Align Extracellular solute-binding protein, family 7 (characterized, see rationale)
to candidate GFF4121 HP15_4061 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component
Query= uniprot:Q48AL6 (362 letters) >FitnessBrowser__Marino:GFF4121 Length = 361 Score = 448 bits (1153), Expect = e-131 Identities = 205/352 (58%), Positives = 273/352 (77%), Gaps = 2/352 (0%) Query: 7 VKAALVVSLGLSSLGLSALAHADDDKKYRWKLAETWGPNFPIFGDATKNMAKMVKEMSNG 66 ++ L+ ++ ++ S + A+++ Y +LA+TWGPN P+ G+ ++MA M + MS+G Sbjct: 8 IRKTLLAAMAAAATVFSVSSVAEEN--YTLRLAQTWGPNSPVLGETVQHMADMAETMSDG 65 Query: 67 RLTIRIDSSNKHKSALGIFDFVKSGQYQMGHSASYYWKGKNFNTMFFTTVPFGMIASEQH 126 RL IRID SNKHK+ GIFD V++GQY MGH+ASYY+KG N M+FTT+PFG+IA E + Sbjct: 66 RLQIRIDPSNKHKAPFGIFDLVRNGQYDMGHTASYYYKGSIPNAMYFTTIPFGLIAPEMY 125 Query: 127 AWFYYGGGMELMKKVYDQYGIMSFPGGNTGNQMGGWFKKEINSVEDLKGLKMRIPGFAGE 186 AWFY+G GMELM+KVY+ YG++SFPGGNTGNQMGGWF+KEINS+EDLKGLKMR PGFAGE Sbjct: 126 AWFYHGEGMELMQKVYEPYGMLSFPGGNTGNQMGGWFRKEINSLEDLKGLKMRTPGFAGE 185 Query: 187 VLAKLGAKPTNIPSGELYTALERNTIDALEWVGPSLDLRMGFHKIAPYYYTGWHEPGTEL 246 V+++LG TN+P GELYTALER T+DA+EWVGP+LD +MGFH+IA YYY+GW EPG E+ Sbjct: 186 VMSELGVAVTNLPPGELYTALERGTVDAVEWVGPALDFQMGFHQIAKYYYSGWQEPGAEV 245 Query: 247 QFMVNQKAYNSLPKDLQKILTVAMKAAAYDMYSQSMHASGVNLASLKKDYPNVQMRSFPK 306 QF++N+K + LPKDLQ+IL V+M+ AAYDMY QS H SGV +K+DYP+V + FP Sbjct: 246 QFLINKKTWEELPKDLQEILRVSMRTAAYDMYIQSTHQSGVAWDRMKEDYPDVTHKVFPP 305 Query: 307 PVMEAIVQANDELLEEFAAKDPMTAEILKSLNDYKHQIRAWTNLSDRAYLDN 358 V++A+ + LL E A KDP+ EI+ S DY Q+R WTN+SD+AYL++ Sbjct: 306 EVIDALRSTTNRLLAEAAEKDPLAKEIIDSQRDYLKQVRQWTNISDKAYLNS 357 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: 469 Number of extensions: 17 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: 362 Length of database: 361 Length adjustment: 29 Effective length of query: 333 Effective length of database: 332 Effective search space: 110556 Effective search space used: 110556 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