Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_013450517.1 CALNI_RS01940 C4-dicarboxylate ABC transporter substrate-binding protein
Query= reanno::psRCH2:GFF85 (317 letters) >NCBI__GCF_000183405.1:WP_013450517.1 Length = 334 Score = 142 bits (359), Expect = 9e-39 Identities = 98/298 (32%), Positives = 151/298 (50%), Gaps = 14/298 (4%) Query: 31 ILTGGTSGVYYPIGVALSQQYNKIDGAKTSVQATK----ASVENLNLLQAGRGELAFSLG 86 I T G YYP+GVA+ + A +QAT S EN+++++ +LA Sbjct: 29 IATATPGGTYYPVGVAIGTLISIKLKASHGIQATAINSAGSGENISMMKKKEADLALLQS 88 Query: 87 DSVEDAWNGVEDAGFKAPLKRLRAIAGTYNNYIQIVASAE----SGIKTLDDLKGKRISV 142 +A+ G KA K RAI + N E I L +LKGK S+ Sbjct: 89 LFAHEAYAGEGMYAGKAE-KDFRAITMLWQNVEHFPILKEYVKTGTITDLHNLKGKPFSI 147 Query: 143 GAPKSGTELNARAIFKAAGLDYKDMGRVEFLPYAESVELIKNRQLDATLQSSGLGMAAIR 202 G SGTE + RAI K+ G D ++E+L Y +SV+ + ++++ A +G+ +AI Sbjct: 148 GKRGSGTEGSGRAILKSLGFDVDKEFKLEYLDYNQSVQAMMDKRVGAANIPAGVPASAIT 207 Query: 203 DLASTMP---VTFVEIPAEVVEKIESD--AYLAGVIPAGTYDGQDADVPTVAITNILVTH 257 L + + ++ E ++KI + VI GTY GQ D+ T+ NILV Sbjct: 208 QLYAQLGEKGAIVLDFTDEQLKKIRDHYPIWTRYVIKKGTYPGQTKDINTIGQPNILVAR 267 Query: 258 EKVSDEVAYQMTKLMFDNLAALGNAHSAAKDIKLENATKNLPIPLHPGAERFYKEAGV 315 + +S+E Y +TK +F+NL L N H A K++ L+ A LP+PLHPGA +++KE G+ Sbjct: 268 KDLSEETVYLVTKTIFENLQFLSNIHPATKELSLKEALDGLPVPLHPGAYKYFKEKGL 325 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: 247 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: 334 Length adjustment: 28 Effective length of query: 289 Effective length of database: 306 Effective search space: 88434 Effective search space used: 88434 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