Align Citrate uptake transporter, substrate binding protein, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate SM_b20724 SM_b20724 hypothetical protein
Query= TCDB::S5XTE7 (334 letters) >FitnessBrowser__Smeli:SM_b20724 Length = 314 Score = 223 bits (569), Expect = 4e-63 Identities = 114/291 (39%), Positives = 173/291 (59%), Gaps = 4/291 (1%) Query: 48 SNMTLIAPAAAGGGWDTFQREQQQSMRVNKIVNNIQVVNIPGAGGTIALGKLSTMTA--P 105 ++ T+IAPA GGGWD R Q M+ I N+QV N+PGAGGTI L + ++ P Sbjct: 21 ADYTIIAPANPGGGWDQTARSLQTVMQQEGISGNVQVQNVPGAGGTIGLAQFASQQKGNP 80 Query: 106 NTLMVGGTGHIAAQIQFDTPAKIQDVTPIARVVEEFDIITVPADSPYNTLEELIEGWKAD 165 N L+VGG + A + ++P ++DVTPIAR+ E++ I VPA S T+++L+E K D Sbjct: 81 NALLVGGYVMVGAILTNNSPVTLKDVTPIARLTGEYEAIVVPAASEIQTMKDLVEALKKD 140 Query: 166 PAGVSWTGG--GSFDQLVMTEIALSAGIDPKQTTFIPSDGGGEAIQALLNGTAKASTGGF 223 P VSW GG G D + + IA +AG+DP + +I GGGEA+ A+L A G+ Sbjct: 141 PGAVSWAGGSAGGTDHIAVGLIAKAAGVDPTKINYIAYSGGGEALAAILGNQVTAGISGY 200 Query: 224 ADMYPQVEAGRLKVLGIAAEERLPGSDIPTLVEQGYDVTLTNWRAMFAPPGLSDDQIAEL 283 + QV+AG L++L +++ ERL G D PTL E G DV + NWR + A PGL+++Q A + Sbjct: 201 GEFESQVKAGTLRLLAVSSAERLEGIDAPTLKESGVDVVVENWRMVAAAPGLTEEQKAAV 260 Query: 284 RAIVAESVETAEWQSAVERNYWMNASLEGEELDQFVEDEIDRIDQLFKEMG 334 A + + ++A WQ ++ W + L G D+ + +I + + K++G Sbjct: 261 SADIEKLAKSAGWQEVLKTKGWQDTYLAGAAFDEQLAKDISATETVLKDIG 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: 344 Number of extensions: 22 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 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