Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate PP_0226 PP_0226 sulfur compound ABC transporter - permease subunit
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__Putida:PP_0226 Length = 222 Score = 129 bits (325), Expect = 4e-35 Identities = 63/208 (30%), Positives = 115/208 (55%) Query: 38 LDNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLV 97 +D+ + G YT+ +S+ + + G +M S+ + R+YV F+ PL+ Sbjct: 10 VDSAPFLLKGAGYTVLLSVGGMFFGLVLGFALALMRLSKILPLNWLARVYVSFFRGTPLL 69 Query: 98 IQIFFLFYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFT 157 +Q+F +++ +P +GI LD ++G+ AY+ E++R+ I ++ RGQ+EA+AS G T Sbjct: 70 VQLFVIYFGMPQIGIELDPIPASLIGLSLNMAAYICEILRAAISSIDRGQWEAAASIGMT 129 Query: 158 YIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPA 217 +Q MR I+PQ +R LPP+ N ++L+K+T++ + EL A A Sbjct: 130 RVQAMRRAILPQALRTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTFEVFTM 189 Query: 218 YIFAAVLYFIICYPLAYFAKAYENKLKK 245 Y+ AV+Y+++C LA+F E ++ + Sbjct: 190 YVAVAVIYWVLCSILAHFQNRMEARVNQ 217 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: 144 Number of extensions: 9 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