Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_106709787.1 CU102_RS04475 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_003010955.1:WP_106709787.1 Length = 514 Score = 394 bits (1013), Expect = e-114 Identities = 229/516 (44%), Positives = 326/516 (63%), Gaps = 30/516 (5%) Query: 10 KAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGG 69 + P+L++RN+ K F V+AL V GEVHAL GENGAGKSTLM I++G D G Sbjct: 2 REPVLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEG- 60 Query: 70 ECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVAR-GDMV 128 E +DG+ V+I P +A+ LG+ +++QE++L P+ SVAENI++ ++R L+ + Sbjct: 61 EIVLDGKTVRIGSPAAAQSLGLGLVHQEIALCPDASVAENIFMASISRQRSLLMNYRKLE 120 Query: 129 RACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 188 R ++RL A V L I+ +QLVEIA+A+ + R+L+ DEPT L+ E Sbjct: 121 REAQAVMSRL-APIDVRRKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEARI 179 Query: 189 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248 LF +IR L+ G++I+YISHRMAEI EL DRVTVLRDG +V T A L+ +V+ MVG Sbjct: 180 LFEIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMVG 239 Query: 249 RDLSGFYT-KTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307 R+++ Y K +EV+ SVR + D R + DL GE+LG+ GL+G+GRTE+A Sbjct: 240 REITQLYPPKQPAGERPQEVVFSVRGLGDNERFRDVDIDLTRGEILGIGGLIGSGRTEIA 299 Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367 + G A T G++ I + G A+ AG+ YL+EDRK GLFLD S+ Sbjct: 300 EGICGLRATTNGQILIHGKQQAIGTYA-------DAVKAGLVYLSEDRKGSGLFLDLSIA 352 Query: 368 ENINLI--------VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGN 419 +NI+++ + D +G G L R A+R L IR+ V +LSGGN Sbjct: 353 KNISVLNLDALTGHLGLIDTVGEGDLARDFAQR--------LNIRMGSIGAPVSSLSGGN 404 Query: 420 QQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVG 479 QQKV +++ L IQP+V+++DEPTRG+D+GAKSEI+ L+ LAQSG+ I++ISSELPE++G Sbjct: 405 QQKVAIAKQLAIQPKVILMDEPTRGIDVGAKSEIHALLRELAQSGIGIIVISSELPELLG 464 Query: 480 LCDRVLVMREGTLAGEVRPAGSAAETQERIIALATG 515 LCDRV+V+REG +AGE+ G T+ER+I LA+G Sbjct: 465 LCDRVIVIREGEVAGEL---GMDDMTEERVIRLASG 497 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: 681 Number of extensions: 37 Number of successful extensions: 8 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: 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 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