Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate GFF197 Psest_0198 TRAP transporter solute receptor, TAXI family
Query= reanno::psRCH2:GFF85 (317 letters) >FitnessBrowser__psRCH2:GFF197 Length = 321 Score = 146 bits (369), Expect = 6e-40 Identities = 98/310 (31%), Positives = 140/310 (45%), Gaps = 4/310 (1%) Query: 11 AAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKTSVQATKASVE 69 AA A S A F+ I TGG +GVYY G ++ + N+ + K + A+ V Sbjct: 12 AALAGTGLSGVVQAQEKFVTIGTGGQTGVYYVAGQSICRFVNRNAENIKCNAPASGGGVA 71 Query: 70 NLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAESGI 129 N+N L++G D A GV + + +RA+ + ++A + I Sbjct: 72 NVNGLRSGEFNFGIMQSDHQYKAMEGVAPFEKEGKMDDIRAVFSLQSEVFTVLARRSANI 131 Query: 130 KTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLDA 189 K LDDLKGKR+++G P SG I K G D L AE + + +DA Sbjct: 132 KGLDDLKGKRVNIGNPGSGQRDTLEEIMKVKGWDQSVFSLAAELKPAEQASALGDNNIDA 191 Query: 190 TLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKI--ESDAYLAGVIPAGTYDGQDADVPT 247 G AI++ +T V I ++K+ E Y IP G Y G D + Sbjct: 192 MTYFVGHPNGAIQEATTTTDAVLVPITGPEIDKLLEEKSYYTKAEIPGGLYKGNDQATQS 251 Query: 248 VAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATK-NLPIPLHPGA 306 + +L T KV EV YQ+ K +F+N+ H A KD+K E + L PLH GA Sbjct: 252 IGGKAVLSTTSKVDAEVVYQLVKSVFENIERFQRLHPAFKDLKPEEMIEVGLSAPLHEGA 311 Query: 307 ERFYKEAGVL 316 ER+YKE G L Sbjct: 312 ERYYKERGWL 321 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: 228 Number of extensions: 14 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