Align Lmo2663 protein (characterized, see rationale)
to candidate PP_3839 PP_3839 short-chain alcohol dehydrogenase
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Putida:PP_3839 Length = 336 Score = 124 bits (312), Expect = 3e-33 Identities = 94/334 (28%), Positives = 159/334 (47%), Gaps = 10/334 (2%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTLG 60 MKA V PG ++ P +G+ + +K+ G+C +D+H G++ + T V LG Sbjct: 1 MKAAVVA-PGRRVDVIEKSLRPLEHGEAL-LKMQCCGVCHTDLHVKNGDFGDKTG-VVLG 57 Query: 61 HEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGSF 120 HE GVV EVGP VTS+K GDR + ++ CG C YC + LC + + G +G Sbjct: 58 HEGIGVVQEVGPGVTSLKPGDRASVAWFYQGCGHCEYCNSGNETLCRDVKNSGYTVDGGM 117 Query: 121 AEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLLL 180 AE + + + + + + AA+ + A++ + +RP + ++G G +G L Sbjct: 118 AEACIVKADYSVKVPDGLDSAAASSITCAGVTTYKAVKISNVRPGQWIAIYGLGGLGNLA 177 Query: 181 AQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYGAERVFD 240 Q K ++A I + ++LR A E+G D +V+ L ED A+V+ TGG A V Sbjct: 178 LQYAKNVFNAKVIA-IDVNEEQLRFASEMGADLVVNPLNEDAAKVIQAKTGGAHAAVV-- 234 Query: 241 CSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKPSSWILA 300 + A A N + + G V VGL +E + ++ ++ I +GS A Sbjct: 235 TAVAKGAFNSAVDALRAGGRLVAVGLPSESMD-LNIPRLVLDGIEVVGSLVGTRQDLQEA 293 Query: 301 LDLLANGKIDTDKMITKVYGLDDWREAFEAVMAG 334 A GK+ + + +D + F+ ++ G Sbjct: 294 FQFAAEGKVVPKVTLRPI---EDINQIFDEMLEG 324 Lambda K H 0.317 0.135 0.392 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: 298 Number of extensions: 17 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: 343 Length of database: 336 Length adjustment: 28 Effective length of query: 315 Effective length of database: 308 Effective search space: 97020 Effective search space used: 97020 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: 49 (23.5 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