Align Fructose import binding protein FrcB (characterized)
to candidate GFF2763 PGA1_c28060 putative sugar transport system, periplasmic protein
Query= SwissProt::Q9F9B2 (341 letters) >FitnessBrowser__Phaeo:GFF2763 Length = 338 Score = 500 bits (1287), Expect = e-146 Identities = 257/342 (75%), Positives = 286/342 (83%), Gaps = 5/342 (1%) Query: 1 MKKTVLSAAFGALAM-GVAFASPSQAAEVSACLITKTDTNPFFVKMKEGAAAKAKELGVT 59 MKK +L A G AM G AFA A V+ACLITKTDTNPFFVKMKEGA AKA ELG+T Sbjct: 1 MKKLLLGTAIGFAAMTGSAFA----AEGVTACLITKTDTNPFFVKMKEGAEAKAAELGMT 56 Query: 60 LKSYAGKIDGDSESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTP 119 LKS+AGK+DGD E+QVAAIETCIADGAKGIL+ ASDT IVP VQ+ARDAGL+VIALDTP Sbjct: 57 LKSFAGKVDGDHETQVAAIETCIADGAKGILLTASDTSSIVPAVQQARDAGLVVIALDTP 116 Query: 120 LEPLDAADATFATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFM 179 LEP+D+ADATFATDN LAG+LIG+WAAA+LGD A AK+A LDL SQP+V VLRDQGF+ Sbjct: 117 LEPIDSADATFATDNFLAGELIGKWAAASLGDEAANAKIAMLDLAVSQPTVGVLRDQGFL 176 Query: 180 IGFGIDPKDPNKIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAA 239 GFGID DPNK GDE DPRIVG+DIT GNEEGGR AMENLL KDP INVV+TINEPAAA Sbjct: 177 QGFGIDLGDPNKWGDETDPRIVGNDITAGNEEGGRRAMENLLAKDPMINVVYTINEPAAA 236 Query: 240 GAYEALKSVGREKDVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADT 299 GAYEALKS+GRE DVLIVSVDGGCPGV+N+ +GVIGATSQQYPL+MA+ GIEAI +A T Sbjct: 237 GAYEALKSIGRENDVLIVSVDGGCPGVQNIKDGVIGATSQQYPLLMASKGIEAISAWATT 296 Query: 300 GEKPTPTEGKDFVDTGVSLVADKPVSGVESIDTKTGMEKCWG 341 GEKP PT GK F DTGV+LV D+P GV+SIDT G CWG Sbjct: 297 GEKPAPTPGKAFFDTGVALVTDQPAEGVDSIDTAEGTNLCWG 338 Lambda K H 0.313 0.132 0.372 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: 488 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: 341 Length of database: 338 Length adjustment: 28 Effective length of query: 313 Effective length of database: 310 Effective search space: 97030 Effective search space used: 97030 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 (21.9 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