Align Fructose import binding protein FrcB (characterized)
to candidate BPHYT_RS22745 BPHYT_RS22745 sugar ABC transporter
Query= SwissProt::Q9F9B2 (341 letters) >FitnessBrowser__BFirm:BPHYT_RS22745 Length = 334 Score = 333 bits (853), Expect = 5e-96 Identities = 183/329 (55%), Positives = 229/329 (69%), Gaps = 18/329 (5%) Query: 14 AMGVAFASPSQAAEVSAC-LITKTDTNPFFVKMKEGAAAKAKELGVTLKSYAGKIDGDSE 72 A V AS SQAA+ LITKTDTNPFFVKMK+GA A A + G L + AGK DGD+ Sbjct: 21 ASAVWCASASQAADQPVVGLITKTDTNPFFVKMKQGAEAAASKDGAKLITAAGKFDGDNA 80 Query: 73 SQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTPLEPLDAADATFAT 132 SQV AIE + GAK ILI SDT+ IVP ++KAR AG++V+ALDTP +P DA DA FAT Sbjct: 81 SQVTAIENMMTAGAKAILITPSDTKAIVPSIKKARAAGVMVVALDTPTDPQDATDALFAT 140 Query: 133 DNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFMIGFGIDPKDPNKI 192 DN AG LIG++A A L K AK+A LDL P SV VLR GF+ GFG+ DP+ + Sbjct: 141 DNFKAGVLIGKYAKAALN--GKPAKIATLDLAPG-VSVGVLRHNGFLEGFGVKEGDPSVV 197 Query: 193 GDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAAGAYEALKSVGREK 252 +D T G++ G+TAMEN LQK P INVV+TINEPAAAGAY ALK+ G++K Sbjct: 198 CSQD---------TRGDQAKGQTAMENCLQKSPDINVVYTINEPAAAGAYRALKAAGKDK 248 Query: 253 DVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADTGEKPTPTEGKDFV 312 V+IVS+DGGC GV+NV G I ATSQQYPL MA+LG+ A ++A TG+K + + Sbjct: 249 SVMIVSIDGGCEGVRNVKAGAIAATSQQYPLKMASLGVTAGVEYAKTGKKVS-----GYQ 303 Query: 313 DTGVSLVADKPVSGVESIDTKTGMEKCWG 341 DTGV+L+ DKP++G++S DTK G++ CWG Sbjct: 304 DTGVTLITDKPMAGIDSKDTKFGLDNCWG 332 Score = 23.9 bits (50), Expect = 0.006 Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%) Query: 102 QVQKARDAGLLVIALDTPLEPLDAADATFATDNLLAGK 139 +V +D G+ +I D P+ +D+ D F DN K Sbjct: 298 KVSGYQDTGVTLIT-DKPMAGIDSKDTKFGLDNCWGNK 334 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: 394 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 341 Length of database: 334 Length adjustment: 28 Effective length of query: 313 Effective length of database: 306 Effective search space: 95778 Effective search space used: 95778 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