Align Fructose import binding protein FruE (characterized)
to candidate SM_b21345 SM_b21345 sugar uptake ABC transporter substrate-binding protein precursor
Query= SwissProt::Q8G848 (327 letters) >FitnessBrowser__Smeli:SM_b21345 Length = 327 Score = 138 bits (348), Expect = 2e-37 Identities = 96/323 (29%), Positives = 164/323 (50%), Gaps = 8/323 (2%) Query: 5 KKAIALVASAAALVSVAACGS-SNAGGSSDSGKKTVGFVAVGPEGGFRTANEKDIQKAFE 63 ++A L A+AA +++A + + + VGF +R A ++ E Sbjct: 6 RRAFMLAATAAGAIAIAGTVAFAELPKLAQKETYKVGFAQTESNNPWRIAQTNSMKAEAE 65 Query: 64 DAGFDLTYSPTQNNDQQKQIQAFNKFVNDEVDAIILSSTEDSGWDDSLKKAAEAEIPVFT 123 G L Y+ + KQ+ N + VD I L+ E+ ++ A +A IPV Sbjct: 66 KLGHQLVYTDAAGS-AAKQVADVNSMIAQGVDLIFLAPREEKPLIPAVMAAKKAGIPVIL 124 Query: 124 VDRNVDVKDAEAKKAIVAHIGPSNVWCGEQAAEFVNKNFPDGANGFILEGPAGLSVVKDR 183 +DR+VD A+A + V IG + G++ AE++ KN + LEG G S DR Sbjct: 125 LDRSVDPSLAKAGEDYVTFIGSDFIEEGKRIAEWLVKNANGKSKIIELEGTTGSSPANDR 184 Query: 184 GTGWGN--KVASNVKVLESQSANWSTDEAKTVTAGLLDKYKSDNPQFIFAQNDEMGLGAA 241 G+ K A +++ SQS +++ D+ + V LL + + ++A NDEM +GA Sbjct: 185 KKGFDETIKAAGGFEIVASQSGDFARDKGRQVAEALLQAH--PDADIVYAHNDEMAIGAI 242 Query: 242 QAVDAAG-LKGK-VKIITIDGTKNALQALVDGDLSYVIEYNPIFGKETAQAVKDYLDGKT 299 A++AAG + GK V +++IDG K A+QA++DG ++ V+E NP FG + + + Y G+ Sbjct: 243 AAIEAAGKVPGKDVLVLSIDGGKEAVQAVIDGKIAAVVECNPRFGPKAFETMLRYAKGEK 302 Query: 300 VEKDIEIESKTFDAASAKEALDN 322 ++ + E K +D+++A L N Sbjct: 303 IDPMVINEDKFYDSSNAAAELAN 325 Lambda K H 0.310 0.128 0.360 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: 231 Number of extensions: 16 Number of successful extensions: 3 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: 327 Length of database: 327 Length adjustment: 28 Effective length of query: 299 Effective length of database: 299 Effective search space: 89401 Effective search space used: 89401 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 48 (23.1 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