Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate RR42_RS29645 RR42_RS29645 ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__Cup4G11:RR42_RS29645 Length = 199 Score = 155 bits (392), Expect = 6e-43 Identities = 87/183 (47%), Positives = 116/183 (63%), Gaps = 3/183 (1%) Query: 71 NEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDTPESL 130 N FDGMIPAL+ARKFDAI SSM+ R K+IDF+ +L+ +++ +K + T ESL Sbjct: 10 NSFDGMIPALQARKFDAINSSMSKNEQRLKVIDFTSKLYAPIEALVVKKGSPLVATAESL 69 Query: 131 MGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQLNF 190 GK+VGVLQGS QE YAR + G I YQ+QD + DL GR+DA + +A F Sbjct: 70 KGKRVGVLQGSTQETYARKYWGGNGVDIVPYQTQDLIWPDLIAGRIDAAMAFAPQADAGF 129 Query: 191 LSKPEGSD--FKTGPAFKDPTL-PLDIAMGLRKNDQALRALINKGIAAVQADGTYAQIQK 247 L P G D F GPA KD ++ +++G+RK+D ALR IN I +++ DGTY +I K Sbjct: 130 LKTPPGKDFVFAQGPAIKDDSIFGPGVSIGVRKDDTALRDAINGAIDSLRKDGTYDKIAK 189 Query: 248 KYF 250 KYF Sbjct: 190 KYF 192 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: 145 Number of extensions: 5 Number of successful extensions: 2 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: 199 Length adjustment: 22 Effective length of query: 236 Effective length of database: 177 Effective search space: 41772 Effective search space used: 41772 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: 46 (22.3 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