Align Extracellular solute-binding protein, family 7 (characterized, see rationale)
to candidate GFF3854 HP15_3795 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component
Query= uniprot:Q48AL6 (362 letters) >FitnessBrowser__Marino:GFF3854 Length = 341 Score = 164 bits (415), Expect = 3e-45 Identities = 101/334 (30%), Positives = 165/334 (49%), Gaps = 11/334 (3%) Query: 26 AHADDDKKYRWKLAETWGPNFPIFGDATKNMAKMVKEMSNGRLTIRIDSSNKHKSALGIF 85 A ADD RWK+ + N P G +A + S+G + +R+ K I Sbjct: 12 AFADD---LRWKMPVAFATNLPGLGSPAAWVADNLTTASDGSIQVRVYEPGKLVPPFDIL 68 Query: 86 DFVKSGQYQMGHSASYYWKGKNFNTMFFTTVPFGMIASEQHAWFYYGGGMELMKKVYDQY 145 V G+ G++ Y +GK F VPFGM W+Y+GGG E++++ Y Sbjct: 69 QSVSDGKVSAGYTWIGYDQGKVPAIPLFAAVPFGMKPPAYIGWYYFGGGHEMLQETYANK 128 Query: 146 G--IMSFPGGNTGNQMGGWFKKEINSVEDLKGLKMRIPGFAGEVLAKLGAKPTNIPSGEL 203 G + + G G + GW+ + I ++ED KGLK+R G G+VL KLGA T +P GEL Sbjct: 129 GFNVHAQLCGIIGPETAGWYSEPIETLEDYKGLKIRFAGLGGKVLEKLGASVTMMPGGEL 188 Query: 204 YTALERNTIDALEWVGPSLDLRMGFHKIAPY-YYTGWHEPGTELQFMVNQKAYNSLPKDL 262 Y ALE+ TIDA E+ P++D +GF+++ Y + GWH+ T ++N+ + + Sbjct: 189 YQALEKGTIDATEFSMPAIDQILGFNQVVKYNLFPGWHQQFTAQYMLINKDEWARATEAQ 248 Query: 263 QKILTVAMKAAAYDMYSQSMHASGVNLASLKKDYPNVQMRSFPKPVMEAIVQANDELLEE 322 + ++ + AA ++ + +G LA + VQ P+ V+ + + E+LEE Sbjct: 249 KALVEASCTAATTRGLAEGEYKNGKVLAEFQD--KGVQADQIPRDVLLKLREVTQEVLEE 306 Query: 323 FAAKDPMTAEILKSLNDYKHQIRAWTNLSDRAYL 356 A+KD + +S ++ + W RAY+ Sbjct: 307 EASKDADFKRVYESQQEFMESYKIW---DTRAYV 337 Lambda K H 0.318 0.133 0.402 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: 330 Number of extensions: 18 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: 362 Length of database: 341 Length adjustment: 29 Effective length of query: 333 Effective length of database: 312 Effective search space: 103896 Effective search space used: 103896 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: 49 (23.5 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