Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_106711277.1 CU102_RS11775 ATP-binding cassette domain-containing protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_003010955.1:WP_106711277.1 Length = 509 Score = 718 bits (1854), Expect = 0.0 Identities = 371/509 (72%), Positives = 432/509 (84%), Gaps = 2/509 (0%) Query: 4 TILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGE 63 TILEMRNITKTFPGVKAL NVNL V++GEIHALVGENGAGKSTLMKVLSGVYP G+YEGE Sbjct: 3 TILEMRNITKTFPGVKALNNVNLDVRKGEIHALVGENGAGKSTLMKVLSGVYPHGSYEGE 62 Query: 64 IHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNR 123 I Y G ++FR I DSE GIIIIHQELALVPLLSIAENIFLGNE A GVI W NR Sbjct: 63 IIYNGQEQHFRDIADSERQGIIIIHQELALVPLLSIAENIFLGNEPAKFGVIDWHVAENR 122 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 TRELL KVGLKE P TLIT++GVGKQQLVEIAKALSK V+LLILDEPTASLNE DS+ALL Sbjct: 123 TRELLAKVGLKEDPLTLITNLGVGKQQLVEIAKALSKEVELLILDEPTASLNEKDSDALL 182 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243 LL+EF+ G++SI+I+HKLNEV KVAD+ITVLRDG T++TLD +++ISED I+ +MVG Sbjct: 183 ALLLEFKAHGISSILISHKLNEVGKVADRITVLRDGATIETLD--KKDISEDRIVTSMVG 240 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 R L DR+P R+ IGE + EVK+W +H H DR V++ IN++VRKGEVVGIAGLMGAGR Sbjct: 241 RQLADRFPQREPDIGEVVFEVKDWVVHHHIHSDRTVINGINLSVRKGEVVGIAGLMGAGR 300 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 TEFAMSVFGK+YG +I+G+V + GK VDVST+ KAID G+AYVTEDRK GL L D+I H Sbjct: 301 TEFAMSVFGKAYGRKISGEVFLKGKKVDVSTIGKAIDNGIAYVTEDRKTFGLNLIDHIKH 360 Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 NTT+ NLAGVS+ ++DD+ E+KVA+++R + IRSS I+Q+T NLSGGNQQKVVLSKWL Sbjct: 361 NTTIVNLAGVSQNGVLDDMAELKVANEYRRKTNIRSSSIYQKTGNLSGGNQQKVVLSKWL 420 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 F+NPD+LILDEPTRGIDVGAKYEIYTIINQL ++GK VLMISSEMPELLG CDRIYVMN+ Sbjct: 421 FANPDLLILDEPTRGIDVGAKYEIYTIINQLVSEGKSVLMISSEMPELLGVCDRIYVMNQ 480 Query: 484 GRIVAELPKGEASQESIMRAIMRSGEKNS 512 GR+V E+P EASQE IMRAI+R+ K S Sbjct: 481 GRLVGEMPASEASQEKIMRAIIRAEGKAS 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: 872 Number of extensions: 31 Number of successful extensions: 6 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: 509 Length adjustment: 35 Effective length of query: 477 Effective length of database: 474 Effective search space: 226098 Effective search space used: 226098 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