Align tagaturonate reductase (EC 1.1.1.58) (characterized)
to candidate 350353 BT0825 altronate oxidoreductase (NCBI ptt file)
Query= ecocyc::ALTRO-OXIDOREDUCT-MONOMER (483 letters) >FitnessBrowser__Btheta:350353 Length = 479 Score = 403 bits (1035), Expect = e-117 Identities = 217/482 (45%), Positives = 298/482 (61%), Gaps = 8/482 (1%) Query: 1 MKTLNRRDFPGAQYPERIIQFGEGNFLRAFVDWQIDLLNEHTDLNSGVVVVRPIETSFPP 60 MK LN+ P Q PERIIQFGEGNFLRAFVDW I +N+ TD NS VVVV+PI+ Sbjct: 1 MKALNKETAPKVQRPERIIQFGEGNFLRAFVDWIIYNMNQKTDFNSSVVVVQPIDKGMVD 60 Query: 61 SLSTQDGLYTTIIRGLNEKGEAVSDARLIRSVNREISVYSEYDEFLKLAHNPEMRFVFSN 120 L+ QD LY ++GL +KGE V+ +I ++R ++ Y++ DEF+KLA PEMRFV SN Sbjct: 61 MLNAQDDLYHVNLQGL-DKGEVVNSLTMIDVISRALNPYTQNDEFMKLAEQPEMRFVISN 119 Query: 121 TTEAGISYHAGDKFDDAPAVSYPAKLTRLLFERFSHFNGALDKGWIIIPCELIDYNGDAL 180 TTEAGI++ K +DAPA SYP KLT+LL+ RF FNG KG II PCELI NG L Sbjct: 120 TTEAGIAFDPTCKLEDAPASSYPGKLTQLLYHRFKTFNGDKTKGLIIFPCELIFLNGHKL 179 Query: 181 RELVLRYAQEWALPEAFIQWLDQANSFCSTLVDRIVTGYPRDEVAKLEEELGYHDGFLDT 240 +E + +Y W L F W ++A +TLVDRIV G+PR ++A ++E++ Y D + Sbjct: 180 KETIYQYIDLWNLGNEFKTWFEEACGVYATLVDRIVPGFPRKDIAAIKEKIQYDDNLVVQ 239 Query: 241 AEHFYLFVIQGPKSLATELRLDKYPLNVLIVDDIKPYKERKVAILNGAHTALVPVAFQAG 300 AE F+L+VI+ P+ +A E DK LNVL V PY ERKV +LNG HT L PVA+ +G Sbjct: 240 AEIFHLWVIEAPQEVAKEFPADKAGLNVLFVPSEAPYHERKVTLLNGPHTVLSPVAYLSG 299 Query: 301 LDTVGEAMNDAEICAFVEKAIYEEIIPVLDLPRDELESFASAVTGRFRNPYIKHQLLSIA 360 ++ V +A I ++ K +++E++ L+LP++EL+ FA V RF NP++ H + SI Sbjct: 300 VNIVRDACQHEVIGKYIHKVMFDELMETLNLPKEELKKFAEDVLERFNNPFVDHAVTSIM 359 Query: 361 LNGMTKFRTRILPQLLAGQKANGTLPARLTFALAALIAFYRG--ERNGETYPVQDDAHWL 418 LN K+ TR LP L + G LP L LAA+I +Y+G +G D + Sbjct: 360 LNSFPKYETRDLPGLKTYLERKGELPKGLVLGLAAIITYYKGGVRADGAEIVPNDAPEIM 419 Query: 419 ERYQQLWSQHRDRVIGTQELVAIVLAEKDHWEQDLTQVPGLVEQVANDLDAILEKGMREA 478 ++LW+ T+++ VLA + W +DL ++PGL V DLD+I EKGM E Sbjct: 420 NLLKELWATG-----CTKKVTEGVLAAEFIWGEDLNKIPGLAAAVKADLDSIQEKGMLET 474 Query: 479 VR 480 V+ Sbjct: 475 VK 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: 651 Number of extensions: 34 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: 479 Length adjustment: 34 Effective length of query: 449 Effective length of database: 445 Effective search space: 199805 Effective search space used: 199805 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