Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS21615 HSERO_RS21615 ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS21615 Length = 271 Score = 99.0 bits (245), Expect = 9e-26 Identities = 64/223 (28%), Positives = 112/223 (50%), Gaps = 5/223 (2%) Query: 30 GVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKCTWVHNEFDGMIPALRARKFDAIM 89 GV Y PF S + GFDI++ A+ K+ ++ +V F+G L D ++ Sbjct: 52 GVESAYAPFSSENEQKDVVGFDIDIMKALAKKIGIEVKFVPTPFEGFFNFLAQGDRDLLI 111 Query: 90 SSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDTPESLMGKQVGVLQGSLQEAYARA 149 S++ +T R+K + FS+ F++ ++ + E L VG + + + Sbjct: 112 SAITITDERKKSVAFSEPYFVATQTIALPAADTKVSKMEDLKPLTVGTQSATSGDELVQQ 171 Query: 150 HLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQLNFLSKPEGSDFKTGPAFKDPT 209 L K A+IK + S +L++G +DA + D+ + N+++ S +T DP+ Sbjct: 172 VLGKNSAKIKRFDSTPLALKELESGGVDAVVADEPVVK-NYIANNPNSKLRT---VTDPS 227 Query: 210 LPL-DIAMGLRKNDQALRALINKGIAAVQADGTYAQIQKKYFG 251 P D + +RK+D L A INKG+A ++ADG++A I +YFG Sbjct: 228 FPKEDYGIAVRKDDPELLAKINKGLAEMKADGSFAAISAQYFG 270 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: 153 Number of extensions: 8 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: 271 Length adjustment: 25 Effective length of query: 233 Effective length of database: 246 Effective search space: 57318 Effective search space used: 57318 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