Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 123 bits (309), Expect = 3e-33 Identities = 71/206 (34%), Positives = 123/206 (59%), Gaps = 6/206 (2%) Query: 16 VLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVNNLV---LNHKNKIE 72 VLK ++L + E++ I+G SGSGKST + + GL+ + GEV++ L + Sbjct: 24 VLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLLLGQPFSKLGEAARGR 83 Query: 73 ICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKYLKVVGLLDKANVY 132 + ++ V+Q +L P +T +N+ + P+ ++++S+ A + A L VGL + Sbjct: 84 LRNRHMGFVYQFHHLLPELTAEENVMM-PLLIRRESEATARDKALALLDAVGLSRRTAHK 142 Query: 133 PATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMKEISHQSNTTMVVV 192 P+ LSGG++QRVA+AR+L T+ +L DEPT LD + ++VL +M +++ + T ++VV Sbjct: 143 PSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFGTALLVV 202 Query: 193 THEMGFAKEVADRIIFMEDGAI-VEE 217 TH++ A + DR + + DG I VEE Sbjct: 203 THDVNIAARM-DRTLTLRDGMIRVEE 227 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: 105 Number of extensions: 2 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: 242 Length of database: 227 Length adjustment: 23 Effective length of query: 219 Effective length of database: 204 Effective search space: 44676 Effective search space used: 44676 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