Align Fructose import permease protein FruF (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 133 bits (335), Expect = 6e-36 Identities = 92/304 (30%), Positives = 155/304 (50%), Gaps = 19/304 (6%) Query: 25 IVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAGI 84 ++AF L +I TI FL L N +++ SA ++A G+T V+ + + Sbjct: 19 LIAFALFIIGFTIANPKFLTLDNFEN----------VVRSSAILGVMALGVTFVVISGNL 68 Query: 85 DLSVGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLI 144 DLSVGS+M+ + + L + + L+I A+ L +G + G LV +L L I TL Sbjct: 69 DLSVGSMMSFSTIVVLD-LHDKLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLG 127 Query: 145 MMLAGRGMAKVITSGENTDASAVAGNEPLKWFA---NGFILGIPANFVIAVIIVILVGLL 201 M+ A G+ + G+N D + G WFA G ILGI +I + + L+G++ Sbjct: 128 MLSAIHGLTLTYSGGKNMDIADKEGT----WFAIFGQGNILGIQTPILIFIALAALLGII 183 Query: 202 CRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVK 261 KT G + AVG N A+ +GI+ +++FL Y +S A AGL + M Sbjct: 184 LAKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNT- 242 Query: 262 TGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAV 321 GQ LE+ + AV++GG SLLGG ++ + +G +I+ I+ ++ +G++ + Sbjct: 243 VGQGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWI 302 Query: 322 VVIV 325 ++I+ Sbjct: 303 IIIL 306 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: 293 Number of extensions: 16 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: 356 Length of database: 324 Length adjustment: 28 Effective length of query: 328 Effective length of database: 296 Effective search space: 97088 Effective search space used: 97088 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