Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_000204075.1:WP_011318959.1 Length = 517 Score = 498 bits (1282), Expect = e-145 Identities = 280/516 (54%), Positives = 361/516 (69%), Gaps = 10/516 (1%) Query: 2 SDMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSG 61 +D S +T P+L ++ I K F GV AL+ V LT Y GEVHALMGENGAGKSTLMKIL+G Sbjct: 7 TDFSPPATATPVLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAG 66 Query: 62 AYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL 121 AY AD G E I+G+ V+I P +AR G+ +IYQEL++APNL+V ENI++G L R Sbjct: 67 AYIADEG-EIRINGKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMGSELTRGQF 125 Query: 122 VARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPL 181 + R M LA LGA F+P V +L+IA++Q VEIARA+ +RILVMDEPT L Sbjct: 126 LDRKAMELEAQQVLASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAAL 185 Query: 182 STHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAA 241 S ET+RLF +IR+LR +G+AI+YISHRM EI LADR++VLRDG ++G+L R +S Sbjct: 186 SDRETERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQR 245 Query: 242 LVKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGA 301 LV+MMVGR + FY + Q+ V+L VR+++DGR+V+ SF LRAGE+LGLAGLVGA Sbjct: 246 LVQMMVGRSMQDFY-EHQRQSNPGPVVLEVRNISDGRKVQPASFQLRAGEILGLAGLVGA 304 Query: 302 GRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLF 361 GRTE++RL+FGAD + GEV + L P AI GI Y+ EDRK QGLF Sbjct: 305 GRTEVSRLIFGADRKVSGEVFLNGK-------KLEIHSPSDAIAVGIGYVPEDRKDQGLF 357 Query: 362 LDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQ 421 L+ S +NI L +DA LG +N + + T+A++ IR+A+ ++ LSGGNQQ Sbjct: 358 LEMSSRKNIGLNRLKQDA-NLGIVNWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQ 416 Query: 422 KVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLC 481 K++L+R L I PRVL+LDEPTRGVDIGAKSEIYR+I+ L+ GVAILM+SSELPE+VGL Sbjct: 417 KLLLARWLAINPRVLMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLS 476 Query: 482 DRVLVMREGTLAGEVRPAGSAAETQERIIALATGAA 517 DRVLVMREG L GE+ + TQE I+ ATGA+ Sbjct: 477 DRVLVMREGQLVGELDNSIGKEITQENIMHYATGAS 512 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: 667 Number of extensions: 30 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 540 Length of database: 517 Length adjustment: 35 Effective length of query: 505 Effective length of database: 482 Effective search space: 243410 Effective search space used: 243410 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