Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 379 bits (973), Expect = e-109 Identities = 229/508 (45%), Positives = 310/508 (61%), Gaps = 15/508 (2%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 +L L+ + K FPGV AL ++L AGEVHA+ GENGAGKSTLMKI+SG Y AD G Sbjct: 23 ILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEG-VVR 81 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132 G VQ A+ G+A+I+QEL+L P+LSVAENIYL R +R V + Sbjct: 82 YRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNSNAQ 141 Query: 133 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 192 L R+G + SP+ V +LS+AQ+Q+VEIA+A+ +AR+L+MDEPT+ L+ ET +LF + Sbjct: 142 RCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRI 201 Query: 193 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 252 IR+LR G+AILYISHR+ E+ E+ DRVTVLRDG + T D A + +V MVGR L Sbjct: 202 IRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRPLD 261 Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312 Y +++L VRD+ SF+LR GE+LG AGL+GAGRTE AR +FG Sbjct: 262 DAYPPRQ-STPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAIFG 320 Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372 A+ G + + + VT+ G PR+AI GIAYL+EDRK GL L V NI L Sbjct: 321 AERPDSGSITLGDEP-----VTI--GSPREAIRHGIAYLSEDRKKDGLALSMPVSANITL 373 Query: 373 I-VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 V A + G R + A + LGIR + LSGGNQQK+++S+ L Sbjct: 374 ANVRAISSRGFLRFSEETA--IAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYR 431 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 R+L DEPTRG+D+GAK IY L++ LA GV +++ISSELPE++G+ DR+ V EG Sbjct: 432 GSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGR 491 Query: 492 LAGEVRPAGSAAETQERIIALATGAAAA 519 + + + +QE I+ A+G + A Sbjct: 492 ITAVLE---TRQTSQEEILHHASGRSHA 516 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: 645 Number of extensions: 39 Number of successful extensions: 8 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