Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_002095475.1:WP_084931811.1 Length = 504 Score = 385 bits (988), Expect = e-111 Identities = 216/487 (44%), Positives = 316/487 (64%), Gaps = 12/487 (2%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 PL+ LR+I KTF G+ AL+ +L AGEVHAL+GENGAGKSTLM++L G +T D G Sbjct: 4 PLIELRDIVKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPD-SGTV 62 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 + G+ VQI GP++A G+ +I+QE++LA L+VAENI+L +A + Sbjct: 63 YDKGEAVQIKGPKAAMARGITLIHQEMALAQELTVAENIFLH---DLPTFIAWPKLRAKA 119 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 A L RLG + PAA V LS+A +Q+VEIARA+ +AR++V DEPT LST + +RL Sbjct: 120 ANILRRLGFEIDPAATVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLE 179 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 +I LR G+AI+YISHR+ E+ +ADR+T+++DG ++ T + ++++MVGR + Sbjct: 180 IISDLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIATESPQQTTLQEVIRLMVGRPV 239 Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311 ++ + EV L V + R+V+ SF +RAGEV+GL GLVG+GRTE+ARL+F Sbjct: 240 DQLFSDRATYGMGEEV-LRVEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIF 298 Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371 GAD G++ + G V+L + P+QA+ AGIA + EDRK QG+ LD + N+ Sbjct: 299 GADRCDSGDIYL-----HGKKVSLRS--PQQAVKAGIALVPEDRKRQGVVLDMPIRANVT 351 Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 + LG ++ + + ++ + ++ A V +LSGGNQQKV+L++ + Sbjct: 352 MANDKAVMAPLGFIHSSRETQVVSKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNL 411 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 +V+ILDEPTRGVD+GAK EIY+LI LAQ G+A+++ISSE E+ GLC+RVLVM EG Sbjct: 412 GGQVIILDEPTRGVDVGAKREIYQLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGA 471 Query: 492 LAGEVRP 498 + GE++P Sbjct: 472 ICGELQP 478 Score = 78.2 bits (191), Expect = 7e-19 Identities = 59/228 (25%), Positives = 111/228 (48%), Gaps = 12/228 (5%) Query: 27 RALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSA 86 R +R V + AGEV L G G+G++ + +++ GA D G+ ++ G++V + PQ A Sbjct: 265 RKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCD-SGDIYLHGKKVSLRSPQQA 323 Query: 87 RDLGVAVIYQE---------LSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLAR 137 G+A++ ++ + + N+++A + + L +V A + Sbjct: 324 VKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVVSKLAQQMRL 383 Query: 138 LGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLR 197 A A V+SLS +Q V +A+ + +++++DEPT + ++ LI +L Sbjct: 384 KCAGLH--APVSSLSGGNQQKVVLAKWFNLGGQVIILDEPTRGVDVGAKREIYQLIAELA 441 Query: 198 GEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKM 245 +GMA++ IS E+ L +RV V+ +G G L S+ L+ M Sbjct: 442 QQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSM 489 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: 622 Number of extensions: 34 Number of successful extensions: 9 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: 504 Length adjustment: 35 Effective length of query: 505 Effective length of database: 469 Effective search space: 236845 Effective search space used: 236845 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 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