Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 435 bits (1119), Expect = e-126 Identities = 240/501 (47%), Positives = 334/501 (66%), Gaps = 10/501 (1%) Query: 13 EILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEIL 72 EIL+ KG+ KRFPGVVA+D +D ++ E+ ++ GENGAGKSTL+KI++G D G I Sbjct: 21 EILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVIC 80 Query: 73 VNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENY 132 G+ V+F S DA GI++IHQELNL +++VAENI+LA E RG VD Sbjct: 81 YEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPF------VDYRT 134 Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192 + ++ L IG SP LV L+ AQ+QMVEI KAL + R++ MDEPTSSLT ET Sbjct: 135 LNANAQRCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESET 194 Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252 +LF II L++ G++++++SHRLDE+ I DR+ V+RDG+ I ++ I+ M Sbjct: 195 VQLFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARM 254 Query: 253 VGREVEFFPHGIETRPGE-IALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311 VGR ++ E+ P E + + VR+L+ D +SF++RKGE+LGFAGL+GAGRTE Sbjct: 255 VGRALDDAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVA 314 Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371 +FG + +SG I + V I++P +AI+ GI + EDRK GL L M V NI L + Sbjct: 315 RAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSN 374 Query: 372 LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431 ++ IS G L +E I+E YV+ L+I+TP++ QI NLSGGNQQK+V++KWL + Sbjct: 375 VRAISSRGF-LRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSR 433 Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491 IL FDEPTRGIDVGAK I++++ LAA G V++ISSELPE+L ++DRI V EG ITA Sbjct: 434 ILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITA 493 Query: 492 VLDNREKRVTQEEIMYYASGQ 512 VL+ R+ +QEEI++YASG+ Sbjct: 494 VLETRQ--TSQEEILHYASGR 512 Lambda K H 0.319 0.138 0.381 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: 29 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: 520 Length of database: 515 Length adjustment: 35 Effective length of query: 485 Effective length of database: 480 Effective search space: 232800 Effective search space used: 232800 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 (21.7 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