Align Fructose import permease protein FrcC (characterized)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 183 bits (465), Expect = 5e-51 Identities = 119/337 (35%), Positives = 180/337 (53%), Gaps = 23/337 (6%) Query: 30 AHDKTLLQKLQHFLHSSPAAVPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIV 89 A D+ + Q+ + + A L+VL+ +AF + FFS + + QV + + Sbjct: 11 ALDRQVQQRRRDLIQKFAALGSLVVLI---VAFS-LTSAAFFSVGNLMTVALQVTSIAYL 66 Query: 90 GAAQTLVILTAGIDLSVGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTL 149 G A T VI+T GIDLSVG+++ L+ V + G P ++++ G+ VGA CG++NG Sbjct: 67 GVAATCVIITGGIDLSVGSVLALAGVAAALLV-KAGVPIPVAMLGGMLVGAACGWVNGIC 125 Query: 150 VARMKLPPFIVTLGMWQIVLASNFLYSANETIRAQDISANASILQFFGQN--FRIGN--- 204 V RM LPPFI TLGM + A + A+ +S G FRI + Sbjct: 126 VTRMGLPPFIATLGMMLVARGL-----ALQITGARPVSGLGDAFGELGNGALFRISHIGA 180 Query: 205 -----AVFT---YGVVVMVLLVCLLWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLI 256 VF Y VV+MV+L + +L+RT+ GR++YAVG + EAA+L+GVNV + + Sbjct: 181 DGFPDTVFPGIPYPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKL 240 Query: 257 SIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFG 316 Y LSGL+ G L+ R+ + P G +++I + VIGG SL GG G+I G G Sbjct: 241 FTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIG 300 Query: 317 ALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAIDQ 353 A ++GV GL + G ++IG++I+ V IDQ Sbjct: 301 AFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWIDQ 337 Lambda K H 0.327 0.141 0.420 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: 362 Number of extensions: 14 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: 360 Length of database: 343 Length adjustment: 29 Effective length of query: 331 Effective length of database: 314 Effective search space: 103934 Effective search space used: 103934 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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