Align Putative amino-acid binding periplasmic protein (characterized, see rationale)
to candidate WP_010936197.1 DET_RS02300 basic amino acid ABC transporter substrate-binding protein
Query= uniprot:Q92PA9 (260 letters) >NCBI__GCF_000011905.1:WP_010936197.1 Length = 260 Score = 96.7 bits (239), Expect = 4e-25 Identities = 68/226 (30%), Positives = 115/226 (50%), Gaps = 11/226 (4%) Query: 29 KVVIGTEGAYPPFNNL-ESDGTLTGFDIDIAKALCEEMKAECTFVTQDWDGIIPALIAKK 87 +V + T+ +PPF + E + GFDID+ KA+ E+ E TF WD ++ L + Sbjct: 40 QVTVVTDATWPPFEYVNEQTHAIEGFDIDLMKAIAEKGNLEVTFQNVAWDALLAGLATGQ 99 Query: 88 FDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPKDSPITEATAAALSGKALGAQGSTTH 147 + ++S++I ER ++ F++ Y+N + V K++ T + L+GK + AQ TT Sbjct: 100 YKVAISSITINAERAEKWLFSDPYFNAGQMVCVQKNN-TTILSHNDLTGKKVAAQTGTT- 157 Query: 148 SNYAEAHMKE-SEVKLYPTADEYKLDLANGRIDAAIDDVVVLSEWLKTEDGACCKLLGTL 206 + EA E + VK Y DL NG+IDA I D V +++ K +GT Sbjct: 158 -GFIEAQKIEGATVKSYDEIGLAFQDLMNGQIDAVICDTPVAIDYVNANPDK-IKKVGTA 215 Query: 207 PIDPVINGEGAGIAIRKGDDALREKLNKAIEAIRANGKYKQINEKY 252 D E GI++ KG + ++N+ + A+ A+G + Q+ K+ Sbjct: 216 FTD-----EFYGISVAKGQTEILARINQGLAAVIADGTFDQLVAKW 256 Lambda K H 0.315 0.132 0.377 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: 173 Number of extensions: 9 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 (21.6 bits) S2: 47 (22.7 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