATDKGVVLLPCELIDHNGDALKQAVIHFAALWKLG 192 Query: 195 EAFIQWLDQANSFCSTLVDRIVTGYPRDEVAKLEEELGYHDGFLDTAEHFYLFVIQGPKS 254 +AF WLD A +FCSTLVDRIVTGYPR E+A +E+ELGY D FL TAE+FYLFVI+GP Sbjct: 193 DAFNGWLDSACTFCSTLVDRIVTGYPRGEIAAIEKELGYTDAFLVTAEYFYLFVIEGPAW 252 Query: 255 LATELRLDKYPLNVLIVDDIKPYKERKVAILNGAHTALVPVAFQAGLDTVGEAMNDAEIC 314 LA EL+L LN+ +VDDI PYK+RKV +LNG HT++VPVA AGL+TVG AM+D + Sbjct: 253 LADELKLAGADLNIQLVDDITPYKQRKVGVLNGGHTSMVPVALLAGLETVGAAMDDPLVS 312 Query: 315 AFVEKAIYEEIIPVLDLPRDELESFASAVTGRFRNPYIKHQLLSIALNGMTKFRTRILPQ 374 F+ + + EEIIP L LPR EL+ FA+ V RFRNPYI+H+L SIALN +KF R++PQ Sbjct: 313 RFLLRTLDEEIIPALPLPRAELDPFAADVLLRFRNPYIQHRLESIALNSWSKFAARVMPQ 372 Query: 375 LLAGQKANGTLPARLTFALAALIAFYRGERNGETYPVQDDAHWLERYQQLWSQHRDRVIG 434 LL QK NG LP RL FALAA + YR G + DD L ++ W + R I Sbjct: 373 LLQYQKTNGVLPQRLVFALAANMLLYR----GLMVTLTDDPAHLAWFEDAWEKFRTHRIN 428 Query: 435 TQELVAIVLAEKDHWEQDLTQVPGLVEQVANDLDAILEKGMREAVRPL 482 E+ LA K W DL QVP L E + L I G+R+A+ L Sbjct: 429 FAEIAQGWLANKAVWGADLNQVPQLTESLEKTLQLIDINGVRKALLEL 476 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: 701 Number of extensions: 31 Number of successful extensions: 2 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: 477 Length adjustment: 34 Effective length of query: 449 Effective length of database: 443 Effective search space: 198907 Effective search space used: 198907 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 24 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