Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Btheta:353166 Length = 218 Score = 144 bits (364), Expect = 1e-39 Identities = 81/220 (36%), Positives = 130/220 (59%), Gaps = 5/220 (2%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 MI+L+ + K +G+ VLK I+L + +GE + I+GPSG+GK+T ++ M L+E +G V + Sbjct: 1 MIKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAI 60 Query: 61 NNLVLNHKNKIEIC---RKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAF 117 + V++ + E+ K VFQ L P T L+N+ + P + S KEA E A Sbjct: 61 DGTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMI-PAFIAGVSSKEANERAM 119 Query: 118 KYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDV 177 + L +GL D+A+ P LSGG++QRVA+AR+L IL DEP+ +LD +++ + Sbjct: 120 EILAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQL 179 Query: 178 MKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEE 217 ++ + T V+VTH+ G AK + DR + M DG I ++ Sbjct: 180 FFDLRDRLGQTFVIVTHDEGLAK-ITDRTVHMVDGTIKKD 218 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: 122 Number of extensions: 6 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: 218 Length adjustment: 23 Effective length of query: 219 Effective length of database: 195 Effective search space: 42705 Effective search space used: 42705 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