Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate RR42_RS09485 RR42_RS09485 amino acid ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__Cup4G11:RR42_RS09485 Length = 216 Score = 134 bits (337), Expect = 2e-36 Identities = 67/194 (34%), Positives = 114/194 (58%) Query: 50 YTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLFYALPV 109 +TL V++LA + T+ G + + TSR ++R + +Y+++ Q P++I +F +Y L V Sbjct: 19 WTLWVTLLAFVGGTLAGFLVALARTSRSALLRLASTVYIQIVQGTPVLIVLFLSYYGLSV 78 Query: 110 LGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYIIVPQ 169 LG++L T +L + Y AY+ E+ R I AVP+GQ+EAS + T QQ+R++++PQ Sbjct: 79 LGLKLSPMTAAMLAMSIYASAYLGEIWRGCIEAVPQGQWEASEALALTRWQQLRHVVLPQ 138 Query: 170 TIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVLYFIIC 229 +R+ LPP V L+KNTS+ I+G EL + ++ A++YF +C Sbjct: 139 AVRLALPPTVGFSVQLVKNTSITSIIGVIELTRAGQLINNATFQPFAVFVVVALIYFALC 198 Query: 230 YPLAYFAKAYENKL 243 +PL+ A+ E +L Sbjct: 199 FPLSSAARRMERRL 212 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: 148 Number of extensions: 4 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