Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate AO353_28165 AO353_28165 ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28165 Length = 259 Score = 229 bits (585), Expect = 3e-65 Identities = 120/258 (46%), Positives = 171/258 (66%), Gaps = 4/258 (1%) Query: 4 LRSL-FAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKL 62 LR+L + +L L T +Q + I+FGV P YPPFE DGSL GFDI+LGNA+CA+L Sbjct: 3 LRTLQYTVMLFGLIITPLSQAQQVIKFGVDPSYPPFEQKQPDGSLSGFDIDLGNALCAEL 62 Query: 63 EVKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSAD 122 VKC WV FDGM+PAL+A+KFDAI+S+ + T AR + +DFS +++ +P+S++ RK+A Sbjct: 63 SVKCIWVEQNFDGMVPALKAKKFDAILSAFSATEARRQQVDFSHKIYTAPSSLVARKNAG 122 Query: 123 FGDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTD 182 T SL GK VGV+QGSLQE++A++ G +I +YQ+QDQ ++DL NGRL+A Sbjct: 123 LLPTAASLKGKSVGVVQGSLQESFAKSEWGSQGVEILSYQTQDQVFSDLINGRLEAAFQA 182 Query: 183 KLEAQLNFLSKPEGSDFK-TGPAFKDPTLPLD-IAMGLRKNDQALRALINKGIAAVQADG 240 ++A + L KP+G F G D + D +A+G+RKN+ LR +N IA ++ G Sbjct: 183 SVQADIGLLQKPQGQGFAFAGDPITDKRIIGDGVAIGVRKNEPDLREQLNTAIAGIRQSG 242 Query: 241 TYAQIQKKYFGDQDIYHE 258 Y +I K+YF + DIY E Sbjct: 243 QYDRIAKQYF-NFDIYGE 259 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: 201 Number of extensions: 9 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: 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