Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_041936477.1 RL_RS21805 L-arabinose ABC transporter ATP-binding protein AraG
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000009265.1:WP_041936477.1 Length = 501 Score = 361 bits (927), Expect = e-104 Identities = 202/504 (40%), Positives = 313/504 (62%), Gaps = 19/504 (3%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 LE NI+K +PGV+AL NV+ V++G +H L+GENGAGKSTL++VLSG A G I Sbjct: 4 LEFSNISKGYPGVQALANVSFTVEKGAVHGLMGENGAGKSTLIRVLSGDQAADA--GNIL 61 Query: 66 YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125 +G + + ++ D+ G+I+IHQEL LVP L++AEN++LG A GVI + R Sbjct: 62 IDGEEQKYGSVRDAFHAGVIVIHQELQLVPELTVAENLWLGRFPAKGGVIHSKTLIETVR 121 Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185 L+++G+ P + + +G +Q+VEIAKA+ +++ LDEPT+SL+ +SE L +L Sbjct: 122 SKLEEIGIDIDPSAKVASLSIGARQMVEIAKAVMLDARVIALDEPTSSLSSRESEILFSL 181 Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISE---DVIIRNMV 242 + + +G + ++H+L+E+ ++ D +TVLRDG L H +I+E + II MV Sbjct: 182 IDRLKAKGTVILYVSHRLDEIFRLCDSLTVLRDG----KLAAHHPQIAETTREQIISEMV 237 Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302 GR++ + + R+ P+G LEV + ++ H I+ +VR+GE++G GL+GAG Sbjct: 238 GREISNVWGWRERPLGGIRLEVNGLSG-------PRLRHPISFSVRQGEILGFFGLIGAG 290 Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362 R+E A ++G H+ G V IDG V + + AI+AG+ EDRK G+V +I Sbjct: 291 RSEMARLLYGADARHQ--GQVTIDGVAVSPNNPKAAINAGMVLCPEDRKFDGIVQGRSIE 348 Query: 363 HNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422 N +++ S I+ +E +A F +LR+R+ Q+ +NLSGGNQQKV+L +W Sbjct: 349 ENIAISSRRHFSPFGILSPRQEAALADRFIAKLRVRTPSRKQDIINLSGGNQQKVILGRW 408 Query: 423 LFSNP-DVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 L VL++DEPTRGIDVGAK EIY I+ +LAA G +++ISSE+PE++G DRI VM Sbjct: 409 LSEQGIKVLVIDEPTRGIDVGAKSEIYEILYELAAGGMAIVVISSELPEVMGISDRIMVM 468 Query: 482 NEGRIVAELPKGEASQESIMRAIM 505 +GR+ A + + + + SI+ A + Sbjct: 469 CQGRVAANVARPDFDERSILTAAL 492 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: 590 Number of extensions: 27 Number of successful extensions: 11 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: 501 Length adjustment: 34 Effective length of query: 478 Effective length of database: 467 Effective search space: 223226 Effective search space used: 223226 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