Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012046028.1 BBTA_RS28795 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000015165.1:WP_012046028.1 Length = 500 Score = 383 bits (984), Expect = e-111 Identities = 214/505 (42%), Positives = 319/505 (63%), Gaps = 15/505 (2%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M LE+ +I KT+PGV AL++V+L V GE+ AL+GENGAGKSTLM+VL GV + Sbjct: 1 MGEPFLELIDIGKTYPGVVALDHVSLSVAPGEVVALLGENGAGKSTLMRVLGGVVAPSS- 59 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGV---ISW 117 G I +G R ++ D+ GI +HQEL L L +A N+F+G E G+ I Sbjct: 60 -GTIRIDGVARTSYSVADAIAAGIAFVHQELNLFDNLDVAGNVFIGREPVHGGLLKLIDR 118 Query: 118 QQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNES 177 + + R L+ ++G +P+T + ++ + ++QLVEI KALS + +I+DEPT+SL S Sbjct: 119 KTLLAKVRPLIDRLGADFAPDTPLAELSLAQRQLVEIIKALSLDARCVIMDEPTSSLTLS 178 Query: 178 DSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVI 237 ++E L+ ++ + G++ I ITH+LNEV + AD VLRDG V L +EE++ + Sbjct: 179 ETERLMQVIAGLKADGVSVIFITHRLNEVMQCADHAIVLRDGRMVGALT--REELNPAAM 236 Query: 238 IRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAG 297 IR M+GRDL Y P P GETIL+V + H+ +++ +R+GE++G+AG Sbjct: 237 IRLMIGRDLRSLYVPPAAPPGETILDVADAVTSTYPHQA------VSLQLRRGEILGLAG 290 Query: 298 LMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVL 357 L+GAGRTE A ++FG + G + +DG+P+ +++ R+AID G+ + EDRK GL+L Sbjct: 291 LVGAGRTELARAIFGVD--PLLAGGISVDGEPIRIASPREAIDRGIYLIPEDRKACGLLL 348 Query: 358 NDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKV 417 ++ N +L +LA S ++D ++E A R RL+IR++ + LSGGNQQKV Sbjct: 349 ELSMAQNVSLPDLASYSSFGLVDTVRETANADHQRERLKIRAADVKAPVGTLSGGNQQKV 408 Query: 418 VLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDR 477 VL+KWL P VLI DEPTRGIDVGAK EIY ++ +L+ G +LMISS+M E++G DR Sbjct: 409 VLAKWLSMRPKVLIFDEPTRGIDVGAKQEIYDMLRRLSDAGVAILMISSDMEEVIGVSDR 468 Query: 478 IYVMNEGRIVAELPKGEASQESIMR 502 I VM+EGRI L + E S+ ++++ Sbjct: 469 IAVMHEGRISGFLARSEFSEHNVLQ 493 Score = 65.1 bits (157), Expect = 6e-15 Identities = 58/235 (24%), Positives = 111/235 (47%), Gaps = 23/235 (9%) Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAI 339 L ++++V GEVV + G GAG++ M V G +G + IDG +V AI Sbjct: 21 LDHVSLSVAPGEVVALLGENGAGKSTL-MRVLGGVVAPS-SGTIRIDGVARTSYSVADAI 78 Query: 340 DAGLAYVTEDRKHLGLVLNDNILHNTTLAN-------LAGVSKASIIDDIKEM--KVASD 390 AG+A+V ++ L L N ++ N + L + + +++ ++ + ++ +D Sbjct: 79 AAGIAFVHQE---LNLFDNLDVAGNVFIGREPVHGGLLKLIDRKTLLAKVRPLIDRLGAD 135 Query: 391 FRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTI 450 F + LS +Q V + K L + +I+DEPT + + + + Sbjct: 136 FAPDTPL---------AELSLAQRQLVEIIKALSLDARCVIMDEPTSSLTLSETERLMQV 186 Query: 451 INQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 I L ADG V+ I+ + E++ D V+ +GR+V L + E + +++R ++ Sbjct: 187 IAGLKADGVSVIFITHRLNEVMQCADHAIVLRDGRMVGALTREELNPAAMIRLMI 241 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: 608 Number of extensions: 33 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: 500 Length adjustment: 34 Effective length of query: 478 Effective length of database: 466 Effective search space: 222748 Effective search space used: 222748 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