Align Fructose import permease protein FruG (characterized)
to candidate 7024901 Shewana3_2075 inner-membrane translocator (RefSeq)
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__ANA3:7024901 Length = 405 Score = 132 bits (331), Expect = 2e-35 Identities = 98/327 (29%), Positives = 164/327 (50%), Gaps = 22/327 (6%) Query: 14 KGFKLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFID----HAYLIILAVAM 69 K + R + P LA ++ + + + + F + + ID A + +L++ M Sbjct: 55 KSTSMGRYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGM 114 Query: 70 TLPILTGGIDLSVGAIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLLAGT----LI 125 +L I TGGIDLSVGA++AI V AN + + ++ ++ G + GLLAG L+ Sbjct: 115 SLVIATGGIDLSVGAVMAIAGAV---CANLLLVPDISLVTVIAAGLIVGLLAGCINGGLV 171 Query: 126 EEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFN 185 +QP +ATL M RG+A +I+ + Q F+ I + L Sbjct: 172 SFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIG----------VGQFLGLP 221 Query: 186 VGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAAL 245 + V I + ++ F + L T G I A+G + ++ +G+ K + Y + AAL Sbjct: 222 MPVWIVIGMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAAL 281 Query: 246 ASIVYTANI-GSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLT 304 A ++ TA+I GS N G+ ELDAV +VVIGG +TGG ++ SV+G+L+ L Sbjct: 282 AGMISTADIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTI 341 Query: 305 SDFGVPAEWTTIVIGLMILVFVVLQRA 331 G+PA++ ++ ++IL ++LQ A Sbjct: 342 IVSGLPAKFNLLIKAIVILTVLLLQSA 368 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: 239 Number of extensions: 11 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: 405 Length adjustment: 30 Effective length of query: 310 Effective length of database: 375 Effective search space: 116250 Effective search space used: 116250 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