Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate WP_086510876.1 BZY95_RS15895 nickel transporter
Query= uniprot:E4PNW5 (250 letters) >NCBI__GCF_002151265.1:WP_086510876.1 Length = 249 Score = 210 bits (535), Expect = 2e-59 Identities = 110/237 (46%), Positives = 144/237 (60%), Gaps = 8/237 (3%) Query: 13 ALIAGGAQAQERDLRIAFDVPYEPFEYKDENGELTGFEVELAEAMCEEMNANCEFVIQAW 72 AL+ G A A+E+ LRI DVPYEP++YK +G +TGFEVEL A CE M C +V QAW Sbjct: 14 ALLGGVANAEEKPLRIGVDVPYEPYQYKLPDGTITGFEVELVNAACERMQRECVWVEQAW 73 Query: 73 DGMIPGLLARKFDLIMSSMSITPERAERVLFSEPYYNTPGGWFGPESFNTDVTDMSAMEG 132 DG+IP L R FDLI S+M+IT ER+ +VLFS+PYY P W G DV +E Sbjct: 74 DGIIPALQVRNFDLIASAMNITEERSHQVLFSDPYYQVPSVWVGKADAEHDVD--GPLED 131 Query: 133 KTVGVQRGTTMDTYVTENMGGIVTIKRYTTADDMVLDLEGQRLDVVFVDYPVGEQTVLTK 192 +GVQ+GT D YVT+ I+RY + +V D+ RLD+VF +P+ ++T+ Sbjct: 132 MAIGVQQGTIQDEYVTQFYPD-TEIRRYADSGSVVADMHAGRLDLVFTAFPLAQRTMFND 190 Query: 193 EGFKEVGEAVK-----LGEGVGVAMRQRDTDLAEEVNAALRTLKEDGTYDTIMQKYF 244 + F GE V G G+G A RQRD LAE N A+ LK DGT+D I ++YF Sbjct: 191 DRFTRQGELVTGPESIYGPGIGAAFRQRDEALAEAFNEAMAELKADGTFDQIFERYF 247 Lambda K H 0.318 0.135 0.389 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: 196 Number of extensions: 9 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: 250 Length of database: 249 Length adjustment: 24 Effective length of query: 226 Effective length of database: 225 Effective search space: 50850 Effective search space used: 50850 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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