Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate SMc00140 SMc00140 amino-acid binding periplasmic protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__Smeli:SMc00140 Length = 260 Score = 156 bits (395), Expect = 4e-43 Identities = 87/250 (34%), Positives = 151/250 (60%), Gaps = 6/250 (2%) Query: 4 LRSLFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLE 63 L + +A + L A E +++ G YPPF ++ +DG+L GFDI++ A+C +++ Sbjct: 7 LAATASAAVFVLMAGVAMAEGEKVVIGTEGAYPPFNNLESDGTLTGFDIDIAKALCEEMK 66 Query: 64 VKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADF 123 +CT+V ++DG+IPAL A+KFDAI++SM++T R++ +DF+++ + +P +++ K + Sbjct: 67 AECTFVTQDWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPKDSPI 126 Query: 124 GD-TPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTD 182 + T +L GK +G + YA AH+ + +++K Y + D+ DL NGR+DA + D Sbjct: 127 TEATAAALSGKALGAQGSTTHSNYAEAHMKE--SEVKLYPTADEYKLDLANGRIDAAIDD 184 Query: 183 KLEAQLNFLSKPEGSDFK-TGPAFKDPTLPLDIA-MGLRKNDQALRALINKGIAAVQADG 240 + +L +G+ K G DP + + A + +RK D ALR +NK I A++A+G Sbjct: 185 VVVLS-EWLKTEDGACCKLLGTLPIDPVINGEGAGIAIRKGDDALREKLNKAIEAIRANG 243 Query: 241 TYAQIQKKYF 250 Y QI +KYF Sbjct: 244 KYKQINEKYF 253 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: 186 Number of extensions: 13 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 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