Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_084932744.1 HA51_RS05190 ribose ABC transporter ATP-binding protein RbsA
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_002095475.1:WP_084932744.1 Length = 502 Score = 382 bits (981), Expect = e-110 Identities = 218/505 (43%), Positives = 312/505 (61%), Gaps = 15/505 (2%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 PLL L+ I K+FPGV+AL L Y G V AL+GENGAGKST+MK+L+G Y+ D G Sbjct: 3 PLLQLKGIEKSFPGVKALNGASLAVYPGRVMALVGENGAGKSTMMKVLTGIYSMDAGSLQ 62 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRA 130 + G+ V GP+++++ G+ +I+QEL+L P L+VAENI+LGR R G + M Sbjct: 63 WL-GKDVAFSGPKASQEAGIGIIHQELNLIPQLTVAENIFLGREFVNRFGRIEWNRMYAE 121 Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190 L RL F+ V LSI +Q+VEIA+ + FE+++++MDEPT L+ ET LF Sbjct: 122 ADALLHRLNLRFNSHKLVGDLSIGDQQMVEIAKVLSFESQVIIMDEPTDALTDTETLSLF 181 Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250 +I +L+ +G I+YISHRM EI E+ D VTV RDG F+ + LS+ +L++MMVGR Sbjct: 182 RVINELKAQGCGIVYISHRMKEIFEICDDVTVFRDGQFIAERAVSDLSEESLIEMMVGRK 241 Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310 L Y H ++ L+V ++ G V SF+LR GE+LG++GL+GAGRTEL +++ Sbjct: 242 LEDQYP--HIDQAPGDIRLTVEHLS-GPGVDNVSFNLRKGEILGISGLMGAGRTELMKVL 298 Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370 +GA R++G V + + P+ + GI Y++EDRK GL L SV EN+ Sbjct: 299 YGALPRSKGTVTLNGRE-------IMTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENM 351 Query: 371 NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430 +L + G L + + + I ++ + +G LSGGNQQKV ++R L Sbjct: 352 SLTALRYFSHATGNLKHSEEQLAVGDFIRLFNVKTPSMEQPIGLLSGGNQQKVAIARGLM 411 Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490 +P VLILDEPTRGVD+GAK EIY+LIN G++I+++SSE+PEV+G+ DR+LVM EG Sbjct: 412 TRPNVLILDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEG 471 Query: 491 TLAGEVRPAGSAAETQERIIALATG 515 L+GE TQE ++A A G Sbjct: 472 HLSGEF---SREQATQESLMAAAVG 493 Score = 84.3 bits (207), Expect = 1e-20 Identities = 66/242 (27%), Positives = 106/242 (43%), Gaps = 23/242 (9%) Query: 24 PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83 PGV V GE+ + G GAG++ LMK+L GA G ++G+ + P Sbjct: 266 PGVD---NVSFNLRKGEILGISGLMGAGRTELMKVLYGALPRSKG-TVTLNGREIMTRSP 321 Query: 84 QSARDLGVAVIYQELS---LAPNLSVAENIYL----------GRALQRRGLVARGDMVRA 130 Q G+ I ++ L +SV EN+ L G +A GD +R Sbjct: 322 QDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSHATGNLKHSEEQLAVGDFIRL 381 Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190 S + LS +Q V IAR + +L++DEPT + ++ Sbjct: 382 FNVKTP------SMEQPIGLLSGGNQQKVAIARGLMTRPNVLILDEPTRGVDVGAKKEIY 435 Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250 LI Q + EG++I+ +S M E+ ++DR+ V+ +G G R +Q +L+ VG+ Sbjct: 436 QLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSREQATQESLMAAAVGKQ 495 Query: 251 LS 252 S Sbjct: 496 HS 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: 578 Number of extensions: 28 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: 502 Length adjustment: 35 Effective length of query: 505 Effective length of database: 467 Effective search space: 235835 Effective search space used: 235835 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 24 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