Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_011383332.1 AMB_RS04535 C4-dicarboxylate ABC transporter
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_000009985.1:WP_011383332.1 Length = 312 Score = 378 bits (971), Expect = e-110 Identities = 198/310 (63%), Positives = 242/310 (78%), Gaps = 3/310 (0%) Query: 9 LLAAAAAFTASTAAVAAPTFINILTGGTSGVYYPIGVALSQQYNK-IDGAKTSVQATKAS 67 + A A + A AA F+NILTGGTSGVYYP+G ALS Y K + GA+ +VQATKAS Sbjct: 5 VFGAVLATILAVPAFAADQFLNILTGGTSGVYYPLGNALSSIYGKALPGARVTVQATKAS 64 Query: 68 VENLNLLQAGRGELAFSLGDSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAES 127 VENLNLLQ GRGELAF+LGDS+ AW+GVE+AG+KAPLK+LR +A Y NYIQIVA+A+S Sbjct: 65 VENLNLLQMGRGELAFTLGDSLTQAWDGVEEAGYKAPLKKLRTMAAIYPNYIQIVATADS 124 Query: 128 GIKTLDDLKGKRISVGAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQL 187 GIKTL DLKGKR+SVGAPKSGTELNARAIFKAAGL Y DM +V++LP+ ESVEL+KN+QL Sbjct: 125 GIKTLADLKGKRVSVGAPKSGTELNARAIFKAAGLAYSDM-KVQYLPFGESVELMKNKQL 183 Query: 188 DATLQSSGLGMAAIRDLASTMPVTFVEIPAEVVEKIESDAYLAGVIPAGTYDGQDADVPT 247 DATLQS+GLG++++RDLA+ + V I EV+ K AY+A V+PA TY GQ DVPT Sbjct: 184 DATLQSAGLGVSSLRDLATGDDIVIVAISPEVIAKTGDSAYIASVVPANTYRGQTVDVPT 243 Query: 248 VAITNILVTHEKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGAE 307 A+ N LVTHE V E+ Y MTK MF N+ L AHSAA++I +A K+ PIPLHPGAE Sbjct: 244 AAVRNFLVTHEGVPAELVYGMTKAMFTNMPDLLAAHSAAREIDPAHAAKS-PIPLHPGAE 302 Query: 308 RFYKEAGVLK 317 ++Y+EAG+LK Sbjct: 303 KYYREAGLLK 312 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: 334 Number of extensions: 11 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: 312 Length adjustment: 27 Effective length of query: 290 Effective length of database: 285 Effective search space: 82650 Effective search space used: 82650 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