Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate 8500099 DvMF_0862 ABC transporter related (RefSeq)
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Miya:8500099 Length = 248 Score = 251 bits (641), Expect = 9e-72 Identities = 134/241 (55%), Positives = 170/241 (70%), Gaps = 2/241 (0%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 +I + + K++G L +++L V GEK+VI GPSGSGKST +R +N LE V G ++V Sbjct: 9 IIRISHAWKFFGELTALNDVSLDVMPGEKVVICGPSGSGKSTLLRSINRLETVDKGTIIV 68 Query: 61 NNLVLNHK-NKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119 + +N N I R+ MVFQ FNL+PH TVLQNLT+APM+L+K + EAE A + Sbjct: 69 DGQDVNSPDNDINKIRQELGMVFQSFNLFPHKTVLQNLTMAPMRLRKTPRAEAESRALEL 128 Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179 LK VG+ DKANV+PA LSGGQQQRVAIAR+L +LFDEPTSALDPE I EVLDVM Sbjct: 129 LKKVGISDKANVFPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVLDVMV 188 Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239 ++ + TMV VTHEMGFA+EVADRIIFM+ G ++EEN P +FF PK R + FL +I Sbjct: 189 TLARE-GMTMVCVTHEMGFAREVADRIIFMDHGQVLEENAPQDFFGAPKHPRLQKFLNQI 247 Query: 240 L 240 L Sbjct: 248 L 248 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: 3 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: 248 Length adjustment: 24 Effective length of query: 218 Effective length of database: 224 Effective search space: 48832 Effective search space used: 48832 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