Align Fructose import permease protein FruF (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__ANA3:7024902 Length = 320 Score = 124 bits (310), Expect = 4e-33 Identities = 87/294 (29%), Positives = 150/294 (51%), Gaps = 31/294 (10%) Query: 23 WSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLIT-MLQESARYLMIATGMTLVIST 81 W + +L + + FQ D G +G ++T +L+++A L+ A GMTLVI + Sbjct: 10 WITASLLLTMFLVGTFQFD----------GFASGRVVTNLLRDNAFLLITALGMTLVIIS 59 Query: 82 AGIDLSVGSVMAVAGAAAMQTLSNGM-NVWLSILIALAVGLAIGCVNGALVSFLGLQPFI 140 GIDLSVG+V+A++G ++ + L+ ++ L +G G + G ++ LQPFI Sbjct: 60 GGIDLSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFI 119 Query: 141 TTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPAN------FVIAVII 194 TL M RG+A ++ ++A + P + +P N +I ++ Sbjct: 120 VTLAGMFLARGLATTLSE------ESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILF 173 Query: 195 VILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGL---FAT 251 +++ ++ T G + A+G NQ ++ + GI K +YAIS FLA +AG+ F T Sbjct: 174 FVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYT 233 Query: 252 ASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTI 305 S + + +E+ AI AVVIGGT L GG + G+ +G +++ +I+ I Sbjct: 234 FSGYALGAI----GVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYI 283 Lambda K H 0.325 0.136 0.384 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: 323 Number of extensions: 24 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: 1 Length of query: 356 Length of database: 320 Length adjustment: 28 Effective length of query: 328 Effective length of database: 292 Effective search space: 95776 Effective search space used: 95776 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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