Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate 3607832 Dshi_1240 SMP-30/Gluconolaconase/LRE domain protein (RefSeq)
Query= metacyc::MONOMER-20630 (291 letters) >FitnessBrowser__Dino:3607832 Length = 286 Score = 126 bits (316), Expect = 6e-34 Identities = 97/290 (33%), Positives = 138/290 (47%), Gaps = 12/290 (4%) Query: 1 MTVTRVVDTSCRLGEGPVWHPDEKRLYWVDIESGRLHRYDPETGAHDCPVETSVIAGVTI 60 M+ T D C LGEGP+WHP+ ++L+W DI R+ D +T + + V A + Sbjct: 1 MSATLYDDRPCALGEGPLWHPERQQLFWFDITGQRMLSRDGDTPL-EWQFDEMVSAAGWV 59 Query: 61 QRDGSLLAFMDRGRVGRVVDGDRRESARI-VDSP-TRFNDVIADPAGRVFCGTM--PSDT 116 D L+A + +G+ R A + D P TR ND ADP G + GTM ++ Sbjct: 60 DHDTLLIASETALVTFDLAEGESRFVAPLEADRPETRSNDGRADPWGGFWIGTMGKSAEP 119 Query: 117 AGGRLFRLDTDGTVTTVETGVGIPNGMGFTRDRERFYFTETEARTVYRYAYDEETGAVSA 176 G ++RL DGT+ V V I N + F + Y+ +T R V R D + G S Sbjct: 120 GAGAIYRL-FDGTLRRVVRDVTISNALCFDAAQSCAYYADTPTRQVMRLPLDGD-GWPSG 177 Query: 177 RERFVESPETPGL-PDGMTVDSAGHIWSARWEGGCVVEYDADGTELGRFDVPTEKVTSVA 235 GL PDG D+AG++W A+W G V + DGT L + A Sbjct: 178 PATVAVDLRAEGLNPDGAVTDAAGNLWIAQWGAGRVACHAPDGTFLRALACGGRHSSCPA 237 Query: 236 FGGPDLDSLYVTTAGGDGDGSAGEGDESTGDAAGALFRLDVAATGRPEFR 285 FGGPDLD L++TTA +G + + D + G +F + A G PE R Sbjct: 238 FGGPDLDQLFITTA---REGLSAD-DIAAAPENGCVFAAEGVARGLPEPR 283 Lambda K H 0.317 0.138 0.420 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: 266 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: 291 Length of database: 286 Length adjustment: 26 Effective length of query: 265 Effective length of database: 260 Effective search space: 68900 Effective search space used: 68900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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