Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate BPHYT_RS16690 BPHYT_RS16690 glutamate/aspartate transporter permease GltK
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__BFirm:BPHYT_RS16690 Length = 225 Score = 101 bits (251), Expect = 3e-26 Identities = 70/227 (30%), Positives = 121/227 (53%), Gaps = 13/227 (5%) Query: 210 SALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEF 269 S +P ALP + + G ++ I + AIV + G +LA+ R S + + G + Sbjct: 7 SGIPGALPTL----WTGAIVTFKITLIAIVFGIVWGTILAMMRLSSFKPFEWFAKGYVTI 62 Query: 270 VRGVPLITLLFTASLLLQYFLPP--GTNFDLILRV---VILVTLFAAAYIAEVIRGGLAA 324 R +PL+ +L L++ L G + D+ +R+ ++ +LF AAY +E+IR G+ + Sbjct: 63 FRSIPLVMVLLWFFLIVPQVLQNVLGLSPDIDIRLASAMVAFSLFEAAYYSEIIRAGIQS 122 Query: 325 LPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLK 384 + RGQ A+ ALG+ Y Q+ RLI++PQA + +P +++ I LF+DT+LV + L D + Sbjct: 123 VARGQVNASFALGMTYAQSMRLIVLPQAFRAMVPLLLTQGIVLFQDTSLVYVISLADFFR 182 Query: 385 GISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKR 431 +N+ D GT E +F +F+ S L++K+ R Sbjct: 183 TATNIGDRD----GTNVEMVLFAGACYFVICVVASSLVKGLQKKVAR 225 Lambda K H 0.329 0.143 0.457 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: 231 Number of extensions: 11 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: 434 Length of database: 225 Length adjustment: 27 Effective length of query: 407 Effective length of database: 198 Effective search space: 80586 Effective search space used: 80586 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: 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