Align Citrate uptake transporter, substrate binding protein, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate WP_011842397.1 RSPH17029_RS17585 tripartite tricarboxylate transporter substrate binding protein
Query= TCDB::S5XTE7 (334 letters) >NCBI__GCF_000015985.1:WP_011842397.1 Length = 314 Score = 230 bits (587), Expect = 3e-65 Identities = 115/293 (39%), Positives = 175/293 (59%), Gaps = 4/293 (1%) Query: 46 IRSNMTLIAPAAAGGGWDTFQREQQQSMRVNKIVNNIQVVNIPGAGGTIALGKLSTMTA- 104 + ++ T++APAA GGGWD R Q+ +R I +++QV N+PGAGGT+ L + + A Sbjct: 19 LAADYTILAPAAPGGGWDQTARTMQEVLRSEGISDSVQVQNVPGAGGTVGLAQFAASAAG 78 Query: 105 -PNTLMVGGTGHIAAQIQFDTPAKIQDVTPIARVVEEFDIITVPADSPYNTLEELIEGWK 163 P+ L+VGG + A + +P + DVTP+AR+ E++ + VPA SP T+ EL++ K Sbjct: 79 DPSQLIVGGYVMVGAILTNGSPVGLDDVTPVARLTGEYEAVVVPASSPIQTVGELVDQLK 138 Query: 164 ADPAGVSWTGG--GSFDQLVMTEIALSAGIDPKQTTFIPSDGGGEAIQALLNGTAKASTG 221 ADP VSW GG G D + + +A +AG+DP + +I GGGEA+ A+L A Sbjct: 139 ADPGAVSWAGGSAGGTDHIAVGLLAKAAGVDPTKINYIAFSGGGEALAAILGSQVTAGVS 198 Query: 222 GFADMYPQVEAGRLKVLGIAAEERLPGSDIPTLVEQGYDVTLTNWRAMFAPPGLSDDQIA 281 G ++ PQVEAG +++L + A ERL G D PTL E GYDV L NWR + A PG+SD+Q A Sbjct: 199 GLSEFLPQVEAGTMRLLAVTAPERLEGVDAPTLAEAGYDVVLQNWRMVAAAPGISDEQKA 258 Query: 282 ELRAIVAESVETAEWQSAVERNYWMNASLEGEELDQFVEDEIDRIDQLFKEMG 334 + A + + + WQ A+ W N L G+ + + + + + + +E+G Sbjct: 259 AILADIEKMNASEGWQKALASKGWANTWLAGDAFAEQLAKDREATEGILREIG 311 Lambda K H 0.314 0.131 0.375 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: 382 Number of extensions: 24 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: 334 Length of database: 314 Length adjustment: 28 Effective length of query: 306 Effective length of database: 286 Effective search space: 87516 Effective search space used: 87516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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