Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate WP_046158297.1 VL52_RS17825 ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >NCBI__GCF_000971335.1:WP_046158297.1 Length = 254 Score = 166 bits (420), Expect = 4e-46 Identities = 96/256 (37%), Positives = 149/256 (58%), Gaps = 10/256 (3%) Query: 5 RSLFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEV 64 ++L A+ + L A+ AQ + +R GV YPPF ADG QGFDI++ N++CA ++V Sbjct: 3 KALIASAGIALLASLSAQA-ETLRIGVDLNYPPFSKQGADGKPQGFDIDIANSLCAAMKV 61 Query: 65 KCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFG 124 C V ++DG+IPAL A KFDAI+SSM +TP R+K +DFS + + ++ +R A G Sbjct: 62 TCQIVPQDWDGLIPALNANKFDAIISSMQITPERQKAVDFSHKYY----NIASRMVAKDG 117 Query: 125 DTPE--SLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTD 182 + SL GK++GVL+ S QE +A+ + K GA I +Y +++ DL++GR+DA D Sbjct: 118 TKVDAASLKGKKIGVLRASTQEKFAKDNWGKNGAAIVSYAKSPESFLDLKSGRVDAVFVD 177 Query: 183 KLEAQLNFLSKPEGSDFK-TGPAFKD-PTLPLDIAMGLRKNDQALRALINKGIAAVQADG 240 + FL + + GP + D + ++K ++AL +NK I ++ DG Sbjct: 178 SAVGEQEFLKTAQAKGYAFVGPNYSDVKYFGPGCGIAVKKGNKALVERLNKAIDQIRKDG 237 Query: 241 TYAQIQKKYFGDQDIY 256 Y ++Q KYF DIY Sbjct: 238 AYKKVQDKYF-SFDIY 252 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: 171 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: 258 Length of database: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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