Align Fructose import permease protein FruF (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 169 bits (427), Expect = 1e-46 Identities = 101/284 (35%), Positives = 162/284 (57%), Gaps = 12/284 (4%) Query: 28 FILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAGIDLS 87 FI L+++C + F + S+ S + +L++ + +IA GMT VI T GIDLS Sbjct: 40 FIGLLVVCIVMV--FASDSFLSGAN-----IENVLRQVSINAIIAVGMTCVILTGGIDLS 92 Query: 88 VGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIMML 147 VGSVMA+AG A + GMN ++ I +AVGL G NG V+F G+ P I TL M Sbjct: 93 VGSVMALAGTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMG 152 Query: 148 AGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIVILVGLLCRKTAM 207 RG+A + T G D + + +F +G ILG+ A VI +I ++ +L + Sbjct: 153 IARGLALIYTGGYPIDGLP----DWVSFFGSGKILGVQAPVVIMAVIYVIAWVLLERMPF 208 Query: 208 GMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLE 267 G + A+G N++A+R++G++ ++ +VY I+G +A A + TA +M G E Sbjct: 209 GRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMS-GQPNAGVGFE 267 Query: 268 MYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVN 311 + AI AVV+GGTS+ GG+ S+ G+ +GA+++ ++ + +GVN Sbjct: 268 LDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVN 311 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: 348 Number of extensions: 19 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: 356 Length of database: 335 Length adjustment: 29 Effective length of query: 327 Effective length of database: 306 Effective search space: 100062 Effective search space used: 100062 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