Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 225 bits (573), Expect = 4e-63 Identities = 155/484 (32%), Positives = 254/484 (52%), Gaps = 24/484 (4%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 PL++++ + K F V A + L Y G V AL+GENGAGKSTLM +L+G Y D G Sbjct: 23 PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPD-AGTI 81 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 +DG+ V+ + A + G+ ++YQ L +++VAEN+ LG+ + + +M Sbjct: 82 ALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQ--EGSFFLNPKEMRNRV 139 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 R G D PAA V+ LS+ ++Q VEI + ++ ++R+L+ DEPT L+ ET LF Sbjct: 140 QELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFE 199 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL-SQAALVKMMVGRD 250 + ++ +G +I++ISH++ E+ +AD + +LR G G + + S+A L MVG++ Sbjct: 200 ALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKE 259 Query: 251 L---SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307 + HG AV L VR++ G ++ +FDL GEV+ + G+ G G+ L Sbjct: 260 VLLEVDREAMPHGDAV-----LQVRNLT-GIGLEDITFDLHQGEVVAVVGVAGNGQKALV 313 Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367 + G + I + + +AY+ EDR GL ++++ Sbjct: 314 EAICGLRKPPVDTMFIMGKRWRDFYA-------KPSWKNSLAYIPEDR--LGLATCRNLN 364 Query: 368 ENINLIVAARDALGLGR-LNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 426 NL++ R G L++ A R TTE I IR LSGGN QK +L+ Sbjct: 365 LVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLA 424 Query: 427 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 486 R L PR+++ ++PT+G+DI A +++ + A A+ IL+++ +L E + L DRV V Sbjct: 425 RELYRCPRLIVAEQPTQGLDIAATEQVWNHLLA-AREMAGILLVTGDLNEALQLADRVAV 483 Query: 487 MREG 490 + G Sbjct: 484 IYRG 487 Score = 68.6 bits (166), Expect = 6e-16 Identities = 62/214 (28%), Positives = 98/214 (45%), Gaps = 20/214 (9%) Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPA--GGPR 341 S ++ G V L G GAG++ L ++ G R AG+ L P R Sbjct: 44 SLNIYPGRVKALLGENGAGKSTLMSMLAG---------RYQPDAGTIALDGKPVRFSSAR 94 Query: 342 QAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTL 401 AI+AGI + Q L +S+ N+++ G LN R R E Sbjct: 95 DAIEAGIGMV-----YQHFMLVESMTVAENVLLGQE---GSFFLNPKEMRNRVQELSVRY 146 Query: 402 GIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALA 461 G+ + A V LS G +Q+V + +LL RVLI DEPT + ++ + +A Sbjct: 147 GLDIDPA-ARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIA 205 Query: 462 QSGVAILMISSELPEVVGLCDRVLVMREGTLAGE 495 + G +I+ IS +L EV+ + D + ++R+G + GE Sbjct: 206 EQGKSIVFISHKLEEVLAVADEIAILRQGRIEGE 239 Lambda K H 0.320 0.136 0.382 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: 540 Number of extensions: 20 Number of successful extensions: 6 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: 540 Length of database: 514 Length adjustment: 35 Effective length of query: 505 Effective length of database: 479 Effective search space: 241895 Effective search space used: 241895 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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