Align Fructose import permease protein FrcC (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 136 bits (342), Expect = 9e-37 Identities = 92/301 (30%), Positives = 152/301 (50%), Gaps = 7/301 (2%) Query: 55 LVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSS 114 L+L++ G F S +T +L+ A + I TLVI++ GIDLSVGA++ LS Sbjct: 15 LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74 Query: 115 VIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTL-GMWQIVLASNF 173 V+ Y + P L+ + L +G L G + GT++ KL PFIVTL GM+ LA Sbjct: 75 VVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMF---LARGL 131 Query: 174 LYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWGRY 233 + +E A D ++ + GN ++ +L ++ V++ T +G Sbjct: 132 ATTLSEESIAIDHPFYDAVAEM--SIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTN 189 Query: 234 VYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESI 293 VYA+G + +A+L G+++ + ISIY +S + LAG S +++I Sbjct: 190 VYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAI 249 Query: 294 TAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGT-DPQWTYLLIGLLIIIAVAID 352 AVVIGG L GG G ++G + G +++GV + G+ WT ++IGLL+ + + Sbjct: 250 AAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILLQ 309 Query: 353 Q 353 + Sbjct: 310 K 310 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: 355 Number of extensions: 23 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: 360 Length of database: 320 Length adjustment: 28 Effective length of query: 332 Effective length of database: 292 Effective search space: 96944 Effective search space used: 96944 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