Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_002722395.1 RSPH17029_RS01360 TAXI family TRAP transporter solute-binding subunit
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_000015985.1:WP_002722395.1 Length = 317 Score = 396 bits (1018), Expect = e-115 Identities = 208/312 (66%), Positives = 244/312 (78%), Gaps = 2/312 (0%) Query: 7 LGLLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQY-NKIDGAKTSVQATK 65 L AAAA + AA FIN+LTGGTSGVYYP+GV LS+ Y I+GA+T VQATK Sbjct: 7 LSAAAAAAVLSLQPQVAAAQEFINVLTGGTSGVYYPLGVGLSEIYAENIEGARTQVQATK 66 Query: 66 ASVENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASA 125 ASVENLNLL +GELAF+LGDSV AW G E+AGF PLK LRAIA Y NYIQIVA A Sbjct: 67 ASVENLNLLAQRKGELAFALGDSVTLAWEGNEEAGFPRPLKNLRAIAAIYPNYIQIVADA 126 Query: 126 ESGIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNR 185 SG+ TL+DLKGK +SVGAP SGTELNARAIF AAG+ Y+D+ +VE+LPYAES ELIKNR Sbjct: 127 ASGVTTLEDLKGKTLSVGAPASGTELNARAIFGAAGMSYEDLAKVEYLPYAESAELIKNR 186 Query: 186 QLDATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYDGQDADV 245 QL ATLQSSGLG+A I+DL+ST + V IPAEVVEKI + Y VIPAGTY GQDADV Sbjct: 187 QLQATLQSSGLGVAFIKDLSSTHDINLVSIPAEVVEKIGA-PYQPAVIPAGTYSGQDADV 245 Query: 246 PTVAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPG 305 PT A+ N+LVTHE VS+E AYQMTKLMF+NL L +AH+AA +IK E A + LPIPLHPG Sbjct: 246 PTAAVGNLLVTHEDVSEETAYQMTKLMFENLDRLKSAHAAAGNIKPETAIEALPIPLHPG 305 Query: 306 AERFYKEAGVLK 317 AE++Y+E G+++ Sbjct: 306 AEKYYREIGLIQ 317 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: 331 Number of extensions: 7 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: 317 Length adjustment: 27 Effective length of query: 290 Effective length of database: 290 Effective search space: 84100 Effective search space used: 84100 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 Apr 10 2024. 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