Align Tricarboxylate transport protein TctC (characterized)
to candidate WP_017597377.1 D471_RS0103690 tripartite tricarboxylate transporter substrate binding protein
Query= reanno::Dino:3609740 (326 letters) >NCBI__GCF_000341125.1:WP_017597377.1 Length = 324 Score = 197 bits (501), Expect = 3e-55 Identities = 115/325 (35%), Positives = 167/325 (51%), Gaps = 16/325 (4%) Query: 12 AAAAALAMT---------GGAHAEGE-QMLESIHFLIPGGAGGGWDGTARGTGEALTKAG 61 AAAA L + G +A+G + I P G GGGWD AR + L G Sbjct: 2 AAAAVLPLALSACGGEDGGNTNADGTWEPNGPIEITAPAGTGGGWDTLARTSARLLESEG 61 Query: 62 LVG-SASYENMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTLV 120 LV S N G GG AY+ N L V S PI++ + G+ D T + Sbjct: 62 LVDQSIQVVNKPGAGGAIGWAYIAGNEGDPQ-KLFVTSPPILLVPMAGDSEYDHEDFTPI 120 Query: 121 AGTIGDYAAIVVGKDSPINSMADLIAAYD-ADPNATAVGGGSVPGGMDHLVAAMVMEAAG 179 A DY +V DS + + DL+ D D N +GGGS PG MDH+ A ++AAG Sbjct: 121 ARLATDYIVYLVPADSELETFDDLVETVDEGDAN---IGGGSAPGSMDHVALAGAIDAAG 177 Query: 180 KDALGVKYIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYD 239 +A Y+P+D GG+AM ALL G + A G SEA + EAGE++ + V++PE V A Sbjct: 178 GNAAAASYVPFDGGGEAMTALLGGHVDAAVVGVSEAAGMLEAGELRALAVSSPEPVEAIA 237 Query: 240 SAPTMVEQGIDTTFVNWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIH 299 PT+++Q +D TF WRG A GL E Q+ Y+ + +T W+E A GW + + Sbjct: 238 DVPTLLDQDVDFTFDIWRGVMAPSGLDEAQVTYYEDLFADLLETQAWQEESASLGWTDAY 297 Query: 300 NSGADFQSFLEAQEAQIGDLMKKLG 324 + ADF +FL+ + ++ +++ ++G Sbjct: 298 QNSADFGAFLDEKRSEFTEILTEVG 322 Lambda K H 0.315 0.132 0.378 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: 346 Number of extensions: 17 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: 326 Length of database: 324 Length adjustment: 28 Effective length of query: 298 Effective length of database: 296 Effective search space: 88208 Effective search space used: 88208 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 Apr 09 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