Align Fructose import permease protein FruG (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 213 bits (542), Expect = 5e-60 Identities = 121/313 (38%), Positives = 194/313 (61%), Gaps = 8/313 (2%) Query: 20 RQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGID 79 R+ IP + + M ++G F + +++L D+A+L+I A+ MTL I++GGID Sbjct: 4 RRFIPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGID 63 Query: 80 LSVGAIVAITAVV-GLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLS 138 LSVGA++A++ VV L + L +++L +G +FG L GT+I + +QPFI TL+ Sbjct: 64 LSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA 123 Query: 139 TMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFG 198 MFLARGLA+ +S +S+ D F V ++ + + + + ++ +I ++ V Sbjct: 124 GMFLARGLATTLSEESIAI----DHPFYDAVAEM--SIALPGNGALDLSSLIFILFFVII 177 Query: 199 YVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAK 258 V +H+TR G +YAIGG++ SAELMG+ + +T IY S+ LA LA IV+T S Sbjct: 178 AVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGY 237 Query: 259 NTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDP-LTSDFGVPAEWTTIV 317 +G ELDA+A+VVIGGT++TGG G+VLG+VLG ++ ++ +T D + + WT IV Sbjct: 238 ALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIV 297 Query: 318 IGLMILVFVVLQR 330 IGL++ F++LQ+ Sbjct: 298 IGLLLFFFILLQK 310 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: 295 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: 320 Length adjustment: 28 Effective length of query: 312 Effective length of database: 292 Effective search space: 91104 Effective search space used: 91104 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