Align Tricarboxylate transport protein TctC (characterized)
to candidate 3609052 Dshi_2441 hypothetical protein (RefSeq)
Query= reanno::Dino:3609740 (326 letters) >FitnessBrowser__Dino:3609052 Length = 320 Score = 120 bits (301), Expect = 4e-32 Identities = 95/318 (29%), Positives = 144/318 (45%), Gaps = 6/318 (1%) Query: 8 RTLIAAA-AALAMTGGAHAEGEQMLESIHFLIPGGAGGGWDGTARGTGEALTKAGLVGSA 66 +T IAA A + G + A + + ++P GAGGG D R +A +G Sbjct: 5 KTQIAAVMAGVLALGTSPALADYPERPVTIIVPWGAGGGTDTIIRLFSIGFEEA--MGQP 62 Query: 67 SYENMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTLVAGTIGD 126 GG G I NA TL ++ I G + L++ Sbjct: 63 INVVNRTGGSGVVGHSAIANATPDGYTLGACTSEITYFETIGLAPITPASFDLISRLAVI 122 Query: 127 YAAIVVGKDSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVMEAAGKDALGVK 186 A + V DSP NS+ +LIAA +++ GS GG H+ A +M+ G D V+ Sbjct: 123 PAGVTVAADSPYNSLEELIAAAKKGGLSSS---GSGLGGPWHMAIAGMMKQVGGDVNTVQ 179 Query: 187 YIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYDSAPTMVE 246 +IP G A+ L++G I+ + EA LA+AGEVKI+G+ + ER A+ PT+ E Sbjct: 180 FIPSQGGAPALQDLVAGGISMFTGSPIEARALADAGEVKILGIMSDERSPAFPDVPTLKE 239 Query: 247 QGIDTTFVNWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIHNSGADFQ 306 G+D + NW A GLPE+ A +A E+ + + E +E A+ G + + F Sbjct: 240 SGVDWSLTNWFSLCAPAGLPEDVKARIEAAAEQAHGSAEVQEALAQRGITPLFDGSEAFS 299 Query: 307 SFLEAQEAQIGDLMKKLG 324 S+ A L+ LG Sbjct: 300 SYAAAFANDAAGLLTDLG 317 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: 310 Number of extensions: 23 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: 326 Length of database: 320 Length adjustment: 28 Effective length of query: 298 Effective length of database: 292 Effective search space: 87016 Effective search space used: 87016 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 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