Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_083790252.1 CALHY_RS03450 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000166355.1:WP_083790252.1 Length = 494 Score = 389 bits (999), Expect = e-112 Identities = 217/500 (43%), Positives = 327/500 (65%), Gaps = 18/500 (3%) Query: 8 MRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIHYE 67 M I K+FPGV+AL+N ++ GEIHALVGENGAGKSTLMK+L+GVY G I Y+ Sbjct: 1 MEGIEKSFPGVQALKNARFELMPGEIHALVGENGAGKSTLMKILTGVYQKDA--GRIVYK 58 Query: 68 GAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGV---ISWQQTFNRT 124 G ++++GI I+HQEL L+P L++A+NIF+G E + ++ +T Sbjct: 59 GREVEIPNPKIAQEMGISIVHQELNLMPHLTVAQNIFIGREPRRKSFSLFLDEEEMNKKT 118 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 +ELL + LK P+T + ++ V KQQ+VEIAKALS + ++LI+DEPTA+L+E + E L N Sbjct: 119 KELLDMLHLKVDPKTKVANLTVAKQQMVEIAKALSFNSEVLIMDEPTAALSEGEVEELFN 178 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 +L + + GM I I+H+L E++++AD++TV+RDG + T +EI+ D II MVGR Sbjct: 179 ILRKLKANGMGIIYISHRLEELKQIADRVTVMRDGQYIGTAKI--DEITIDEIISMMVGR 236 Query: 245 DLEDRYPPRDVPIG-ETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 ++ + ++V E +LEV N ++ + D++ +RKGE++G AGL+GAGR Sbjct: 237 EIYETLREKEVKENSEIVLEVSNLKRGNE-------IKDVSFKLRKGEILGFAGLVGAGR 289 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 TE A +VFG +G++ + GK V + + AI G+AY++EDRK GL+L ++ Sbjct: 290 TEVARAVFGADPVE--SGEIYVRGKKVHIKSPSDAIKHGIAYLSEDRKRYGLMLGLDVES 347 Query: 364 NTTLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422 N L ++ ++ + + ++ +++ +LRI++ + Q+ NLSGGNQQKV+++KW Sbjct: 348 NMVLPSMKEFLNPLGFVKKKRAERICNEYVKKLRIKTPSLNQKVRNLSGGNQQKVIIAKW 407 Query: 423 LFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMN 482 L N D+LI DEPTRGIDVGAK EIY ++N+L +GK ++MISSE+PE+L RI VM Sbjct: 408 LMKNCDILIFDEPTRGIDVGAKNEIYKLLNELVNEGKSIIMISSELPEILRMSHRIIVMC 467 Query: 483 EGRIVAELPKGEASQESIMR 502 EGRI AEL EA++E IM+ Sbjct: 468 EGRITAELSGKEATEELIMK 487 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: 694 Number of extensions: 35 Number of successful extensions: 10 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: 494 Length adjustment: 34 Effective length of query: 478 Effective length of database: 460 Effective search space: 219880 Effective search space used: 219880 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 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