Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2366 PS417_12065 D-ribose transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__WCS417:GFF2366 Length = 495 Score = 369 bits (946), Expect = e-106 Identities = 205/492 (41%), Positives = 302/492 (61%), Gaps = 3/492 (0%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 ++ +V K + GV AL + + L AG VHAL G NGAGKST + IL G+ QRD+G ILL Sbjct: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 +G PV+ P +A A GI +I QEL + +++ A+NI++GREPR+A G +D LNR+ Sbjct: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRA-GCIVDNKALNRRT 124 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 + + D+D ++P+ L+VA+ Q+VEIAKA S D +V+IMDEPT+A+ E LF+ Sbjct: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 IR L AQG GIVY+SH++ EL QIAD S+ RDG ++ + M + D ++ +VG+ L Sbjct: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 Query: 262 DG-EQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320 + ++ + + N L+V L+R D+S LR+GEILG GLMG+GR+E I+ Sbjct: 245 TRIDHKVGRECAAN-TCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303 Query: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380 G ++G + + G I P + G+ ++EDRK GL + + +NIALS+ R Sbjct: 304 GLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRL 363 Query: 381 TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440 + ++ R + A+ V++L IKT S+E +SGGNQQK+V+AK L + L D Sbjct: 364 SSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423 Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500 EPTRGID GAK EIY LLD G A +++SSE PE+L +S R+ V GR+ Sbjct: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483 Query: 501 DATQEKIMQLAT 512 +QE +++LA+ Sbjct: 484 ALSQEALLRLAS 495 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: 566 Number of extensions: 27 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: 495 Length adjustment: 34 Effective length of query: 486 Effective length of database: 461 Effective search space: 224046 Effective search space used: 224046 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 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