Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate SM_b20503 SM_b20503 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Smeli:SM_b20503 Length = 512 Score = 380 bits (976), Expect = e-110 Identities = 218/513 (42%), Positives = 319/513 (62%), Gaps = 16/513 (3%) Query: 9 TKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG 68 T +L +RN+ K F V+AL V+ GEVHAL GENGAGKSTLM +++G G Sbjct: 2 TSETVLEIRNVSKHFGAVKALTAVDFRLARGEVHALCGENGAGKSTLMNVIAGVLQPSEG 61 Query: 69 GECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMV 128 E I+G V+I P A+ LG+A+++QE++L P+ ++AEN+++ +RR + + Sbjct: 62 -EVLIEGAPVKIASPAVAQSLGIALVHQEIALCPDATIAENMFMAATNRRRSALMNYAQL 120 Query: 129 RACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 188 A + A + V L I+ +QLVEIA+A+ + R+L+ DEPT L+ E Sbjct: 121 ERDAQAVMNRLAPIDVSQKVGDLPISSQQLVEIAKALTLDCRVLIFDEPTAALTETEAQV 180 Query: 189 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248 LF +IR L+ G++I+YISHRMAE+ L DRVTV RDG +V T + ++ +V++MVG Sbjct: 181 LFGIIRDLKARGISIIYISHRMAEVFSLCDRVTVFRDGRYVATEMVSDVTPDDVVRLMVG 240 Query: 249 RDLSGFYTKTHGQAVER--EVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306 R++S Y + ER E +LSVRD+ G R + SF+LR GE+LG+ GL+G+GRTE+ Sbjct: 241 REISQLYPDKQPSS-ERLGEPILSVRDLG-GERFRDVSFELRYGEILGVGGLIGSGRTEI 298 Query: 307 ARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSV 366 A + T+GE+R+ + L A AG+ YL+EDRK G+FLD S+ Sbjct: 299 AEGICALRPVTQGEIRLHDK-------VLRLRRYSDAAKAGVVYLSEDRKGSGVFLDLSI 351 Query: 367 HENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 426 +NI + + LG LN R + LG+R+ + V +LSGGNQQKV ++ Sbjct: 352 AQNI-AALDLKALTSLGLLNSREERALAEDLTRRLGVRMGGVDMPVSSLSGGNQQKVAIA 410 Query: 427 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 486 + L + P+V+++DEPTRG+D+GAKSEI+RL+ LA++G+ IL+ISSELPE++GLCDRVLV Sbjct: 411 KQLAVDPKVILMDEPTRGIDVGAKSEIHRLLRELARAGIGILVISSELPELIGLCDRVLV 470 Query: 487 MREGTLAGEVRPAGSAAETQERIIALATGAAAA 519 +REG +AGEV T+E I+ LA+G A Sbjct: 471 VREGRIAGEV---SGNEMTEEVIMRLASGIGPA 500 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: 31 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: 512 Length adjustment: 35 Effective length of query: 505 Effective length of database: 477 Effective search space: 240885 Effective search space used: 240885 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