Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate BPHYT_RS21915 BPHYT_RS21915 ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__BFirm:BPHYT_RS21915 Length = 222 Score = 129 bits (325), Expect = 4e-35 Identities = 68/201 (33%), Positives = 115/201 (57%), Gaps = 1/201 (0%) Query: 45 INGFIYTLEVSILALLIATIFGTIGGV-MATSRFKIIRAYTRIYVELFQNVPLVIQIFFL 103 ++G + T+EV+ +L ++ + G + G+ T + +I+ + Y+ F+ PL++Q+F L Sbjct: 16 LHGAVVTVEVTAASLALSCVLGLLIGIGRLTPKRRIVYGFCTAYLTFFRGTPLLVQLFLL 75 Query: 104 FYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMR 163 F+ LP GI L F G+LG+G Y AYVSE+VR I +V RGQ EA+ S G + Q MR Sbjct: 76 FFGLPQFGILLPAFVCGMLGLGLYSAAYVSEIVRGAIQSVDRGQMEAARSIGMSSGQAMR 135 Query: 164 YIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAV 223 II+PQ I ++PP+ N+ + LIKN++++ ++ +LMH + Y+ A+ Sbjct: 136 AIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQKIISVSYRSLEVYLAIAL 195 Query: 224 LYFIICYPLAYFAKAYENKLK 244 +Y ++ Y E L+ Sbjct: 196 VYLVLTQATNYALHRVERHLR 216 Lambda K H 0.328 0.143 0.422 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: 145 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: 250 Length of database: 222 Length adjustment: 23 Effective length of query: 227 Effective length of database: 199 Effective search space: 45173 Effective search space used: 45173 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: 46 (22.3 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