Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 223 bits (569), Expect = 1e-62 Identities = 147/483 (30%), Positives = 253/483 (52%), Gaps = 16/483 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 ++ ++ +TK F V A ++++L + G + AL+GENGAGKSTLM +L+G Y G I Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDA--GTI 81 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 +G F + D+ + GI +++Q LV +++AEN+ LG E + ++ ++ NR Sbjct: 82 ALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE--GSFFLNPKEMRNRV 139 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 +EL + GL P ++D+ +G++Q VEI K L + ++LI DEPTA L ++ L Sbjct: 140 QELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFE 199 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 L + QG + + I+HKL EV VAD+I +LR G ++ E S+ + MVG+ Sbjct: 200 ALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQG-RIEGEFSESEVTSKADLACRMVGK 258 Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304 ++ +P G+ +L+V+N L DI + +GEVV + G+ G G+ Sbjct: 259 EVLLEVDREAMPHGDAVLQVRNLTGIG--------LEDITFDLHQGEVVAVVGVAGNGQK 310 Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364 ++ G T + I GK + + LAY+ EDR L N N++ N Sbjct: 311 ALVEAICGLRKPPVDT--MFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDN 368 Query: 365 TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424 L G ++ +D K + ++ + IR I LSGGN QK VL++ L+ Sbjct: 369 LLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELY 428 Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484 P +++ ++PT+G+D+ A +++ + A + G+L+++ ++ E L DR+ V+ G Sbjct: 429 RCPRLIVAEQPTQGLDIAATEQVWNHL-LAAREMAGILLVTGDLNEALQLADRVAVIYRG 487 Query: 485 RIV 487 R + Sbjct: 488 RFM 490 Score = 84.0 bits (206), Expect = 1e-20 Identities = 59/220 (26%), Positives = 107/220 (48%), Gaps = 14/220 (6%) Query: 282 DINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDA 341 DI++ + G V + G GAG++ + G+ G + +DGKPV S+ R AI+A Sbjct: 42 DISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPD--AGTIALDGKPVRFSSARDAIEA 99 Query: 342 GLAYVTEDRKHLGLVLNDNILHNTTLANLAG--VSKASIIDDIKEMKVASDFRTRLRIRS 399 G+ V + H LV + + N L ++ + + ++E+ V R Sbjct: 100 GIGMVYQ---HFMLVESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRYGLDIDPAARV 156 Query: 400 SGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGK 459 S +LS G +Q+V + K L+ + VLI DEPT + + ++ + ++A GK Sbjct: 157 S-------DLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGK 209 Query: 460 GVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQES 499 ++ IS ++ E+L D I ++ +GRI E + E + ++ Sbjct: 210 SIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKA 249 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: 581 Number of extensions: 31 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 514 Length adjustment: 35 Effective length of query: 477 Effective length of database: 479 Effective search space: 228483 Effective search space used: 228483 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 Apr 09 2024. 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