Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate Ac3H11_3325 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= uniprot:E4PNW5 (250 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3325 Length = 253 Score = 95.9 bits (237), Expect = 7e-25 Identities = 79/260 (30%), Positives = 127/260 (48%), Gaps = 23/260 (8%) Query: 3 KMIFAASCALALIAG-GAQAQERD-------LRIAFDVPYEPFEYKDENGELTGFEVELA 54 K+ A + ALAL A AQA+ D + IA + + PF + + LTGFEVE+A Sbjct: 2 KLFKAVATALALCAAFAAQARTLDEVKKDGKILIATEGQFAPFNFFNGT-TLTGFEVEVA 60 Query: 55 EAMCEEMNANCEFVIQAWDGMIPGLLARKFDLIMSSMSITPERAERVLFSEPYYNTPGGW 114 E + ++M ++ +D ++ GL ++DL+++S IT ERA+ V F+EP+Y + G Sbjct: 61 ELVAKKMGLTIQWKTLGFDALLTGLRQDRWDLVIASHGITEERAKAVTFTEPHYCSGGMI 120 Query: 115 FGPESFNTDVTDMSAMEGKTVGVQRGTTMDTYVTENMGGIVTIKRYTTADDMVLDLEGQR 174 + D++ GK V VQ GT+ V + + I +K + T D L +R Sbjct: 121 IAMDPAIKSAKDLA---GKIVAVQTGTSYLENV-QKVSSIKEMKNFPTDVDARSALNSRR 176 Query: 175 LDVVFVDYPVGEQTVLTKEGFKEVGEAVKLG-----EGVGVAMRQRDTDLAEEVNAALRT 229 +D D + V K G KLG E + A+ + ++ LA N AL Sbjct: 177 VDAWVTD-----RFVAKAVAEKNPGAGFKLGDMLFIERIAAAVAKGNSSLAGGWNKALAE 231 Query: 230 LKEDGTYDTIMQKYFAYDIK 249 + DG+Y + +KYF D++ Sbjct: 232 VMADGSYAALSKKYFNEDVR 251 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: 139 Number of extensions: 3 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: 253 Length adjustment: 24 Effective length of query: 226 Effective length of database: 229 Effective search space: 51754 Effective search space used: 51754 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 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