Align Ribose import ATP-binding protein RbsA 1; 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:Q9WXX0 (520 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969 Length = 514 Score = 351 bits (901), Expect = e-101 Identities = 192/480 (40%), Positives = 295/480 (61%), Gaps = 7/480 (1%) Query: 15 LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74 L+ GI K FPGV A+ N+ F + ++ +L+GENGAGKSTL+KIL G P +G++ + Sbjct: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 Query: 75 GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134 + + F D+ G++VIHQEL+L MTVAEN+FL + R V+ + Sbjct: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPAR------FGLVNRGVLR 129 Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194 ++ LL + + P V L+ QRQ+VEI KAL + +I DEPTSSL+ E +R Sbjct: 130 QQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDR 189 Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKK-GEFDVDTIIKMMV 253 L II L+ G V++VSHR++EV RI + + V +DG+ + + E D ++ MV Sbjct: 190 LMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMV 249 Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313 GR+++ G++AL+V+ L + VSF+V KGE+LG GLVGAGRTE + L Sbjct: 250 GRDIQDIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRL 309 Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373 + G+ ++ G + ++ +++++++P DAI G+ L PEDRK +G++ +V +NI + + Sbjct: 310 LSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369 Query: 374 KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADIL 433 S G +L E ++ +K L +KTP+ Q LSGGNQQK +L +WL+ +L Sbjct: 370 SHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVL 429 Query: 434 IFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVL 493 + DEPTRGID+GAKAEI+++I LAA G AVI++SS+L E++ +SDRI+V+ EG + L Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489 Score = 89.0 bits (219), Expect = 4e-22 Identities = 67/254 (26%), Positives = 136/254 (53%), Gaps = 15/254 (5%) Query: 8 RGDRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPD 67 RGD L+ KG++ PG+ + V F+V++ EI+ L G GAG++ L+++L+G+ + Sbjct: 264 RGD--VALQVKGLLG--PGLH--EPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQR 317 Query: 68 AGEILVNGERVEFHSPVDAFKKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTL 124 G ++++ + ++ SP DA G+ + ++ + +V ENI ++ R TL Sbjct: 318 EGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINIS---ARPSHSTL 374 Query: 125 SSRVDENYMYTRSKELLDLIGAKFSPDA--LVRNLTTAQRQMVEICKALVKEPRIIFMDE 182 + ++ + + + + K +P A + L+ +Q + + L +++ +DE Sbjct: 375 GCLLRGDWERGNADKQIKSLKVK-TPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDE 433 Query: 183 PTSSLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGE 242 PT + + +++II L + GI+V+ VS L EVM ISDRI+V+ +G GEL + + Sbjct: 434 PTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQ 493 Query: 243 FDVDTIIKMMVGRE 256 + ++++ + R+ Sbjct: 494 ANESNLLQLALPRQ 507 Score = 77.8 bits (190), Expect = 9e-19 Identities = 59/231 (25%), Positives = 113/231 (48%), Gaps = 8/231 (3%) Query: 286 NVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGI 345 N+SF G+V G GAG++ + ++ G SGD+ + + + K D+I G+ Sbjct: 33 NISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQTMAFKGTADSIASGV 92 Query: 346 GLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSI 405 +I ++ L V MTV +N+ L L +R+GLV + + + +K L+ + Sbjct: 93 AVIHQELHL---VPEMTVAENLFLGHLP--ARFGLV-NRGVLRQQALTLLKGLADEIDPQ 146 Query: 406 YQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVI 465 ++ LS G +Q V +AK L+ A ++ FDEPT + + +I L +GK V+ Sbjct: 147 EKVGR-LSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRDEGKVVL 205 Query: 466 MISSELPEILNLSDRIVVMWEGEITAVLDNREKRVTQEEIMYYASGQKKQN 516 +S + E+ + + + V +G +N + +T ++++ G+ Q+ Sbjct: 206 YVSHRMEEVFRICNAVTVFKDGRYVRTFENMSE-LTHDQLVTCMVGRDIQD 255 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: 678 Number of extensions: 43 Number of successful extensions: 7 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: 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 (21.7 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