Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_5969 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969 Length = 514 Score = 359 bits (921), Expect = e-103 Identities = 199/495 (40%), Positives = 305/495 (61%), Gaps = 5/495 (1%) Query: 23 IALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLD 82 + + K FPGV AL N F G+VHALMGENGAGKSTL+KIL G Y SGD+ + Sbjct: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 Query: 83 GKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAA 142 + + + A G+ +IHQEL+L+ ++ A+N+F+G P + GL ++ L +QA Sbjct: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPAR-FGL-VNRGVLRQQAL 133 Query: 143 AIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRI 202 + + ++DP VG L++ ++Q+VEIAKALS + V+ DEPT++L+ EI L I Sbjct: 134 TLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAI 193 Query: 203 IRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVP-MQETSMDTIISMMVGRAL 261 I L+ +G ++Y+SH+M+E+ +I + V+V +DG+Y+ T M E + D +++ MVGR + Sbjct: 194 IGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDI 253 Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321 P R DV L+V+GL VSF + KGEILG GL+GAGRTE+ R + G Sbjct: 254 QDIYDYRP-RERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSG 312 Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT 381 + G +++H + ++SP DA+A G+ EDRK G+ V NI +S+ + Sbjct: 313 LERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHS 372 Query: 382 RVGFMDQRAI-REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440 +G + + R A ++ L +KTP+ Q+ LSGGNQQK ++ +WL +L D Sbjct: 373 TLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432 Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500 EPTRGID+GAK+EIY+++ LA G A++++SS+L EV+ +S R+LV+CEG + GEL+R Sbjct: 433 EPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRD 492 Query: 501 DATQEKIMQLATQRE 515 A + ++QLA R+ Sbjct: 493 QANESNLLQLALPRQ 507 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: 633 Number of extensions: 31 Number of successful extensions: 8 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: 514 Length adjustment: 35 Effective length of query: 485 Effective length of database: 479 Effective search space: 232315 Effective search space used: 232315 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