Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 238 bits (608), Expect = 3e-67 Identities = 165/483 (34%), Positives = 256/483 (53%), Gaps = 22/483 (4%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P++ L ICK+F VRA + L G + AL+GENGAGKSTLM IL+G D G Sbjct: 28 PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQD-AGTI 86 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 +DG P+ A G+ ++YQ L +++VAEN+ LG Q ++ R +R Sbjct: 87 VVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLG---QSPDMLLRPARMRDE 143 Query: 132 APTLA-RLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190 LA R G PAA V LS+ +RQ VEI + ++ ++R+L++DEPT L+ ETD+LF Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203 Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL-SQAALVKMMVGR 249 + ++ +G A+++ISH++ E+ +AD + +LR G V A + +Q L MVGR Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263 Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309 D+ + + +LSV ++ G + S +R GE++ +AG+ G G+ EL Sbjct: 264 DV--VLQVDAKRLTPVDTVLSVEHLS-GAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320 Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369 + G GEVRI AG P + G+AY+ EDR QGL + + Sbjct: 321 ICGLARPEAGEVRILGRPWR----EFFAGPPGR---RGLAYIPEDR--QGLATCRHLDLV 371 Query: 370 INLIVAARDALGLG-RLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRL 428 N ++ R+ G L+RT A + ++ ALSGGN QK+++ R Sbjct: 372 DNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGRE 431 Query: 429 LEIQPRVLILDEPTRGVDIGAKSEIY-RLINALAQSGVAILMISSELPEVVGLCDRVLVM 487 +P V++ + PT+G+DI A E++ RL+ A + SGV L+++ +L E + L DR+ VM Sbjct: 432 FFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTSGV--LLVTGDLNEALELADRIAVM 489 Query: 488 REG 490 G Sbjct: 490 YRG 492 Score = 72.4 bits (176), Expect = 4e-17 Identities = 64/222 (28%), Positives = 105/222 (47%), Gaps = 16/222 (7%) Query: 284 SFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQA 343 + D+R G + L G GAG++ L ++ G + G + + G+ T+ A PR A Sbjct: 49 TLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV------DGVPTVFAS-PRDA 101 Query: 344 IDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGI 403 + AGI + + L +V EN+ L+ + D L L R + G+ Sbjct: 102 LRAGIGMVYQHFMLVD---SMTVAENV-LLGQSPDML----LRPARMRDEVAALAERYGL 153 Query: 404 RVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQS 463 V A VG LS G +Q+V + +LL RVLILDEPT + +++ + +A Sbjct: 154 AVDPA-ARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMWRMADQ 212 Query: 464 GVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAET 505 G A++ IS +L EV+ + D + ++R G + E A +T Sbjct: 213 GKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQT 254 Score = 48.9 bits (115), Expect = 5e-10 Identities = 55/229 (24%), Positives = 98/229 (42%), Gaps = 16/229 (6%) Query: 29 LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQ--RVQIDGPQSA 86 L V L GE+ A+ G G G+ L++ + G + GE I G+ R GP Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPE-AGEVRILGRPWREFFAGPPGR 349 Query: 87 RDLG-VAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLA--RLGADFS 143 R L + Q L+ +L + +N L R A+G + T A R+ +++ Sbjct: 350 RGLAYIPEDRQGLATCRHLDLVDNFLL----TTRNQFAKGVFLDRTEATNAVKRVVWEYN 405 Query: 144 P-----AANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRG 198 A +LS Q + I R + ++V + PT L T+ ++ + + R Sbjct: 406 VQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARS 465 Query: 199 EGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 +L ++ + E ELADR+ V+ G F+ D+ ++ + +M+ Sbjct: 466 TS-GVLLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513 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: 647 Number of extensions: 36 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 540 Length of database: 537 Length adjustment: 35 Effective length of query: 505 Effective length of database: 502 Effective search space: 253510 Effective search space used: 253510 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