Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS10775 HSERO_RS10775 cysteine ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS10775 Length = 267 Score = 108 bits (270), Expect = 1e-28 Identities = 73/221 (33%), Positives = 115/221 (52%), Gaps = 14/221 (6%) Query: 35 YPPFE-SVAADGSLQGFDIELGNAICAKLEVKCTWVHNEFDGMIPALRARKFDAIMSSMA 93 YPPF G L GF++++ + AKL VK + E+ G++ L A K+D I++ + Sbjct: 47 YPPFNFKDPKTGELTGFEVDVAKLLAAKLGVKPVFTTTEWSGILAGLGAGKYDVIINQVG 106 Query: 94 VTPAREKIIDFSDRLFLSPTSVITRK--SADFGDTPESLMGKQVGVLQGSLQEAYARAHL 151 +T R+K DFSD LS +I RK +F + E L GK++G+ QG+ E A+ Sbjct: 107 ITDERQKAFDFSDPYTLSSAQLIVRKDEKREF-KSLEDLKGKKLGLGQGTNFEQKAK--- 162 Query: 152 AKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQLNFLSKPEGSDFKTGPAFKDPTLP 211 A G ++ Y + ADL GR+DA L D L + ++ K K G P Sbjct: 163 AVPGIDVRTYPGSPEYLADLAAGRIDAALNDSL--LVGYILKSTNLPLKAG----SPIGA 216 Query: 212 LD-IAMGLRKNDQALRALINKGIAAVQADGTYAQIQKKYFG 251 +D I + RK + +A +NK +A ++ADG++ +K+FG Sbjct: 217 VDKIGIPFRKGNPEFKAALNKALADIKADGSFKAASEKWFG 257 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: 159 Number of extensions: 15 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: 267 Length adjustment: 25 Effective length of query: 233 Effective length of database: 242 Effective search space: 56386 Effective search space used: 56386 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