Align Fructose import permease protein FruF (characterized)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Dyella79:N515DRAFT_2414 Length = 358 Score = 217 bits (552), Expect = 4e-61 Identities = 126/339 (37%), Positives = 193/339 (56%), Gaps = 11/339 (3%) Query: 13 VKKLLSSNLTWSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIA 72 +++ L+ L W ++ ILL+ +F FLAL W G L G LI + +A +++ Sbjct: 22 LRRCLAHPLLWPLLTLILLLAGNGLFNPGFLALQWRD--GHLYGNLIDIAHRAAPLALVS 79 Query: 73 TGMTLVISTAGIDLSVGSVMAVAGAAAMQTLSNGMN-----VWLSILIALAVGLAIGCVN 127 GMTLVI+ G+D+SVG+V+A+A A T+ + N +WL+I ALA G G N Sbjct: 80 LGMTLVIALRGLDISVGAVLAIAATVAAWTIGHVSNDGLLPLWLAIAAALAAGALCGLWN 139 Query: 128 GALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPAN 187 G LV G+QP + TLI+M+AGRG+A+ I+ G+ P + NGF+LG+P + Sbjct: 140 GWLVVGAGMQPIVATLILMVAGRGIAQSISGGQILTLYYA----PYSFLGNGFVLGLPFS 195 Query: 188 FVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAG 247 + + L+ L RKTA+G+ + A+G N +A+ + G++ + I Y G AA+AG Sbjct: 196 LFVVAAVFALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAG 255 Query: 248 LFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIIT 307 L +++V D G LE+ AILAV +GG+ L GG+FSLAGS +GA+II + TI Sbjct: 256 LLVSSNVNSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYA 315 Query: 308 LGVNAEATPAFFAVVVIVICVMQAPKIHNLSANMKRKRA 346 +GV + A AV+V + ++Q+P + R RA Sbjct: 316 IGVPPQVNLAVKAVLVFAVMLLQSPLCRGQLRALLRLRA 354 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: 350 Number of extensions: 20 Number of successful extensions: 5 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: 358 Length adjustment: 29 Effective length of query: 327 Effective length of database: 329 Effective search space: 107583 Effective search space used: 107583 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