Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 365 bits (938), Expect = e-105 Identities = 221/505 (43%), Positives = 300/505 (59%), Gaps = 14/505 (2%) Query: 6 DTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTA 65 D LAL +I KTFPGV+AL V L+ Y G+V AL+GENGAGKST++KIL+G Y Sbjct: 13 DPPVSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQP 72 Query: 66 DPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVAR 124 D GG +DGQ V PQ+A D GV I+QE L LSVAENI+LG A + GL+ Sbjct: 73 D-GGRILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDW 131 Query: 125 GDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTH 184 L +GA+ P + L IA + LV IARA+ EAR+++MDEPT LS Sbjct: 132 KKTTENARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHK 191 Query: 185 ETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVK 244 E + L+ L+ L+ +G AIL+ISH+ EI +AD TV RDG +G A +++A LVK Sbjct: 192 EIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVK 251 Query: 245 MMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304 MMVGRD+S + + + +L+V+ A SF LR GE+LG GLVGAGR+ Sbjct: 252 MMVGRDVSQIFPQRAPNV--GDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRS 309 Query: 305 ELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQ 364 E + +FG + G V I G+ ++ PA A+D GI Y+ EDR QG LD Sbjct: 310 EFMQSLFGITRPSAGSVEIG---GARAEISSPA----DAVDHGIVYVPEDRGKQGAILDL 362 Query: 365 SVHENINLIVAAR-DALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKV 423 + +N+ L R G RL A R E + L +R A +VG LSGGNQQKV Sbjct: 363 PIFQNVTLPSLGRISRKGFLRLAEEFALAR--EYTERLDLRAASLDTHVGNLSGGNQQKV 420 Query: 424 MLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDR 483 ++++ L +PRV+ILDEPT+GVDIG+K+ ++ + LA G+A++M+SSE+PEV+G+ DR Sbjct: 421 VIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDR 480 Query: 484 VLVMREGTLAGEVRPAGSAAETQER 508 V+VMREG + E+ ET R Sbjct: 481 VIVMREGRIVAELAGDDLQPETLVR 505 Score = 75.5 bits (184), Expect = 5e-18 Identities = 61/226 (26%), Positives = 104/226 (46%), Gaps = 13/226 (5%) Query: 32 VELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGV 91 + T GE+ G GAG+S M+ L G T G I G R +I P A D G+ Sbjct: 288 ISFTLREGEILGFYGLVGAGRSEFMQSLFGI-TRPSAGSVEIGGARAEISSPADAVDHGI 346 Query: 92 AVIYQELSLAP---NLSVAENIYL---GRALQRRGLVARGDMVRACAPTLARLGADFSPA 145 + ++ +L + +N+ L GR + R+G + + RL D A Sbjct: 347 VYVPEDRGKQGAILDLPIFQNVTLPSLGR-ISRKGFLRLAEEFALAREYTERL--DLRAA 403 Query: 146 A---NVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMA 202 + +V +LS +Q V IA+ + R++++DEPT + + + +L +G+A Sbjct: 404 SLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLA 463 Query: 203 ILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248 ++ +S + E+ ++DRV V+R+G V L L LV+ G Sbjct: 464 VIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509 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: 632 Number of extensions: 26 Number of successful extensions: 8 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: 510 Length adjustment: 35 Effective length of query: 505 Effective length of database: 475 Effective search space: 239875 Effective search space used: 239875 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