Align Fructose import permease protein FruF (characterized)
to candidate GFF716 PGA1_c07310 binding protein dependent transport system permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Phaeo:GFF716 Length = 373 Score = 128 bits (321), Expect = 3e-34 Identities = 96/303 (31%), Positives = 155/303 (51%), Gaps = 39/303 (12%) Query: 63 QESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAA-AMQTLSNGMNVWLSILIALAVGL 121 Q SA++++IA G L++ DLSVGS++ AG A+ +++ G VWL+IL+ A+ Sbjct: 62 QISAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIAT 121 Query: 122 AIGCVNGALVSFLGLQPFITTLIMMLAGRGMA---------KVITSG-----ENTDASAV 167 AIG +NG +V GL FI TL + RG A K I G E +A+ Sbjct: 122 AIGALNGFIVVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLAAL 181 Query: 168 AGNEPL----KWFA-NGFIL--------------GIPANFVIAVIIVILVGLLCRKTAMG 208 G + L +WF NG+I G+P V A+++VI+ ++ KT G Sbjct: 182 FGGKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFG 241 Query: 209 MMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDL-- 266 I A G + EA+R +G+ ++ L++ + F A + FAT VM + + L Sbjct: 242 NWIFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATV---FATCQVMEFGGAGSDRGLLK 298 Query: 267 EMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVVIVI 326 E AI+AVVIGG L GG S+ G+A+GA+I ++++ + GV + F ++++ Sbjct: 299 EFEAIIAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFA 358 Query: 327 CVM 329 ++ Sbjct: 359 VIL 361 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: 320 Number of extensions: 26 Number of successful extensions: 2 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: 373 Length adjustment: 29 Effective length of query: 327 Effective length of database: 344 Effective search space: 112488 Effective search space used: 112488 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