Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate AO356_27120 AO356_27120 ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27120 Length = 260 Score = 268 bits (686), Expect = 6e-77 Identities = 136/257 (52%), Positives = 181/257 (70%), Gaps = 1/257 (0%) Query: 1 MTPLRSLFAALLLPLCATA-HAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAIC 59 M L+ L+ + L LC +A A+E+ +RFGV Y PFES AADGSL+GFDI+LGNAIC Sbjct: 1 MISLKKLYLVMGLALCTSAVSAKEYSTLRFGVDANYAPFESKAADGSLKGFDIDLGNAIC 60 Query: 60 AKLEVKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRK 119 AKL VKC WV ++FDG+IP LRA KFD I+SSM VT REK IDFS+ LF TS + +K Sbjct: 61 AKLSVKCIWVESDFDGLIPGLRAGKFDGILSSMTVTATREKAIDFSNELFSGFTSYVFKK 120 Query: 120 SADFGDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDAT 179 + SL GK VG QGS+QEAYA+A L K G +I++YQ+QDQ Y DL GRLDA+ Sbjct: 121 GSGLNTDVASLKGKTVGYFQGSIQEAYAKAVLDKAGVKIQSYQNQDQVYYDLVAGRLDAS 180 Query: 180 LTDKLEAQLNFLSKPEGSDFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQAD 239 L D L+AQL F++ P+G++++ P+ + P LP A+G+ K + L+AL++K I A+ D Sbjct: 181 LQDTLQAQLGFITSPQGAEYEMSPSVESPYLPSKTAIGIAKGNTELKALLDKAIQALHDD 240 Query: 240 GTYAQIQKKYFGDQDIY 256 GTY IQK++FGD ++Y Sbjct: 241 GTYDSIQKQHFGDLNLY 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: 204 Number of extensions: 6 Number of successful extensions: 1 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