Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate H281DRAFT_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Burk376:H281DRAFT_00426 Length = 503 Score = 409 bits (1052), Expect = e-118 Identities = 242/506 (47%), Positives = 330/506 (65%), Gaps = 16/506 (3%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 PL++++ + K+FPGVRAL V+ GEVHALMGENGAGKSTLMKIL+G YT D GE Sbjct: 3 PLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRD-SGEI 61 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRA 130 + GQ V++ P+ A+ G+ +I+QEL L +L+VA+NI++GR + R GL D + A Sbjct: 62 LLGGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLNA 121 Query: 131 CA-PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRL 189 A L+R+ + P A V +L++A +Q+VEIA+A+ F++R+L+MDEPT+ L+ E L Sbjct: 122 KAREILSRMHVNIDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181 Query: 190 FALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249 F +IR+L+ G+ ++YISH+M E+ ++ADRVTVLRDG +V T+ A S A++ MMVGR Sbjct: 182 FRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMVGR 241 Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309 LS A + E+ L VR++ G V+ SF LR GE+LG AGL+GAGRTE+AR Sbjct: 242 TLSD-VAPAGRAASQGEIALEVRNLHAGPLVRDVSFTLRKGEILGFAGLMGAGRTEVARA 300 Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369 VFGAD GE+ + S P A+ GI YL+EDRK GL V N Sbjct: 301 VFGADPVESGEIFVKGAKAS-------IRTPSDAVAHGIGYLSEDRKRFGLATGMDVESN 353 Query: 370 INLIVAARDALGLG-RLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRL 428 I ++ R+ L L L R RRR + I+ L IR A V LSGGNQQK+++++ Sbjct: 354 I-VMSNLRNFLSLNFFLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKW 412 Query: 429 LEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMR 488 LE VL DEPTRG+D+GAKSEIY+L+ +LA G AI+MISSELPE++ + DRV+VM Sbjct: 413 LERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMC 472 Query: 489 EGTLAGEVRPAGSAAETQERIIALAT 514 EG + GE+ PA A TQERI+ LAT Sbjct: 473 EGRITGEL-PAEQA--TQERIMHLAT 495 Score = 77.0 bits (188), Expect = 2e-18 Identities = 62/228 (27%), Positives = 101/228 (44%), Gaps = 8/228 (3%) Query: 29 LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARD 88 +R V T GE+ G GAG++ + + + GA + GE + G + I P A Sbjct: 271 VRDVSFTLRKGEILGFAGLMGAGRTEVARAVFGADPVE-SGEIFVKGAKASIRTPSDAVA 329 Query: 89 LGVAVIYQE---LSLAPNLSVAENIYLG--RALQRRGLVARGDMVRACAPTLARLGADFS 143 G+ + ++ LA + V NI + R R +R A L A + Sbjct: 330 HGIGYLSEDRKRFGLATGMDVESNIVMSNLRNFLSLNFFLRRARMRRRASHFINLLAIRT 389 Query: 144 PAA--NVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGM 201 P+A V LS +Q + IA+ + + +L DEPT + ++ L+R L EG Sbjct: 390 PSAAQQVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADEGK 449 Query: 202 AILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249 AI+ IS + EI ++DRV V+ +G G L +Q ++ + R Sbjct: 450 AIVMISSELPEILRMSDRVVVMCEGRITGELPAEQATQERIMHLATQR 497 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: 588 Number of extensions: 32 Number of successful extensions: 10 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: 503 Length adjustment: 35 Effective length of query: 505 Effective length of database: 468 Effective search space: 236340 Effective search space used: 236340 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