Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate Pf6N2E2_2768 Tricarboxylate transport protein TctC
Query= TCDB::Q9FA46 (325 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2768 Length = 330 Score = 398 bits (1023), Expect = e-116 Identities = 193/319 (60%), Positives = 245/319 (76%), Gaps = 4/319 (1%) Query: 9 LTASILLMSTSVLAQEA---PSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIEKPMRVT 65 L A L+ + +LA + P R ECIAPA PGGGFDLTCKL Q +L+ + KPMRVT Sbjct: 10 LAAGCLMFAGQLLAADPSKEPKRPECIAPASPGGGFDLTCKLAQSALVNQKLLTKPMRVT 69 Query: 66 YMPGGVGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASVGTDYG 125 YMPGGVGAVAYNA+VAQRP + GT+VA+S GSLLNL+QGKFGR+ VRWLA+VGT YG Sbjct: 70 YMPGGVGAVAYNAVVAQRPADAGTLVAWSSGSLLNLAQGKFGRFDESAVRWLAAVGTSYG 129 Query: 126 MIAVRADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPHKMRYV 185 IAV++DSP+K L DL+ A++KDP SVVIG+G ++GSQDWM++AL+A+ A ++P +RYV Sbjct: 130 AIAVKSDSPYKNLDDLVQALKKDPGSVVIGSGGTVGSQDWMQTALIAKAAGINPRDLRYV 189 Query: 186 AFEGGGEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRL-PGQLANIPTAKE 244 A EGGGE TAL+G H+QV S D+S+ +P++ +R+LAVF+E R+ ++ +IPTAKE Sbjct: 190 ALEGGGEIATALLGGHIQVGSTDISDSMPHIQSGDMRLLAVFAEKRIDEPEMKDIPTAKE 249 Query: 245 QGYDLVWPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMTGQQLD 304 QGYD+VWP++RGFY+GPKVSD DY WW D F KL ++EF K RD R LF F MTG +LD Sbjct: 250 QGYDIVWPVVRGFYLGPKVSDEDYAWWKDAFDKLLASEEFAKLRDQRELFPFAMTGPELD 309 Query: 305 DYVKKQVTDYREQAKAFGL 323 YVKKQV DY+ AK FGL Sbjct: 310 AYVKKQVADYKVLAKEFGL 328 Lambda K H 0.318 0.135 0.401 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: 419 Number of extensions: 12 Number of successful extensions: 2 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: 325 Length of database: 330 Length adjustment: 28 Effective length of query: 297 Effective length of database: 302 Effective search space: 89694 Effective search space used: 89694 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: 41 (21.7 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