Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_043458758.1 H537_RS42805 ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000430725.1:WP_043458758.1 Length = 527 Score = 226 bits (576), Expect = 2e-63 Identities = 157/492 (31%), Positives = 258/492 (52%), Gaps = 13/492 (2%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 L++ +ITK +P V A +V+L V+ GEIHA++GENGAGKSTLMK++ G +G + Sbjct: 6 LQLAHITKRYPSVVANSDVSLTVQPGEIHAVLGENGAGKSTLMKIIYGSVKPD--QGTVM 63 Query: 66 YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125 ++G + ++ +GI ++ Q +L L++AEN++LG ++ + Sbjct: 64 FDGTPVHIANPKEARALGISMVFQHFSLFDTLTVAENVWLG----LGNHLTLSEVAGGIE 119 Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185 + GL P + + VG+ Q VEI +AL S KLLILDEPT+ L E L + Sbjct: 120 AKAAEYGLDIDPSRPVHTLSVGEMQRVEIIRALLGSPKLLILDEPTSVLTPQAVERLFVV 179 Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGRD 245 L + +G + + I+HKL+E+R++ TVLR+G T C+ S + R M+G + Sbjct: 180 LRKLAAEGCSILYISHKLHEIRELCTACTVLRNGKV--TGACNPSMESNASLSRMMIGSE 237 Query: 246 LEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTE 305 P G +L V+ + + LH+I + VR GEVVGIAG+ G G+ E Sbjct: 238 PPALEHHARQP-GAVVLNVQGLSLPREDLFGVN-LHNIALDVRAGEVVGIAGVSGNGQRE 295 Query: 306 FAMSVFGKSYGHRITGDVL-IDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364 F ++ G+ R D + + GK V + GL +V E+R G V ++ N Sbjct: 296 FLYALSGED--RRSDPDAIRLSGKSVGRLGPVQRRRLGLHFVPEERLGRGAVPTLSLAQN 353 Query: 365 TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424 L + ID + A+D +R +++ G + +LSGGN QK ++ + + Sbjct: 354 LLLTRTDALRTGGWIDVKAMHRQAADIISRFNVKAGGPTSQAKSLSGGNLQKFIVGREID 413 Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484 + P +LI+ +PT G+DVGA +I I +G VL++S E+ EL CDR++V+ +G Sbjct: 414 AKPKLLIISQPTWGVDVGAAAQIRGEILARRDEGCAVLVVSEELDELFEICDRLHVIAKG 473 Query: 485 RIVAELPKGEAS 496 ++ + + +A+ Sbjct: 474 QLSPSIDRAQAT 485 Score = 76.3 bits (186), Expect = 3e-18 Identities = 58/226 (25%), Positives = 105/226 (46%), Gaps = 12/226 (5%) Query: 282 DINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDA 341 D+++TV+ GE+ + G GAG++ ++G + G V+ DG PV ++ ++A Sbjct: 23 DVSLTVQPGEIHAVLGENGAGKSTLMKIIYGSVKPDQ--GTVMFDGTPVHIANPKEARAL 80 Query: 342 GLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSG 401 G++ V + H L + N L G+ + ++ A L I S Sbjct: 81 GISMVFQ---HFSLFDTLTVAENVWL----GLGNHLTLSEVAGGIEAKAAEYGLDIDPS- 132 Query: 402 IFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGV 461 + LS G Q+V + + L +P +LILDEPT + A ++ ++ +LAA+G + Sbjct: 133 --RPVHTLSVGEMQRVEIIRALLGSPKLLILDEPTSVLTPQAVERLFVVLRKLAAEGCSI 190 Query: 462 LMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRS 507 L IS ++ E+ C V+ G++ S S+ R ++ S Sbjct: 191 LYISHKLHEIRELCTACTVLRNGKVTGACNPSMESNASLSRMMIGS 236 Score = 60.1 bits (144), Expect = 2e-13 Identities = 49/229 (21%), Positives = 106/229 (46%), Gaps = 25/229 (10%) Query: 21 LENVNLKVKEGEIHALVGENGAGKSTLMKVLSG---------VYPAGTYEGEIHYEGAVR 71 L N+ L V+ GE+ + G +G G+ + LSG + +G G + G V+ Sbjct: 270 LHNIALDVRAGEVVGIAGVSGNGQREFLYALSGEDRRSDPDAIRLSGKSVGRL---GPVQ 326 Query: 72 NFRAINDSEDIGIIIIHQEL---ALVPLLSIAENIFLGNEVA--SNGVISWQQTFNRTRE 126 R +G+ + +E VP LS+A+N+ L A + G I + + + Sbjct: 327 RRR-------LGLHFVPEERLGRGAVPTLSLAQNLLLTRTDALRTGGWIDVKAMHRQAAD 379 Query: 127 LLKKVGLKES-PETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185 ++ + +K P + + G Q + + + KLLI+ +PT ++ + + Sbjct: 380 IISRFNVKAGGPTSQAKSLSGGNLQKFIVGREIDAKPKLLIISQPTWGVDVGAAAQIRGE 439 Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISE 234 ++ R++G ++++ +L+E+ ++ D++ V+ G ++D Q I++ Sbjct: 440 ILARRDEGCAVLVVSEELDELFEICDRLHVIAKGQLSPSIDRAQATITQ 488 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: 518 Number of extensions: 29 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 512 Length of database: 527 Length adjustment: 35 Effective length of query: 477 Effective length of database: 492 Effective search space: 234684 Effective search space used: 234684 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