Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate Pf6N2E2_321 TRAP transporter solute receptor, unknown substrate 1
Query= reanno::psRCH2:GFF85 (317 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_321 Length = 316 Score = 454 bits (1167), Expect = e-132 Identities = 242/317 (76%), Positives = 267/317 (84%), Gaps = 2/317 (0%) Query: 1 MRLTKRLGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKT 59 MR+ K LLAAAAA ST A AAP +INILTGGTSGVYYPIGV LSQ Y+ I AKT Sbjct: 1 MRVNKHFTLLAAAAALVVSTTAQAAPVYINILTGGTSGVYYPIGVGLSQIYSSGIQDAKT 60 Query: 60 SVQATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYI 119 SVQATKASVENLNLLQAGRGELA +LGDSV DA NGVEDAGFKAPL +LRAIAG Y NYI Sbjct: 61 SVQATKASVENLNLLQAGRGELALALGDSVADAKNGVEDAGFKAPLTKLRAIAGAYPNYI 120 Query: 120 QIVASAESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESV 179 QIVAS ESGIKTL DLKGK +SVGA KSGTELNARAIFKAAGL Y+DM +V++LP+AESV Sbjct: 121 QIVASQESGIKTLADLKGKTVSVGAAKSGTELNARAIFKAAGLTYQDM-KVQYLPFAESV 179 Query: 180 ELIKNRQLDATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYD 239 +LIKNRQLDATLQSSGLGMAAIRDLASTM +++V +P +VVEKI + AY + +IPA TYD Sbjct: 180 DLIKNRQLDATLQSSGLGMAAIRDLASTMALSYVAVPTDVVEKIGNPAYQSAMIPANTYD 239 Query: 240 GQDADVPTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLP 299 GQ VPTVAITNILVT E V DEVAYQMTKL+F+NL LG +HSAAKDI L+NA KNLP Sbjct: 240 GQAEAVPTVAITNILVTREDVPDEVAYQMTKLLFENLTRLGTSHSAAKDITLKNAAKNLP 299 Query: 300 IPLHPGAERFYKEAGVL 316 I LHPGAER+YKE G L Sbjct: 300 IALHPGAERYYKEVGAL 316 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: 347 Number of extensions: 6 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: 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