Align Fructose import permease protein FruF (characterized)
to candidate WP_106713880.1 CU102_RS25515 ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >NCBI__GCF_003010955.1:WP_106713880.1 Length = 331 Score = 166 bits (420), Expect = 8e-46 Identities = 103/316 (32%), Positives = 172/316 (54%), Gaps = 23/316 (7%) Query: 24 SIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVISTAG 83 +I+A +LL++ F +F + L L + +++A GMTLVI+T G Sbjct: 25 TILALVLLILFNLAFTRNFATMQ----------TLNVNLTQVCTIVIVAVGMTLVIATGG 74 Query: 84 IDLSVGSVMAVAGAAAMQTL--------SNGMNVWLSILIALAVGLAIGCVNGALVSFLG 135 IDLSVGS+MA++GA A S G+ V +++I++ V G NG L++ Sbjct: 75 IDLSVGSLMAISGALAPMIFLGKIVPIDSVGIAVVAAMVISVGVAGLFGLFNGWLIAKFR 134 Query: 136 LQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEPLKWFANGFILGIPANFVIAVIIV 195 +QP + TL++ +AGRG+A+V+T+G N V ++ G + G+P V+ +++V Sbjct: 135 IQPIVATLVLFIAGRGIAQVMTNG-NLQTFRVP---QFQFIGLGRVFGVPVQVVLMLLLV 190 Query: 196 ILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFATASVM 255 I + ++T G I A+G N+ A+ ++GI + +VY ISG A +AGL A Sbjct: 191 IAAAWVLKRTVFGRQIIAIGGNERAAELSGIAVSTVKLVVYTISGLCAGVAGLVVIAINS 250 Query: 256 RVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGV-NAEA 314 D G +E+ AI AV +GGT L GGK ++ G+ +GA+ I ++R T++ GV +A A Sbjct: 251 SSDANLVGLGMELDAIAAVAVGGTLLSGGKATIVGTLLGAMTIQLVRYTLLANGVPDAAA 310 Query: 315 TPAFFAVVVIVICVMQ 330 ++V+ + + Q Sbjct: 311 LVVKAGIIVLAVWIQQ 326 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: 316 Number of extensions: 17 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: 331 Length adjustment: 29 Effective length of query: 327 Effective length of database: 302 Effective search space: 98754 Effective search space used: 98754 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 24 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