Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate HSERO_RS07530 HSERO_RS07530 amino acid ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__HerbieS:HSERO_RS07530 Length = 216 Score = 130 bits (328), Expect = 2e-35 Identities = 74/208 (35%), Positives = 111/208 (53%), Gaps = 4/208 (1%) Query: 37 ALDNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPL 96 + DN + +TL +S LA L I G I +M TS +R + +Y+++ Q P+ Sbjct: 6 SFDNFVFLLEAARWTLLLSALAFLGGGIAGFIVALMRTSHLAPLRLLSAVYIQIIQGTPV 65 Query: 97 VIQIFFLFYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGF 156 +I +F FY L + G +L + + Y AY+ E+ R I AVP Q+EAS + Sbjct: 66 LILLFLSFYGLAIFGYKLPPMVAATIAMTIYSSAYLGEIWRGCIEAVPVPQWEASTALAM 125 Query: 157 TYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAP 216 T QQ+RY+I+PQ +RI LPP +V ++KNTS+ I+G EL + + P Sbjct: 126 TRWQQLRYVILPQAVRISLPPTVGFLVQIVKNTSIASIIGLVELAQAGK--LVSNATFQP 183 Query: 217 AYIFAAV--LYFIICYPLAYFAKAYENK 242 +F V +YF+ CYPL+ FA A E K Sbjct: 184 FLVFPIVAGIYFVFCYPLSRFAFALERK 211 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: 138 Number of extensions: 5 Number of successful extensions: 2 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: 216 Length adjustment: 23 Effective length of query: 227 Effective length of database: 193 Effective search space: 43811 Effective search space used: 43811 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