Align Tricarboxylate transport protein TctC (characterized)
to candidate WP_092347638.1 BLU87_RS10045 tripartite tricarboxylate transporter substrate binding protein
Query= reanno::Dino:3609740 (326 letters) >NCBI__GCF_900107645.1:WP_092347638.1 Length = 326 Score = 367 bits (943), Expect = e-106 Identities = 178/317 (56%), Positives = 231/317 (72%), Gaps = 1/317 (0%) Query: 10 LIAAAAALAMTGGAHAEGEQMLESIHFLIPGGAGGGWDGTARGTGEALTKAGLVGSASYE 69 + A ALA+ G +++ + +HFLIPGGAGGGWDGTARG G+ L +GL+ S+E Sbjct: 10 IFLALFALALPVGTSLASDEV-DELHFLIPGGAGGGWDGTARGVGKVLLDSGLLKHTSFE 68 Query: 70 NMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTLVAGTIGDYAA 129 NMSGGGGGKA+ +LI A T++VNSTPI+IRSLTG QSF DLT +A I DYAA Sbjct: 69 NMSGGGGGKALNHLIGTAKRQQNTMLVNSTPIIIRSLTGVFPQSFHDLTPIAAVIADYAA 128 Query: 130 IVVGKDSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVMEAAGKDALGVKYIP 189 +VV KDS ++ ++A + ADP + +GGGSV GGMDHLV AM+++AAG + L + YIP Sbjct: 129 LVVPKDSKYQTLDQVLADFKADPRSIKIGGGSVKGGMDHLVPAMIIKAAGGNPLDLGYIP 188 Query: 190 YDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYDSAPTMVEQGI 249 YDAGGKAMA LLSG+I L+TGFSEA+ LA GEV+II VT+ ER+A T+ E GI Sbjct: 189 YDAGGKAMAGLLSGDIKVLATGFSEALGLANQGEVRIIAVTSEERLAQAPGVQTVKESGI 248 Query: 250 DTTFVNWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIHNSGADFQSFL 309 D TF NWRGFF APGLPE + AY+ L+KMYDTPEWE++R++ GW N++ G +F +FL Sbjct: 249 DVTFANWRGFFGAPGLPEARAQAYRDLLKKMYDTPEWEDIRSKRGWQNLYKPGTEFTAFL 308 Query: 310 EAQEAQIGDLMKKLGFL 326 + QE IGD+M++LGF+ Sbjct: 309 DNQEKAIGDMMRELGFI 325 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: 406 Number of extensions: 20 Number of successful extensions: 1 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: 326 Length adjustment: 28 Effective length of query: 298 Effective length of database: 298 Effective search space: 88804 Effective search space used: 88804 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 24 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