Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_086005351.1 RHSP_RS08730 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_000359745.1:WP_086005351.1 Length = 477 Score = 355 bits (910), Expect = e-102 Identities = 205/476 (43%), Positives = 293/476 (61%), Gaps = 11/476 (2%) Query: 32 VELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGV 91 + L G VH L+GENGAGKSTLMKIL+G Y GE + G+ Q P+ AR G+ Sbjct: 1 MNLKVRRGRVHTLLGENGAGKSTLMKILAGVYKPT-SGEILLAGKAYQPQNPRDARGHGI 59 Query: 92 AVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADFSPAANVASL 151 ++++QELSL NLSVA+NI+ R G V +V + LG + A V L Sbjct: 60 SIVFQELSLCRNLSVAQNIFASHEPSRFGFVRDRVLVAKAEALIEDLGLPVNVHAKVGDL 119 Query: 152 SIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMA 211 SIAQRQLVEIA+ + A ++++DEPT+ LS E + LF++I +L+ G AI+YISHRM Sbjct: 120 SIAQRQLVEIAKGLSLPADVIILDEPTSSLSDSEAEILFSIIERLKARGKAIIYISHRME 179 Query: 212 EIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSGFYTKTHGQ--AVEREVML 269 EI L+D +TV+RDG +V T +++ S L+ +MVGR++ Y A +L Sbjct: 180 EIMRLSDDITVIRDGEYVTTTEKSETSIDKLIALMVGREMQDIYPPRVAPRPAESTAPVL 239 Query: 270 SVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGS 329 + +++ + S D++ GEV+GL GL+G+GR+++ + +FG + R G++ + Sbjct: 240 ATKNLTVPGKFHEVSIDVKPGEVVGLFGLIGSGRSDIMKALFGME-RPEGQIFL-----D 293 Query: 330 GGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTA 389 G +TL + P AI GIA++TE+RK +GL L SV N+N++ + A G + +A Sbjct: 294 GKPLTLAS--PSDAIRHGIAFVTENRKEEGLVLAHSVERNVNMVALKQLAGPFGLMRGSA 351 Query: 390 ARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGA 449 R + L I+ A + G+LSGGNQQK++L++ L+I+PRVLILDEPTRGVD+GA Sbjct: 352 ERAAAKAEVLRLAIKAASIDTSTGSLSGGNQQKIVLAKWLQIRPRVLILDEPTRGVDVGA 411 Query: 450 KSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAET 505 K EIYR+I LA G AILM+SSELPEV+GL DRV VM +LA + G ET Sbjct: 412 KFEIYRIIRELAAEGAAILMVSSELPEVLGLSDRVAVMHNRSLAAVLDAEGLTPET 467 Score = 90.5 bits (223), Expect = 1e-22 Identities = 73/245 (29%), Positives = 117/245 (47%), Gaps = 13/245 (5%) Query: 11 APLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGE 70 AP+LA +N+ T PG +V + GEV L G G+G+S +MK L G P G+ Sbjct: 236 APVLATKNL--TVPG--KFHEVSIDVKPGEVVGLFGLIGSGRSDIMKALFGMER--PEGQ 289 Query: 71 CHIDGQRVQIDGPQSARDLGVAVIYQ---ELSLAPNLSVAENIYLGRALQRRGL--VARG 125 +DG+ + + P A G+A + + E L SV N+ + Q G + RG Sbjct: 290 IFLDGKPLTLASPSDAIRHGIAFVTENRKEEGLVLAHSVERNVNMVALKQLAGPFGLMRG 349 Query: 126 DMVRACAPT-LARLGADFSPA-ANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLST 183 RA A + RL + + SLS +Q + +A+ + R+L++DEPT + Sbjct: 350 SAERAAAKAEVLRLAIKAASIDTSTGSLSGGNQQKIVLAKWLQIRPRVLILDEPTRGVDV 409 Query: 184 HETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALV 243 ++ +IR+L EG AIL +S + E+ L+DRV V+ + LD L+ ++ Sbjct: 410 GAKFEIYRIIRELAAEGAAILMVSSELPEVLGLSDRVAVMHNRSLAAVLDAEGLTPETVM 469 Query: 244 KMMVG 248 G Sbjct: 470 TYAAG 474 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: 619 Number of extensions: 28 Number of successful extensions: 7 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: 477 Length adjustment: 34 Effective length of query: 506 Effective length of database: 443 Effective search space: 224158 Effective search space used: 224158 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