Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012385982.1 BIND_RS15565 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000019845.1:WP_012385982.1 Length = 511 Score = 706 bits (1823), Expect = 0.0 Identities = 357/508 (70%), Positives = 423/508 (83%) Query: 3 NTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEG 62 N ILEMR I+K+F GVKAL +VNL VK GEIHALVGENGAGKSTLMKVLSGVYP G+YEG Sbjct: 2 NAILEMRGISKSFTGVKALNDVNLTVKAGEIHALVGENGAGKSTLMKVLSGVYPHGSYEG 61 Query: 63 EIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122 I Y+G R+F IND+E +GIIIIHQELAL+PL+SIAENIF+ N + GVI + Sbjct: 62 AIFYDGEERHFHDINDTEALGIIIIHQELALIPLMSIAENIFIANPPSRFGVIDRDTVYT 121 Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 R +ELL KVGL E+P+TLIT+IGVGKQQLVEIAKALSK V+LLILDEPTASLNE+DSEAL Sbjct: 122 RAKELLAKVGLNEAPDTLITNIGVGKQQLVEIAKALSKKVRLLILDEPTASLNENDSEAL 181 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 L+LL+EFR QG+TSI+I+HKLNEV +VADQITVLRDG TV T+DCH E I ED IIR MV Sbjct: 182 LDLLIEFRAQGITSILISHKLNEVSRVADQITVLRDGRTVDTMDCHAEAIEEDRIIRKMV 241 Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302 RDLE RYP R+ IG I ++NW+ YH QH DRQ++ ++N V++GE+VGIAGLMGAG Sbjct: 242 DRDLEHRYPKREPKIGAAIFSIENWSVYHPQHPDRQLIKNVNFHVKRGEIVGIAGLMGAG 301 Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362 RTEFAMSVFG+S+G +ITG +++G+ VD+STV +AI+AGLAYVTEDRK LGL+L+D+I Sbjct: 302 RTEFAMSVFGRSWGQKITGRAVLNGREVDLSTVSRAINAGLAYVTEDRKELGLLLSDDIR 361 Query: 363 HNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422 N TLANL GV+ +IDD+KE KVASD+R+R+RIRSSG++QE LSGGNQQKVVLSKW Sbjct: 362 KNVTLANLEGVANQRVIDDMKEFKVASDYRSRMRIRSSGVYQEVGKLSGGNQQKVVLSKW 421 Query: 423 LFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMN 482 LF+ P++LILDEPTRGID+GAKYEIY IIN LA GKGV++ISSEMPELLG DRIYVMN Sbjct: 422 LFAGPEILILDEPTRGIDIGAKYEIYCIINDLANAGKGVVVISSEMPELLGISDRIYVMN 481 Query: 483 EGRIVAELPKGEASQESIMRAIMRSGEK 510 EG V E P EA+QE IMR+IMR GEK Sbjct: 482 EGAFVGEFPTAEATQEKIMRSIMRKGEK 509 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: 832 Number of extensions: 29 Number of successful extensions: 5 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: 511 Length adjustment: 35 Effective length of query: 477 Effective length of database: 476 Effective search space: 227052 Effective search space used: 227052 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