Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Smeli:SMc02325 Length = 503 Score = 391 bits (1004), Expect = e-113 Identities = 209/504 (41%), Positives = 320/504 (63%), Gaps = 9/504 (1%) Query: 18 KGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGER 77 +GI K FPGV A+ +V +Y + +L+GENGAGKSTL+KILTG+ +PDAG I + Sbjct: 8 EGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIRLGDTE 67 Query: 78 VEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRS 137 F + + A + G++ IHQE L D ++VAENIFL + R +D + + Sbjct: 68 TTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAP-----RNRFGLIDWKQLNADA 122 Query: 138 KELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFE 197 + LL GA F P +R+L A++ +V I +AL + R++ MDEPT++L+ +E L++ Sbjct: 123 QALLGRAGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELYD 182 Query: 198 IIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV 257 +IE LK+ G +V+F+SH+ DE+ RI+DR V RDG IGE + D +++MMVGR V Sbjct: 183 LIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGRAV 242 Query: 258 EFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGV 317 E G+ L V + + ++++FE+R+GE+LGF GLVGAGR+E M + G+ Sbjct: 243 GSVYPKKEVTIGQPVLTVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFMQSLIGI 302 Query: 318 NQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISR 377 + +G + ++G + I++P +AI+ GI +PE+R QG ++ M + N+ LPSL SR Sbjct: 303 TRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPSLSHTSR 362 Query: 378 WGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDE 437 G L +E ++ +Y RL ++ ++ Q LSGGNQQKVV+AKWLAT ++I DE Sbjct: 363 SGF-LRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKVIILDE 421 Query: 438 PTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLDNRE 497 PT+GID+G+KA +H + ELAAQG +VIM+SSE+PEI+ +SDR++VM EG + + E Sbjct: 422 PTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYERSE 481 Query: 498 KRVTQEEIMYYASGQKKQ-NGRVA 520 +T E+++ A+G + Q +GR A Sbjct: 482 --LTAEKLVRAAAGIETQADGRAA 503 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: 631 Number of extensions: 29 Number of successful extensions: 7 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: 503 Length adjustment: 35 Effective length of query: 485 Effective length of database: 468 Effective search space: 226980 Effective search space used: 226980 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