Align Fructose import permease protein FruF (characterized)
to candidate SM_b21343 SM_b21343 sugar uptake ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Smeli:SM_b21343 Length = 334 Score = 184 bits (468), Expect = 2e-51 Identities = 116/317 (36%), Positives = 183/317 (57%), Gaps = 25/317 (7%) Query: 24 SIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAG 83 ++ AF+ L++ +F +FL+L L L + A +++A GMTLVI+T G Sbjct: 28 TVAAFLALILFNVVFTPNFLSLQ----------TLNVNLTQVATIVIVAIGMTLVIATGG 77 Query: 84 IDLSVGSVMAVAGAAA----MQTLSNGMNVWLSILIA-----LAVGLAIGCVNGALVSFL 134 IDLSVGS+MA+ GA A M TL ++ +++ +A +A GL +G NG LV+ Sbjct: 78 IDLSVGSLMAIGGALAPMIFMGTLFPVSSMPVAVALAFVLPVVATGL-LGLFNGLLVTRF 136 Query: 135 GLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVII 194 +QP I TL++ +AGRG+A+V+T+G V NE ++ A G + GIPA ++ + I Sbjct: 137 AIQPIIATLVLFIAGRGIAQVMTNGN----LQVFRNEGFQFIALGRVAGIPAQVILMIAI 192 Query: 195 VILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASV 254 + R T G + AVG N++ASR+TGI ++ LVY ISG LA +AGL A Sbjct: 193 AAIAWAAIRYTVFGRQVIAVGGNEKASRLTGIPVHRVKLLVYMISGALAGVAGLIVVARN 252 Query: 255 MRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGV-NAE 313 D G +E+ AI AV +GGT L GG+ ++ G+ +GA++I ++R T++ GV +A Sbjct: 253 SASDANLVGLGMELDAIAAVAVGGTLLTGGRANIVGTVIGALVIQLVRYTLLANGVPDAA 312 Query: 314 ATPAFFAVVVIVICVMQ 330 A A++++ + + Q Sbjct: 313 ALIVKAALILLAVFIQQ 329 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: 335 Number of extensions: 17 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: 334 Length adjustment: 29 Effective length of query: 327 Effective length of database: 305 Effective search space: 99735 Effective search space used: 99735 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