Align Fructose import permease protein FruG (characterized)
to candidate Pf6N2E2_163 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_163 Length = 325 Score = 126 bits (316), Expect = 9e-34 Identities = 88/297 (29%), Positives = 151/297 (50%), Gaps = 12/297 (4%) Query: 33 ILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAIVAITA-V 91 + M+ + AL ++ S+L L++LAV MT ++ GGIDLSVG+++A+ A Sbjct: 28 LAMVALFSALSSHFLSYDTFSTLANQIPDLMVLAVGMTFILIIGGIDLSVGSVLALAAST 87 Query: 92 VGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLARGLASIIS 151 V + + G + ++ + + A+ G + G++ + + FI +L + +ARGLA + Sbjct: 88 VSVAVLGWGWSVWPSALLGMAVAALAGTVTGSITVAWRIPSFIVSLGVLEMARGLAYQM- 146 Query: 152 TDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLHHTRTGRTI 211 T S T G+ F+++SN I +P IIAL+V+ L T GR + Sbjct: 147 TGSRTAYIGDSFAWLSNPIAFGISPSF----------IIALLVIFIAQAVLTRTVFGRYL 196 Query: 212 YAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGVGWELDAVA 271 IG + + L G+ K + +++ LA +A++ + + +A G G EL +A Sbjct: 197 IGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIA 256 Query: 272 SVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGLMILVFVVL 328 +VVIGGT + GG G V+ + G L+ S+L + G I+ G +I+V VVL Sbjct: 257 AVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVL 313 Score = 25.8 bits (55), Expect = 0.002 Identities = 33/130 (25%), Positives = 58/130 (44%), Gaps = 10/130 (7%) Query: 26 LAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAI 85 +A +VIFI ++ + +FG Y+ +G ++ + A + IL + + + Sbjct: 175 IALLVIFIAQAVLTRTVFGRYL-IGIGTN---EEAVRLAGINPKPYKILVFSLMGLLAGV 230 Query: 86 VAITAVVGLKLA--NAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLA 143 A+ + L+ A NAG L +I ++IG L+ G + F L LA Sbjct: 231 AALFQISRLEAADPNAGSGLELQVIAAVVIGGT-SLMGG---RGSVISTFFGVLIISVLA 286 Query: 144 RGLASIISTD 153 GLA I +T+ Sbjct: 287 AGLAQIGATE 296 Lambda K H 0.327 0.142 0.400 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: 267 Number of extensions: 17 Number of successful extensions: 4 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: 340 Length of database: 325 Length adjustment: 28 Effective length of query: 312 Effective length of database: 297 Effective search space: 92664 Effective search space used: 92664 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