Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 354 bits (908), Expect = e-102 Identities = 191/499 (38%), Positives = 306/499 (61%), Gaps = 12/499 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +LEM I K+FPGVKAL+NVNLKV+ IHAL+GENGAGKSTL+K L G+Y + G I Sbjct: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GTI 70 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 ++G +F + ++ + GI ++HQEL LV S+ +N++LG + + + T Sbjct: 71 LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRET 130 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 + + ++ + P + + V + Q++EIAKA S + K++I+DEPT+SL E + L Sbjct: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 ++ + + +G + I+HK+ E+ ++ D++TVLRDG + T ++ D II MVGR Sbjct: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPL--AGLTMDKIIAMMVGR 248 Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304 L R+P ++ GE ILEV+N + Q + D++ + KGE++GIAGL+GA RT Sbjct: 249 SLNQRFPDKENKPGEVILEVRNLTSLRQPS-----IRDVSFDLHKGEILGIAGLVGAKRT 303 Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364 + ++FG + G + + GK ++ +AI+ G A VTE+R+ G+ +I N Sbjct: 304 DIVETLFG--IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFN 361 Query: 365 TTLANLAGV-SKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 + ++N+ +K ++D+ + +R+++ G + +LSGGNQQKV++ +WL Sbjct: 362 SLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 + P++L+LDEPTRGIDVGAK+EIY +I +LA GKG+++ISSEMPELLG DRI VM+ Sbjct: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481 Query: 484 GRIVAELPKGEASQESIMR 502 G + + +Q I+R Sbjct: 482 GLVSGIVDTKTTTQNEILR 500 Lambda K H 0.316 0.135 0.374 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: 639 Number of extensions: 37 Number of successful extensions: 8 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: 512 Length of database: 506 Length adjustment: 34 Effective length of query: 478 Effective length of database: 472 Effective search space: 225616 Effective search space used: 225616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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