Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate WP_053937455.1 WG78_RS08855 transporter substrate-binding domain-containing protein
Query= uniprot:A0A1N7UK26 (258 letters) >NCBI__GCF_001294205.1:WP_053937455.1 Length = 260 Score = 121 bits (304), Expect = 1e-32 Identities = 86/254 (33%), Positives = 130/254 (51%), Gaps = 19/254 (7%) Query: 7 LFAALLLPLCATAHAQEWKE-------IRFGVFPEYPPFESVAADGSLQGFDIELGNAIC 59 L AALL A+A A + + +R V YPPF + +G L GFD+E+ A+ Sbjct: 7 LIAALLGITAASAMAADLLDSVKQRGTLRVAVEGTYPPF-NYKDNGQLTGFDVEIAQALA 65 Query: 60 AKLEVKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRK 119 KL VK + E+ G++ L A K+D I++ + +T R++ DFSD LS ++ RK Sbjct: 66 QKLGVKAEFTTTEWSGILAGLSAGKYDVIVNQVGITAKRQESFDFSDPYVLSQAQLVVRK 125 Query: 120 --SADFGDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLD 177 S +F T + L GK+VGV QG+ +A A G +K Y + + DL R+D Sbjct: 126 DDSRNF-KTLDDLKGKKVGVGQGT---NFAEMLKAVNGIDVKTYPGEQEYLQDLALSRID 181 Query: 178 ATLTDKLEAQLNFLSKPEGSDFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQ 237 A L D L + +L K G +P+L + KN+ +A +NK +A ++ Sbjct: 182 AALNDTL--MIPYLIHKTNLPLKAGAGVGEPSLN---GIPFVKNNPKFKAALNKALADIK 236 Query: 238 ADGTYAQIQKKYFG 251 ADGTY +I K+FG Sbjct: 237 ADGTYNKISTKWFG 250 Lambda K H 0.319 0.135 0.393 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: 146 Number of extensions: 9 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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