Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate HSERO_RS00320 HSERO_RS00320 peptide ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__HerbieS:HSERO_RS00320 Length = 240 Score = 248 bits (633), Expect = 8e-71 Identities = 126/241 (52%), Positives = 173/241 (71%), Gaps = 2/241 (0%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 MI++ + K +G H+L+ I+ ++ E + +IGPSGSGKST +RC+NGLEEVS G++ + Sbjct: 1 MIKVNQLQKRFGQAHILRGIDCEIRAREVVCVIGPSGSGKSTFLRCLNGLEEVSDGDIFI 60 Query: 61 NNLVLNH-KNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119 + LN K + R MVFQ FNL+PHMTVL+NL +APM+++K S++EA A K Sbjct: 61 EGVKLNDPKVNLNALRAELGMVFQRFNLFPHMTVLENLIMAPMQVKKLSRREAVLVAEKL 120 Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179 L+ VGLLDK + +P LSGGQQQRVAIAR+L + +LFDEPTSALDPE + EVL VMK Sbjct: 121 LQKVGLLDKIDAFPNQLSGGQQQRVAIARALAMEPKVMLFDEPTSALDPELVGEVLTVMK 180 Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239 +++ + TMVVVTHEMGFA+EV+DR++F++ G I+EE P + +P ER R FL K+ Sbjct: 181 QLA-EEGMTMVVVTHEMGFAREVSDRVLFIDQGVIMEEGPPQQVLGDPHHERTRDFLRKV 239 Query: 240 L 240 L Sbjct: 240 L 240 Lambda K H 0.317 0.133 0.372 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: 160 Number of extensions: 7 Number of successful extensions: 3 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: 242 Length of database: 240 Length adjustment: 23 Effective length of query: 219 Effective length of database: 217 Effective search space: 47523 Effective search space used: 47523 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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