Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_084931762.1 HA51_RS02835 sugar ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >NCBI__GCF_002095475.1:WP_084931762.1 Length = 500 Score = 395 bits (1014), Expect = e-114 Identities = 213/502 (42%), Positives = 331/502 (65%), Gaps = 10/502 (1%) Query: 15 LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74 L +GI K + +A+ +VDF V E+ +LIGENGAGKSTL+ IL+GV D+G I VN Sbjct: 6 LMMRGITKTYGSAIALQDVDFMVRPGEVHALIGENGAGKSTLLNILSGVRPADSGAIHVN 65 Query: 75 GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSR-VDENYM 133 GE+V+ +P+ A GI++IHQEL ++VA+N+FL TL+ VD+ Sbjct: 66 GEQVQMKNPLSARHAGIAMIHQELQHVPELSVAQNMFLGRPLT-----TLNGLFVDKRAQ 120 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 R+ +L + +P ++NL +Q+Q+VEI +AL+ E +II MDEPTSSLT E E Sbjct: 121 LARATHILKQLDPSINPAEPIKNLKVSQQQIVEIARALLDEAKIIAMDEPTSSLTPREFE 180 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 RL E+I LKS G+S+++VSH+++E+ ++ DR +MRDG+++G + + +TI+ MV Sbjct: 181 RLAELIADLKSTGVSLIYVSHKMNEIFQVCDRATIMRDGRQVGVVNICDETEETIVAKMV 240 Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313 GR+++ H ++ L+V N+ ++K SF V GEVLG AGLVGAGRTE + L Sbjct: 241 GRKIDKQAHQSWATDRKV-LQVENVARGTEIKPASFSVCAGEVLGVAGLVGAGRTELLKL 299 Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373 + G++++ +G++ VNG+ V N AI+ GIGL+PEDRK +G++ VK N+ LPS++ Sbjct: 300 IAGIDKRSAGEVRVNGQLVRNHNVSAAIRAGIGLVPEDRKKEGIIKARAVKVNMALPSMR 359 Query: 374 KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADIL 433 + G V+ + K ++++ + L ++ +I + LSGGNQQKV++ +W+A +A++ Sbjct: 360 NFTLAG-VIRKVKLNAVAQEVMSDLKLRPLNIEKPIGTLSGGNQQKVIIGRWVAADAEVF 418 Query: 434 IFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVL 493 +FDEPTRGID+GAKAEI+ +I +LA QGKA++++SSE+ EIL +SDR++VM EG+IT L Sbjct: 419 LFDEPTRGIDIGAKAEIYNLIEKLAQQGKAIVVVSSEMTEILRVSDRVLVMREGKITREL 478 Query: 494 DNREKRVTQEEIMYYASGQKKQ 515 + +T+E I +A K+ Sbjct: 479 TGDD--ITEENIARFAINDIKE 498 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: 643 Number of extensions: 36 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: 500 Length adjustment: 34 Effective length of query: 486 Effective length of database: 466 Effective search space: 226476 Effective search space used: 226476 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 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