Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate PP_3954 PP_3954 periplasmic binding subunit of unknown solute
Query= reanno::psRCH2:GFF85 (317 letters) >FitnessBrowser__Putida:PP_3954 Length = 316 Score = 448 bits (1152), Expect = e-131 Identities = 232/311 (74%), Positives = 261/311 (83%), Gaps = 1/311 (0%) Query: 7 LGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKTSVQATK 65 L L A+ F S AA AAPTFINILTGGTSGVYYP+GV +SQ Y+ I+G+KT+VQATK Sbjct: 5 LRLALASTLFAVSAAAQAAPTFINILTGGTSGVYYPVGVGISQIYSHGIEGSKTTVQATK 64 Query: 66 ASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASA 125 ASVENLNLLQAGRGELAF+LGDSV DAW G +AGFK PLK+LRAIAGTY NYIQIVAS Sbjct: 65 ASVENLNLLQAGRGELAFALGDSVADAWKGDAEAGFKTPLKKLRAIAGTYPNYIQIVASK 124 Query: 126 ESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNR 185 ESGI +L DLKGKRISVGAPKSGTELNARAIFKAAGL Y+DMG+VE+LPYAESVELIKNR Sbjct: 125 ESGITSLSDLKGKRISVGAPKSGTELNARAIFKAAGLTYQDMGKVEYLPYAESVELIKNR 184 Query: 186 QLDATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYDGQDADV 245 QLDATLQSSGLG AAIRDLA+T+PV FV IPAEVV +I ++AY IPA TYDGQ ADV Sbjct: 185 QLDATLQSSGLGQAAIRDLAATLPVVFVPIPAEVVTRIGNNAYQPATIPANTYDGQSADV 244 Query: 246 PTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPG 305 T AI NILVT + D++AYQMTKL+F+NL L AH+AAKDI+ ENA KNLPIPLHPG Sbjct: 245 STAAINNILVTRADIGDDLAYQMTKLIFENLPRLVTAHAAAKDIQAENAAKNLPIPLHPG 304 Query: 306 AERFYKEAGVL 316 A R++KE +L Sbjct: 305 AARYFKEKNLL 315 Lambda K H 0.314 0.131 0.359 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: 360 Number of extensions: 6 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: 317 Length of database: 316 Length adjustment: 27 Effective length of query: 290 Effective length of database: 289 Effective search space: 83810 Effective search space used: 83810 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: 42 (22.0 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