Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate WP_086508345.1 BZY95_RS02045 nickel transporter
Query= uniprot:E4PNW5 (250 letters) >NCBI__GCF_002151265.1:WP_086508345.1 Length = 255 Score = 263 bits (673), Expect = 2e-75 Identities = 130/252 (51%), Positives = 173/252 (68%), Gaps = 8/252 (3%) Query: 1 MKKMIFAASCALALIAGGAQAQERD-LRIAFDVPYEPFEYKDENGELTGFEVELAEAMCE 59 MKK++ + +AL AG AQA++ D +R DVPYEP EY+ +GELTGF+++L A+C Sbjct: 1 MKKLLTVSLLGVALAAGTAQARDYDHVRFGVDVPYEPMEYRTPDGELTGFDIDLGNALCA 60 Query: 60 EMNANCEFVIQAWDGMIPGLLARKFDLIMSSMSITPERAERVLFSEPYYNTPGGWFGPES 119 EM CE++ Q WDG+IPGLLAR +D IMSSM+I ER + +LFS+PY PG WF P Sbjct: 61 EMGITCEWIEQEWDGIIPGLLARNYDAIMSSMTINDERRQTLLFSDPYITIPGAWFAPAG 120 Query: 120 FNTDVTDMSAMEGKTVGVQRGTTMDTYVTENMGGIVTIKRYTTADDMVLDLEGQRLDVVF 179 + + + + GK++GVQRGTT D+YVT+N G + + RY+TADDMVLDL+ QRLD+VF Sbjct: 121 SDVEEINEETLAGKSIGVQRGTTFDSYVTDNYGRVANVSRYSTADDMVLDLQAQRLDLVF 180 Query: 180 VDYPVGEQTVLTKEG--FKEVGEAVK-----LGEGVGVAMRQRDTDLAEEVNAALRTLKE 232 +++ VG+ T+L F+ VGE V GEG G+A R RD LA+ N AL TLKE Sbjct: 181 LEFIVGQATLLDNHSGEFEVVGEMVTEPEEYFGEGFGIAFRPRDEALAQRFNEALATLKE 240 Query: 233 DGTYDTIMQKYF 244 DGTYD I Q+YF Sbjct: 241 DGTYDEIYQRYF 252 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: 237 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: 250 Length of database: 255 Length adjustment: 24 Effective length of query: 226 Effective length of database: 231 Effective search space: 52206 Effective search space used: 52206 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