Align Tricarboxylate transport protein TctB (characterized)
to candidate GFF781 PGA1_c07950 hypothetical protein
Query= reanno::Dino:3609739 (162 letters) >FitnessBrowser__Phaeo:GFF781 Length = 164 Score = 211 bits (536), Expect = 6e-60 Identities = 101/161 (62%), Positives = 126/161 (78%) Query: 1 MALDRWIALVLLGVCLIYGYTAWFTMDADLAPFMRRNPIWPSTFPKVLSVLGAVAALVIL 60 MALDRWIALV+L + L YGYTA+FTMD L PFM+ N IWPSTFPK LSV+ + AL+IL Sbjct: 1 MALDRWIALVILMISLAYGYTAFFTMDEGLPPFMKFNAIWPSTFPKGLSVMAVICALIIL 60 Query: 61 LGLEGPQKPPKAGDIDYRRLGDYKIGQAALLLGLMVGYALLLRPAGFLVSTTSFLILGSV 120 L + PKAGDIDYRRL DYK+GQA LL +MV YAL LRP GFL++T +FL++ ++ Sbjct: 61 LSPQKADAGPKAGDIDYRRLLDYKLGQAMALLAMMVIYALALRPVGFLIATIAFLVVSAM 120 Query: 121 ILGERNWPVMIGVAVVATGAIWYLVQEVLGIFLRPLPMFMG 161 +LGER ++I +AV+A G +WYLVQ+VLGI+LRPLP FMG Sbjct: 121 VLGERKLHILIPIAVLAAGVVWYLVQQVLGIYLRPLPFFMG 161 Lambda K H 0.329 0.147 0.467 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: 130 Number of extensions: 4 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: 162 Length of database: 164 Length adjustment: 18 Effective length of query: 144 Effective length of database: 146 Effective search space: 21024 Effective search space used: 21024 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 (21.8 bits) S2: 43 (21.2 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