Align Extracellular solute-binding protein, family 7 (characterized, see rationale)
to candidate 6938423 Sama_2542 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component (RefSeq)
Query= uniprot:Q48AL6 (362 letters) >FitnessBrowser__SB2B:6938423 Length = 363 Score = 316 bits (809), Expect = 7e-91 Identities = 154/328 (46%), Positives = 212/328 (64%), Gaps = 2/328 (0%) Query: 29 DDDKKYRWKLAETWGPNFPIFGDATKNMAKMVKEMSNGRLTIRIDSSNKHKSALGIFDFV 88 D K+ WKLA +W NFP G A ++ A MV EMS GRL I++ + + AL +FD V Sbjct: 32 DSAKQIEWKLATSWPKNFPGLGTAPEHFAVMVDEMSAGRLKIKVYGAGELMPALEVFDAV 91 Query: 89 KSGQYQMGHSASYYWKGKNFNTMFFTTVPFGMIASEQHAWFYYGGGMELMKKVYDQYGIM 148 G QM HSASYYWKGK FFT++PFG+ A E + W YGGG EL ++VY +GI+ Sbjct: 92 SQGSVQMAHSASYYWKGKAPAAQFFTSIPFGLNAQEMNGWLTYGGGQELWEEVYAPFGIL 151 Query: 149 SFPGGNTGNQMGGWFKKEINSVEDLKGLKMRIPGFAGEVLAKLGAKPTNIPSGELYTALE 208 PGGN+G QMGGWF KEIN+++DLKGLKMR+PG GEVL +L P +P ELYTA++ Sbjct: 152 PLPGGNSGVQMGGWFNKEINTIDDLKGLKMRLPGLGGEVLKRLEGVPVTLPGRELYTAMQ 211 Query: 209 RNTIDALEWVGPSLDLRMGFHKIAP-YYYTGWHEPGTELQFMVNQKAYNSLPKDLQKILT 267 IDA EWVGP DL G HK+A YYY GWHEPGT L+FM+N+ A+ LPKDLQ I+ Sbjct: 212 TGAIDATEWVGPYNDLAFGLHKVAKYYYYPGWHEPGTTLEFMINKAAFEKLPKDLQAIVK 271 Query: 268 VAMKAAAYDMYSQSMHASGVNLASLKKDYPNVQMRSFPKPVMEAIVQANDELLEEFAAKD 327 +A KA DM + + L +L ++ V ++ FP+ VM + + E++ E +++D Sbjct: 272 IAAKATNQDMLDEYTARNVGALDALVNEH-GVVLKQFPEEVMAQLRSVSAEVISEQSSQD 330 Query: 328 PMTAEILKSLNDYKHQIRAWTNLSDRAY 355 PM ++ ++ +Y+ +R + +S+ AY Sbjct: 331 PMMKKVNEAYREYEAGVRKYHLISEDAY 358 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: 411 Number of extensions: 16 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: 363 Length adjustment: 29 Effective length of query: 333 Effective length of database: 334 Effective search space: 111222 Effective search space used: 111222 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