Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 385 bits (989), Expect = e-111 Identities = 220/504 (43%), Positives = 318/504 (63%), Gaps = 19/504 (3%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDA--GEI 71 + + +GI K F GV A+D +D + E + L GENGAGKSTL+K+L+GV + GEI Sbjct: 7 LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66 Query: 72 LVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDEN 131 L G+ + S D+ + GI +IHQEL L ++VAENIFL +E R R+D + Sbjct: 67 LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRP-----GGRMDYD 121 Query: 132 YMYTRSKELLDLIGAKFSPDAL-VRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVE 190 MY ++ LL +G AL + +Q+ EI KAL K+ +++ +DEPTSSLT Sbjct: 122 AMYAKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSS 181 Query: 191 ETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIK 250 ETE L I+E LK RG++ +++SH+LDEV R+ D + V+RDG+ I E DVDT+I Sbjct: 182 ETEVLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLIT 241 Query: 251 MMVGREVEFFPHGIETRPGEIALEVRNLKWKD-------KVKNVSFEVRKGEVLGFAGLV 303 +MVGR++E IE GE+ E R+ D +V +VSF++R+GE+LG AGLV Sbjct: 242 LMVGRKLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLV 301 Query: 304 GAGRTETMLLVFGV-NQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMT 362 GAGRTE + +FG K S ++++ GR ++I++P DAI+ G+G++PEDRK G+V + Sbjct: 302 GAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLG 361 Query: 363 VKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVL 422 V DNI L +L + G + D ++E E + +KT S LSGGNQQK VL Sbjct: 362 VGDNITLATLDHYAHAGHI-DRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVL 420 Query: 423 AKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIV 482 AK L +LI DEPTRG+DVGAKAEI+R+I ELAAQG A++++SSE+PE+L ++DR++ Sbjct: 421 AKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVL 480 Query: 483 VMWEGEITAVLDNREKRVTQEEIM 506 VM EG + N + +TQE+++ Sbjct: 481 VMGEGRLRGDFPN--QGLTQEQVL 502 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: 660 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: 513 Length adjustment: 35 Effective length of query: 485 Effective length of database: 478 Effective search space: 231830 Effective search space used: 231830 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