Align Fructose import permease protein FruG (characterized)
to candidate HSERO_RS05185 HSERO_RS05185 ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__HerbieS:HSERO_RS05185 Length = 340 Score = 207 bits (527), Expect = 3e-58 Identities = 118/310 (38%), Positives = 188/310 (60%), Gaps = 9/310 (2%) Query: 25 TLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGA 84 ++ VV+ ++M++ G + ++ + +L ID+A+L+++A+ MT IL+GGIDLSVG+ Sbjct: 18 SMVTVVLLVVMLVAGALGYDGFLSPQVMLNLLIDNAFLLVVAIGMTFVILSGGIDLSVGS 77 Query: 85 IVAITAVVG-LKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLA 143 ++A+T +V L N LV++ +LL+GA FG G +I F +Q FI TL+ MFLA Sbjct: 78 VLALTTMVAAFLLQNWHWHPLLVIVTVLLMGAGFGAAMGAMIHYFKLQAFIVTLAGMFLA 137 Query: 144 RGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLH 203 RGL +IS +S+T + +++ L + V+IAL ++ H Sbjct: 138 RGLCYLISINSITIDDPLFTTLSQTRLELAG-------LFISPSVVIALFMLALAIWMAH 190 Query: 204 HTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGV 263 TR GR +YAIGG+ +SA LMGLPV RT+ ++Y S AA+A ++++ + S Sbjct: 191 CTRFGRAVYAIGGNENSALLMGLPVGRTKVLVYAFSGLCAAVAGVLFSFYMLSGYGLHAQ 250 Query: 264 GWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTS-DFGVPAEWTTIVIGLMI 322 G ELDA+A+VVIGGT++TGG+GYV G++ G L+ ++ L + D + + WT I IG ++ Sbjct: 251 GVELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIFIGALL 310 Query: 323 LVFVVLQRAV 332 VF V QR + Sbjct: 311 FVFCVAQRVI 320 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: 278 Number of extensions: 15 Number of successful extensions: 3 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: 340 Length adjustment: 28 Effective length of query: 312 Effective length of database: 312 Effective search space: 97344 Effective search space used: 97344 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