Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 330 bits (847), Expect = 6e-95 Identities = 213/513 (41%), Positives = 298/513 (58%), Gaps = 29/513 (5%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADP-GGE 70 P+L ++ I KTFPGV+AL V L+ GE+HAL+GENGAGKSTLMK+LSG Y GE Sbjct: 4 PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGE 63 Query: 71 CHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRA 130 GQ G + LG+ +I+QEL+L P LS+ EN++LG RG++ Sbjct: 64 IRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAATLR 123 Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190 L +G P + + + ++QLVEIA+A+ E ++L++DEPT L+ ++D L Sbjct: 124 ARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDALL 183 Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD--RAHLSQAALVKMMVG 248 L+ Q + G+A + ISH++ EI ++ADRVT+LRDG V TLD A +SQ +++ MVG Sbjct: 184 ELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMVG 243 Query: 249 RDLSGFYTKTHGQAVEREVMLSVR------DVADGRR-VKGCSFDLRAGEVLGLAGLVGA 301 R LS Y + V +V+ V+ GRR V+ + +R GEV+G+AGL+GA Sbjct: 244 RALSDRYPRR--TTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGA 301 Query: 302 GRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLF 361 GRTE A +FG R+ G I A G + +A+ G+AY TEDRK GL Sbjct: 302 GRTEFAMSLFG---RSYGR-NIRGQAFLDGR-EIDVSTISRAMANGLAYATEDRKHLGLV 356 Query: 362 LDQSVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSG 417 LD + N+ L VA R + R + A R L IR A LSG Sbjct: 357 LDNDIRHNVTLANLRGVAKRWVIDHEREVQVAEEFRR-----RLRIRCADVFQETVNLSG 411 Query: 418 GNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEV 477 GNQQKV+LS+ L P+VLILDEPTRG+D+GAK EIY +IN L G +++ISSE+PE+ Sbjct: 412 GNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPEL 471 Query: 478 VGLCDRVLVMREGTLAGEVRPAGSAAETQERII 510 +G+ DR+ VM G + E+ PA A +QE+I+ Sbjct: 472 LGVADRIYVMNAGEMVAEM-PAAEA--SQEKIM 501 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: 679 Number of extensions: 40 Number of successful extensions: 7 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: 518 Length adjustment: 35 Effective length of query: 505 Effective length of database: 483 Effective search space: 243915 Effective search space used: 243915 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 17 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