Align Fructose import permease protein FruG (characterized)
to candidate SM_b21590 SM_b21590 inner membrane ABC transporter permease YjfF
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Smeli:SM_b21590 Length = 322 Score = 198 bits (504), Expect = 1e-55 Identities = 114/318 (35%), Positives = 186/318 (58%), Gaps = 8/318 (2%) Query: 18 LDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGG 77 + ++ +P A ++IF+L + A + + I +L D+A+L I AV MT IL+GG Sbjct: 1 MKQKYLPLTATILIFVLSYALCVAQYPNMLSTRVIGNLLTDNAFLGIAAVGMTFVILSGG 60 Query: 78 IDLSVGAIVAITAV-VGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIAT 136 IDLS+GA++A V + + L + G+ + ++L I +FG L G +I M FI T Sbjct: 61 IDLSIGAVIAFAGVFLAVVLEHGGMHPLVAFALLLAITTLFGALMGAIIHYLEMPAFIVT 120 Query: 137 LSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVV 196 L+ MFLARG+A ++S DS+ + S K+ +I+ +G ++ V V Sbjct: 121 LAGMFLARGMAFVLSIDSIPIKHPFYATLKSLYFKLPGGGRITL-----IGGLMLFVFAV 175 Query: 197 FGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGS 256 G + H TR G IYA+GG ++A+LMG+PV T IY S LA L+ IV++ + Sbjct: 176 -GILIAHRTRFGTNIYALGGGTATAKLMGVPVAATTIRIYALSGLLAGLSGIVFSLYTSA 234 Query: 257 AKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDP-LTSDFGVPAEWTT 315 + VG ELDA+ +VVIGGT++TGG G+V G+++G L++ ++ +T D + + WT Sbjct: 235 GYSLAAVGVELDAITAVVIGGTLLTGGSGFVAGTLVGILIQGLIQTYITFDGTLSSWWTK 294 Query: 316 IVIGLMILVFVVLQRAVM 333 I+IGL++ F++LQ+ ++ Sbjct: 295 ILIGLLLFAFILLQKGII 312 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: 294 Number of extensions: 20 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: 340 Length of database: 322 Length adjustment: 28 Effective length of query: 312 Effective length of database: 294 Effective search space: 91728 Effective search space used: 91728 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