Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 362 bits (930), Expect = e-104 Identities = 219/526 (41%), Positives = 304/526 (57%), Gaps = 17/526 (3%) Query: 1 MSDMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILS 60 M+D + T++ PLLA+R + K F GV+AL V+ T GE+HAL+GENGAGKSTL+K L+ Sbjct: 1 MTDPTPTASP-PLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLT 59 Query: 61 GAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRG 120 G Y D G ++G+ + G + A+ L + +YQE++L PNLSVAEN++LGR R G Sbjct: 60 GVYQRD-AGTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFG 118 Query: 121 LVARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTP 180 LV RG M R L G A + S+A +Q+V IARAV A++L++DEPT Sbjct: 119 LVDRGAMRRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTAS 178 Query: 181 LSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQA 240 L E LF ++R LR G+ I++++H + ++ L DR+TVLR+G VG A L + Sbjct: 179 LDAQEVAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRL 238 Query: 241 ALVKMMVGRDLSGFYTKTHGQAVE-----REVMLSVRDVADGRRVKGCSFDLRAGEVLGL 295 LV MM+GR+L + A + R ++ R R V+ D+R GEV+GL Sbjct: 239 DLVAMMLGRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGL 298 Query: 296 AGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDR 355 AGL+G+GRTE ARLVFG D RGE + A + GPR AI G + EDR Sbjct: 299 AGLLGSGRTETARLVFGMDRADRGEAAVDGQA-------VRLRGPRDAIRLGFGFCPEDR 351 Query: 356 KLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGAL 415 K +G+ SV ENI L + AR L + R I L IR HA+ + L Sbjct: 352 KKEGIVGALSVRENIILALQARQG-WLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLL 410 Query: 416 SGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELP 475 SGGNQQK +L+R L +PR+LILDEPTRG+D+GA +EI RLI L G+A+L++SSEL Sbjct: 411 SGGNQQKALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELE 470 Query: 476 EVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAP 521 E+V RV+V+R+ E+R G + A+A+ + P Sbjct: 471 EIVAYSRRVVVLRDRRHVAELR--GGEVAVDRIVAAIASESVPEEP 514 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: 690 Number of extensions: 37 Number of successful extensions: 9 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: 516 Length adjustment: 35 Effective length of query: 505 Effective length of database: 481 Effective search space: 242905 Effective search space used: 242905 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