Align Fructose import binding protein FrcB (characterized)
to candidate Ac3H11_3035 Fructose ABC transporter, substrate-binding component FrcB
Query= SwissProt::Q9F9B2 (341 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3035 Length = 337 Score = 325 bits (833), Expect = 1e-93 Identities = 182/334 (54%), Positives = 229/334 (68%), Gaps = 11/334 (3%) Query: 8 AAFGALAMGVAFASPSQAAEVSACLITKTDTNPFFVKMKEGAAAKAKELGVTLKSYAGKI 67 A GALA G+A A Q +E LITKT+TNPFFVKMKEGA A+AK+LG L S AGK Sbjct: 13 ALTGALACGLAQA---QTSEPVIGLITKTETNPFFVKMKEGATAEAKKLGAKLVSAAGKT 69 Query: 68 DGDSESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTPLEPLDAAD 127 DGD+ QV A+E IA GAK ILI SD + IVP ++KA+ G++VIALD+P EP+DA D Sbjct: 70 DGDNAGQVTAMENLIAAGAKTILITPSDAKAIVPAIKKAQAKGVMVIALDSPTEPMDATD 129 Query: 128 ATFATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFMIGFGIDPK 187 A FATDN AG+LIGQ+A A A K+ +A LDL P P V R GF+ GFG+ Sbjct: 130 ALFATDNYKAGELIGQYAKAAA--AGKKPVIATLDLFPGHP-VGAQRHNGFLKGFGLQAN 186 Query: 188 DPNKIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAAGAYEALKS 247 D +V + G+ G+T MEN LQK+P IN+V+TINEPAAAGAY ALK+ Sbjct: 187 DAKSNELSRPAEVVCMADSFGDRAKGQTGMENCLQKNPDINIVYTINEPAAAGAYNALKA 246 Query: 248 VGREKDVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADTGEKPTPTE 307 G+EK+VLIVSVDGGC G+ +V +GVI ATSQQYPL MAA+G+ A ++A TG+K + Sbjct: 247 AGKEKNVLIVSVDGGCAGIADVGKGVIAATSQQYPLRMAAMGVAAGVEYAKTGKKVS--- 303 Query: 308 GKDFVDTGVSLVADKPVSGVESIDTKTGMEKCWG 341 + DTGV+L+A KP++GV+S D KTG + CWG Sbjct: 304 --GYTDTGVTLIAAKPMAGVDSKDVKTGTDLCWG 335 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: 405 Number of extensions: 31 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: 341 Length of database: 337 Length adjustment: 28 Effective length of query: 313 Effective length of database: 309 Effective search space: 96717 Effective search space used: 96717 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