Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate AO353_25660 AO353_25660 ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25660 Length = 259 Score = 295 bits (754), Expect = 8e-85 Identities = 138/241 (57%), Positives = 182/241 (75%) Query: 17 ATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKCTWVHNEFDGM 76 A A A+EW E+RFG P YPPFES ADG +QGF ++LGNAICA+L++KC WV N+FDG+ Sbjct: 18 AGASAKEWTELRFGTNPSYPPFESTTADGGVQGFGVDLGNAICAELKLKCVWVSNDFDGL 77 Query: 77 IPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDTPESLMGKQVG 136 IPAL+A KFDAI SSM VT AR+K IDF+DRL+ PT+++TRK + T ESL GK +G Sbjct: 78 IPALKAGKFDAIESSMTVTDARKKQIDFTDRLYAGPTAIVTRKDSGLEPTAESLKGKTIG 137 Query: 137 VLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQLNFLSKPEG 196 +QG++QE YARA LA G +++AYQ+QDQ YADL GRLDA++ DKL+AQ++FL P+G Sbjct: 138 FMQGTIQETYARAKLAPGGVKLRAYQNQDQVYADLVYGRLDASIQDKLQAQMSFLESPQG 197 Query: 197 SDFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQADGTYAQIQKKYFGDQDIY 256 + FK DP +P DIA+G+RK++ L+ ++N I A+ G YAQIQKKYFGD D+Y Sbjct: 198 APFKNSQGISDPLVPADIAIGVRKDNDELKGMLNTAIKALHEKGIYAQIQKKYFGDLDLY 257 Query: 257 H 257 + Sbjct: 258 N 258 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: 231 Number of extensions: 9 Number of successful extensions: 1 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: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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 17 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