Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 483 bits (1244), Expect = e-141 Identities = 258/511 (50%), Positives = 351/511 (68%), Gaps = 9/511 (1%) Query: 9 TTGVAASSSSSVP----VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTL 64 TT A +S +VP ++ V K FPGV+ALD+ +F+L G VHALMGENGAGKSTL Sbjct: 6 TTMAAVRASGAVPKSEYLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTL 65 Query: 65 MKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREP 124 MKIL+G+Y D G++ L G + + P A GI +IHQELNLM ++ A+NI+I REP Sbjct: 66 MKILAGIYYPDQGEVKLRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREP 125 Query: 125 RKAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIM 184 + G F+D E+ R A +F R+++D+DP V L+VA +QMVEIAKA+S++S VLIM Sbjct: 126 KNRFG-FVDHGEMRRMTAKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIM 184 Query: 185 DEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPM 244 DEPT+AL E+A LF IIRDL++QG+GIVYI+HKM+EL +IAD SV RDGKYI T Sbjct: 185 DEPTSALTEREVAHLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLS 244 Query: 245 QETSMDTIISMMVGRALDGEQRIP-PDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILG 303 E + D II MMVGR + Q P + DVVL V+ L RDVSF +R GEILG Sbjct: 245 NEVTRDDIIRMMVGREI--TQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILG 302 Query: 304 FAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLA 363 AGL+G+GR+ VA +FG P +G I I G + VI S A+ H + +L+EDRK G Sbjct: 303 VAGLVGSGRSNVAETLFGVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCL 362 Query: 364 VGMDVQANIALSSM-GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQ 422 + +D+ N+ ++ + +F + GF+ +R + A + R+L +KTP+++++ LSGGNQQ Sbjct: 363 LILDILENMQIAVLQDKFVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQ 422 Query: 423 KIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMS 482 K++I +WLL + IL DEPTRGIDVGAK+EI++L+ LA G A++MISSE+PEVL MS Sbjct: 423 KVLIGRWLLTNPRILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMS 482 Query: 483 HRVLVMCEGRITGELARADATQEKIMQLATQ 513 R++VM EGR+TG L RA+ATQ K+M+LA + Sbjct: 483 DRIMVMHEGRVTGILDRAEATQIKVMELAAR 513 Score = 91.3 bits (225), Expect = 8e-23 Identities = 63/229 (27%), Positives = 115/229 (50%), Gaps = 7/229 (3%) Query: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347 A+ DV F L++G + G GAG++ + + + G + GE+ + G +KSP DA+ Sbjct: 38 ALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLRGAGIRLKSPLDALE 97 Query: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIRE-AAQMYVRQLAIKT 406 +GI + ++ L M V NI + + R GF+D +R A+++ R Sbjct: 98 NGIAMIHQE---LNLMPFMTVAENIWIRREPK-NRFGFVDHGEMRRMTAKLFERLKIDLD 153 Query: 407 PSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466 P +E R LS N+Q + IAK + + D+L DEPT + + +++++ L QG Sbjct: 154 PEIE--VRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEIIRDLRSQGI 211 Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515 IV I+ ++ E+ ++ V +G+ G + T++ I+++ RE Sbjct: 212 GIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGRE 260 Lambda K H 0.320 0.135 0.372 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: 641 Number of extensions: 25 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 (21.8 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