Align Fructose import permease protein FruF (characterized)
to candidate SM_b21589 SM_b21589 sugar uptake ABC transporter permease
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Smeli:SM_b21589 Length = 341 Score = 231 bits (588), Expect = 3e-65 Identities = 132/322 (40%), Positives = 200/322 (62%), Gaps = 8/322 (2%) Query: 13 VKKLLSSNLTWSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIA 72 + + + L ++A +V+ +I FL L + G L G ++ +L A +++A Sbjct: 4 IMRTYAGRLLPQLIALAAIVVAISIVFPGFLNLQIQN--GRLYGSMVDILNRGAPVVLLA 61 Query: 73 TGMTLVISTAGIDLSVGSVMAVAGAAAMQTLSNGMNVWLSILIALAVGLAIGCVNGALVS 132 GMT+VI+T GIDLSVG+VMA+ GA A +++G ++ ++L LAVG+ G NG LV+ Sbjct: 62 IGMTVVIATKGIDLSVGAVMAICGAVAASLITSGHSLAETLLATLAVGIVCGIWNGVLVA 121 Query: 133 FLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAGNEP-LKWFANGFILGIPANFVIA 191 L +QP I TL++M+AGRG+A++IT G + + N+P L + +G G+P VI Sbjct: 122 VLDIQPIIATLVLMVAGRGIAQLITEG-----TILTFNDPGLIFIGSGSFAGLPMPLVIW 176 Query: 192 VIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLFAT 251 ++ +LV LL R+TA+GM+IEA+GIN++AS ++G+ +L Y +SG AAIAG+ A Sbjct: 177 LVFGLLVALLVRRTALGMLIEAIGINRQASTLSGVLTPVLLVAAYVLSGLCAAIAGIIAA 236 Query: 252 ASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLGVN 311 A + D G LE+ AILAVV+GGTSLLGG+FS+A S +GAVII I I+ G Sbjct: 237 ADIRGADANNAGLWLELDAILAVVVGGTSLLGGRFSIAASVLGAVIIQAINTGILLSGFP 296 Query: 312 AEATPAFFAVVVIVICVMQAPK 333 E A ++I I V+Q+P+ Sbjct: 297 PEFNLIIKAAIIIFILVLQSPR 318 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: 313 Number of extensions: 20 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: 341 Length adjustment: 29 Effective length of query: 327 Effective length of database: 312 Effective search space: 102024 Effective search space used: 102024 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