Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 160 bits (406), Expect = 2e-44 Identities = 95/223 (42%), Positives = 134/223 (60%), Gaps = 9/223 (4%) Query: 1 MIELKNVNKYYGTHH----VLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56 +IE KN+ K YG VL+ INL +KEGE + I+GPSG GKST + + L+ + G Sbjct: 17 LIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKG 76 Query: 57 EVVVNN---LVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113 V + + + ++ RK +FQ FNL +T L+N+ L P+ L +K+K Sbjct: 77 MVYIKGKKTTMFSENDRAVFRRKISGFIFQQFNLINTLTALENVEL-PLVLDEKNKNYRI 135 Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173 + A K LK++ L + N YP LSGGQQQRVAIAR+L I DEPT LD + +E Sbjct: 136 KKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDSKNSRE 195 Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVE 216 V+D++KE++ + T+++VTHE FAK A RII M+DG IVE Sbjct: 196 VMDILKELNEKEGITVIMVTHEPEFAK-YASRIINMKDGEIVE 237 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: 172 Number of extensions: 8 Number of successful extensions: 4 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: 238 Length adjustment: 23 Effective length of query: 219 Effective length of database: 215 Effective search space: 47085 Effective search space used: 47085 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 Apr 09 2024. 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