Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 345 bits (884), Expect = 3e-99 Identities = 191/480 (39%), Positives = 293/480 (61%), Gaps = 10/480 (2%) Query: 11 RMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGE 70 R +L+A+G+ KRF +A+D VD + E+ +L+G+NGAGKSTLIK+LTGV +PD G Sbjct: 9 RPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGS 68 Query: 71 ILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDE 130 + ++G + +P++A + GI ++QE+NLC N++VAEN++ A R +R +D Sbjct: 69 VELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLY----AGRYPRRRRLRMIDW 124 Query: 131 NYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVE 190 + ++ LL + + DA + + A RQMV I +AL R++ +DEPTSSL Sbjct: 125 RQVRDGARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEG 184 Query: 191 ETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIK 250 E LF +I L+ RG++++FV+H LD+V +SDRI V+RDG R+GE + ++ Sbjct: 185 EVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVN 244 Query: 251 MMVGREVEFFPHGIETR----PGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAG 306 MVGR++ R A++ + L + K+ V +VR+GE+LG GL+G+G Sbjct: 245 AMVGRDLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSG 304 Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366 RTE L+FG+++ E G++ + G +VE+K+P DA+ G+ L PE+RK G+V ++V++N Sbjct: 305 RTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVREN 364 Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426 IVL +L+ W + +++E++ V+ L IK I LSGGNQQKV+LA+WL Sbjct: 365 IVL-ALQARQGW-RGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWL 422 Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWE 486 T +LI DEPTRGIDV AK E+ + A G AV+ IS+E E+ DRI VM E Sbjct: 423 VTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRE 482 Score = 111 bits (277), Expect = 7e-29 Identities = 70/226 (30%), Positives = 124/226 (54%), Gaps = 10/226 (4%) Query: 33 VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92 VD +V E++ L G G+G++ L ++L G+ + + GE+ + GERVE P DA +G++ Sbjct: 285 VDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLA 344 Query: 93 VIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149 + +E + ++V ENI LA +A +G + +R DE +++L+ +G K + Sbjct: 345 LCPEERKTDGIVAELSVRENIVLALQARQGWRGMSRARQDE-----LARQLVQALGIKAA 399 Query: 150 P-DALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGIS 208 + V L+ +Q V + + LV EPR++ +DEPT + V + L + G++ Sbjct: 400 DIETPVGLLSGGNQQKVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMA 459 Query: 209 VVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254 V+F+S E+ R DRI VMR+ ++ GEL G + ++ M+ G Sbjct: 460 VLFISAETGELTRWCDRIAVMRERRKAGELPGGSTEA-RVLAMIAG 504 Score = 80.9 bits (198), Expect = 1e-19 Identities = 53/201 (26%), Positives = 105/201 (52%), Gaps = 5/201 (2%) Query: 287 VSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIG 346 V +R GEV G GAG++ + L+ GV + + G + ++GR + P +A + GIG Sbjct: 31 VDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVELDGRVIAPSTPMEAQRDGIG 90 Query: 347 LIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIY 406 + ++ L ++V +N+ + R ++ D R+ + + +++L ++ + Sbjct: 91 TVYQE---VNLCPNLSVAENLYAGRYPRRRRLRMI-DWRQVRDGARSLLRQLHLEL-DVD 145 Query: 407 QITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIM 466 + +Q V +A+ L +A +LI DEPT +D G E+ R+I +L +G A++ Sbjct: 146 APLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRVIAQLRERGMAILF 205 Query: 467 ISSELPEILNLSDRIVVMWEG 487 ++ L ++ +SDRI V+ +G Sbjct: 206 VTHFLDQVYAVSDRITVLRDG 226 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: 619 Number of extensions: 31 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 520 Length of database: 505 Length adjustment: 35 Effective length of query: 485 Effective length of database: 470 Effective search space: 227950 Effective search space used: 227950 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 Apr 09 2024. 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