Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_009763321.1 MICLODRAFT_RS18455 TAXI family TRAP transporter solute-binding subunit
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_000262405.1:WP_009763321.1 Length = 327 Score = 168 bits (425), Expect = 2e-46 Identities = 119/329 (36%), Positives = 176/329 (53%), Gaps = 17/329 (5%) Query: 1 MRLTKR----LGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNKIDG 56 M+LT+R +GL AA+ A AP F I TGGT+G YYP+G ++ + Sbjct: 3 MKLTRRELAKIGLGLGAASVLGRGAFAQAPAFFRIGTGGTAGTYYPVGGLIANAISNPPQ 62 Query: 57 AKTSVQATKASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYN 116 + QA+ SV N+N + +G E F+ D A+ G K ++ LR +A Y Sbjct: 63 LVLTAQASNGSVANVNSIVSGALESGFTQADVAYWAYTGTGLFEGKGKIEDLRLLANLYP 122 Query: 117 NYIQIVASAESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYA 176 I +VA+ + IK++ DLKGKR+S+ P SGT ++AR I G+ D+ + +FL Sbjct: 123 ESIHLVAAKSANIKSVADLKGKRVSMDEPGSGTLVDARIILAGWGIKESDV-KADFLKPN 181 Query: 177 ESVELIKNRQLDATLQSSGLGMAAIRDLAST------MPVTFVEIPAEVVEKIESDAYLA 230 ++ E +++ LDA G +AI +LA+T +P+ E A+ + K + + A Sbjct: 182 QAAERMRDGGLDAFFFVGGYPTSAITELAATGGGVDLVPLAGPE--ADAIRK-QYSFFAA 238 Query: 231 GVIPAGTYDGQDADVPTVAITNILVTHEKVSDEVAYQMTKLMFDN--LAALGNAHSAAKD 288 IPAGTY A V T+A+ VT KV D V Y++ K ++ + AAL H+ K Sbjct: 239 DEIPAGTYKDVSA-VKTLAVGAQWVTSAKVPDAVVYEVVKGLWGDKTRAALDAGHAKGKM 297 Query: 289 IKLENATKNLPIPLHPGAERFYKEAGVLK 317 I+ ENA IP+H GAERFYKEAG+LK Sbjct: 298 IRKENALAGAGIPIHAGAERFYKEAGLLK 326 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: 246 Number of extensions: 14 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: 327 Length adjustment: 28 Effective length of query: 289 Effective length of database: 299 Effective search space: 86411 Effective search space used: 86411 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 24 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