Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate GFF1596 PGA1_c16180 TRAP transporter solute receptor, TAXI family
Query= reanno::psRCH2:GFF85 (317 letters) >FitnessBrowser__Phaeo:GFF1596 Length = 321 Score = 171 bits (432), Expect = 3e-47 Identities = 110/320 (34%), Positives = 157/320 (49%), Gaps = 8/320 (2%) Query: 1 MRLTKRLGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNKI---DGA 57 M TK A AF A A A FI I TGG +GVYYP G A+ + NK G Sbjct: 1 MTNTKLAVSALVATAFMAPAAM--AEEFITIGTGGVTGVYYPTGGAICRLVNKTRKEHGI 58 Query: 58 KTSVQATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNN 117 + SV++T SV N+N ++ G E + D A+NG + + LRA+ + Sbjct: 59 RCSVESTGGSVYNINTIREGELEFGVAQSDWQYHAYNGTSKFEEQGAFEGLRAVFSVHPE 118 Query: 118 YIQIVASAESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAE 177 +VA A++G+ + DDLKGKR+++G P SG + +A G L AE Sbjct: 119 PFTVVARADAGVTSFDDLKGKRVNIGNPGSGQRGTMEVLLEAKGWGMDAFALATELKAAE 178 Query: 178 SVELIKNRQLDATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESD--AYLAGVIPA 235 + + Q+DA + + G +I++ + V + E VEK+ +D Y IP Sbjct: 179 QSAALCDNQIDAMVYTVGHPSGSIQEATTACDSVLVTVDGEAVEKLIADNSFYRTATIPG 238 Query: 236 GTYDGQDADVPTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLEN-A 294 G Y G DADV T + VT ++VSDE Y + K +F+N H A ++K E A Sbjct: 239 GMYRGSDADVGTFGVGATFVTSDQVSDEAVYTVVKAVFENFDDFKKLHPAFANLKPEEMA 298 Query: 295 TKNLPIPLHPGAERFYKEAG 314 T L PLHPGA ++YKE G Sbjct: 299 TAGLSAPLHPGAAKYYKEQG 318 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: 225 Number of extensions: 8 Number of successful extensions: 4 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: 321 Length adjustment: 28 Effective length of query: 289 Effective length of database: 293 Effective search space: 84677 Effective search space used: 84677 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