Align Citrate uptake transporter, membrane subunit, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate RR42_RS20610 RR42_RS20610 tripartite tricarboxylate transporter TctA
Query= TCDB::S5Y5N9 (510 letters) >FitnessBrowser__Cup4G11:RR42_RS20610 Length = 504 Score = 483 bits (1243), Expect = e-141 Identities = 241/510 (47%), Positives = 348/510 (68%), Gaps = 8/510 (1%) Query: 1 MDILSLLMEGFAGALTPMNLLWVIVGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAA 60 MD L+LLM GFA A+TP+NL+W +VGC LGTA+GV+PG+G ++ VA+LLP+T ++PTAA Sbjct: 1 MDTLNLLMHGFAIAITPINLMWALVGCFLGTAIGVLPGIGPALTVAMLLPLTAKVEPTAA 60 Query: 61 FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMALNGRAPQALATAAIGAFIG 120 IMF+G+Y+G ++G ST +ILMNTPG++S + + EG+ MA +GRA ALATAAIG+F Sbjct: 61 LIMFAGIYYGAMYGGSTTSILMNTPGESSTMVTAMEGNLMAKSGRAGPALATAAIGSFAA 120 Query: 121 GIVSSFIVVFLAPTLAELSTAFGPAEYFALALFAFVATSSVVSDSVFKGLASLIFGLGIA 180 G +++ ++ AP A+++ FGP EYF + L AF S+V+ S+ +G+ SL GLGI Sbjct: 121 GTIATVLLSMFAPVAADVALQFGPGEYFMIMLLAFTTVSAVLGSSLLRGMTSLFLGLGIG 180 Query: 181 TIGIDSVTGIERFTLGAPQLFDGISLVTVTVAILALGEVFYIAARARRDKANLETRSAGR 240 IG+DS++G R+++ +L+DGI +V V V + A+GE + A + + S Sbjct: 181 LIGMDSLSGQTRYSMNVQELYDGIDIVVVAVGLFAVGEALFNAFFPQPAGGFNKLSSV-- 238 Query: 241 PWLTGTEFKEAAPAWARGTIIGLPFGVIPVGGSEVPTFLAYSTERALDKRRKDPQFGDKG 300 +T +++K + PAW RGTIIG PFG+IP GG+E+PTFL+Y+TE+ L K + +FG G Sbjct: 239 -MMTKSDWKRSVPAWIRGTIIGFPFGLIPAGGAEIPTFLSYATEKKLSKHK--DEFGTVG 295 Query: 301 AIRGLAAPEAAGNATTGMAMGALLALGLPVSATAAIMLAAFRQYGIQPGPLLFDRNPELV 360 AI G+A PEAA NA + LL LG+P S T AI+LAAF+ Y +QPGP+LF + +LV Sbjct: 296 AIEGVAGPEAANNAAVTATLAPLLTLGIPTSNTTAILLAAFQNYNLQPGPMLFQTSGDLV 355 Query: 361 WALLASFFIAMIVLLFINLPFAQLWAKLLLIPNHYLYSGIALFCGLGIYATSGAVFDLLM 420 W LLAS +I ++LL +NLP LW ++L IP LY GI +F GLG Y + FDLL+ Sbjct: 356 WGLLASLYIGNVMLLVLNLPAIGLWVRMLRIPTPLLYGGILIFAGLGAYGIRQSWFDLLL 415 Query: 421 LLGIGVVALIMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDFSILVSSPITWSLYA 480 L IGV+ + MRR+ +P AP+++GM+LGP+AE LR+AL S GD+SI V+ PI+ Sbjct: 416 LFIIGVLGMAMRRFDFPTAPVIVGMILGPIAEKQLRNALSISQGDWSIFVTQPIS---AT 472 Query: 481 VLAIFIAVSVITAIRGRRKHLTSQLETIDA 510 +LA+ +AV +I I G +++ + DA Sbjct: 473 ILAMTVAVVLIPRILGWLARRSARGKVADA 502 Lambda K H 0.326 0.141 0.414 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: 795 Number of extensions: 36 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: 510 Length of database: 504 Length adjustment: 34 Effective length of query: 476 Effective length of database: 470 Effective search space: 223720 Effective search space used: 223720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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