Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 392 bits (1007), Expect = e-113 Identities = 217/501 (43%), Positives = 316/501 (63%), Gaps = 16/501 (3%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDA--GTL 61 +L++KGI K FPGVKAL L+V G + AL+GENGAGKST+MKVL+G+Y + + G + Sbjct: 5 ILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGEI 64 Query: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121 + G+ F G S+ GI IIHQEL L+P L+I EN+FLG E +R G IDW Sbjct: 65 RFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASR-GVIDWDAATLR 123 Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181 A +LL + L + L+ D+ +G QQ+VEIAK LS E K++I+DEPT +L ++++++L Sbjct: 124 ARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDALL 183 Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREV--ASLTEDSLIEMMVG 239 ++ + K++G + ISH++ EI ++ D VT+ RDG + + A +++D +I MVG Sbjct: 184 ELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMVG 243 Query: 240 RKLEDQYPHLDKAPGDIRLKV-----DNLCGPG---VNDVSFTLRKGEILGVSGLMGAGR 291 R L D+YP PGD+ +V D+ PG V DV+ T+R+GE++G++GLMGAGR Sbjct: 244 RALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGAGR 303 Query: 292 TELMKVLYGAL--PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349 TE L+G G LDG E+ + +ANG+ Y +EDRK GLVL ++ Sbjct: 304 TEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDIRH 363 Query: 350 NMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARG 409 N++L LR ++ + H E Q +F R ++ + Q LSGGNQQKV +++ Sbjct: 364 NVTLANLRGVAKRW-VIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLSKW 422 Query: 410 LMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMH 469 L P+VLILDEPTRG+DVGAK EIY +INQ A+G ++L+SSEMPE+LG++DRI VM+ Sbjct: 423 LFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYVMN 482 Query: 470 EGHLSGEFTREQATQEVLMAA 490 G + E +A+QE +M A Sbjct: 483 AGEMVAEMPAAEASQEKIMGA 503 Lambda K H 0.318 0.137 0.380 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: 726 Number of extensions: 43 Number of successful extensions: 11 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: 501 Length of database: 518 Length adjustment: 34 Effective length of query: 467 Effective length of database: 484 Effective search space: 226028 Effective search space used: 226028 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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