Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 384 bits (987), Expect = e-111 Identities = 216/486 (44%), Positives = 313/486 (64%), Gaps = 4/486 (0%) Query: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 LR GI K + AL N+ F G+VHALMGENGAGKSTL+KIL G SG + I Sbjct: 10 LRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFID 69 Query: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARF-GLVNRGVLRQQALT 134 Q + + D+ G+A+IHQEL+ VP+MTVAENLFLG P F G+++R + ++A Sbjct: 70 GQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHREAKE 129 Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 L + +IDPQ +G LS+G++Q+VEIA+A+S A V+ DEPT++LS E +L +I Sbjct: 130 KLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRLI 189 Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 ++R +G ++Y+SHRMEEV+++ N VTVF+DG ++ T EN+ ++ +V MVGR I Sbjct: 190 AQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGT-ENLGNVSTTDIVRMMVGRQIV 248 Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314 D+Y + PR GDV L+V+ L G PVSF+V GE++ + GLVG+GRTE+ RLL G + Sbjct: 249 DLYQHEPRTPGDVLLEVRDLAGSATG-PVSFEVSAGEVVSMSGLVGSGRTEVARLLFGAD 307 Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374 + +GS+ L +E + P AIA G+ + EDRK +G+ SV NI+IS+ + Sbjct: 308 PRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNF-VA 366 Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 G +++ R +Q++ L+++ + LSGGNQQKA L RWL ++L+LDEP Sbjct: 367 GGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILDEP 426 Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494 TRG+DIGAK EIY++I LA G A++V+SSDL E +GISDR+LV+ G + +L A Sbjct: 427 TRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSA 486 Query: 495 NESNLL 500 E ++ Sbjct: 487 TEEEVM 492 Score = 92.8 bits (229), Expect = 3e-23 Identities = 63/227 (27%), Positives = 118/227 (51%), Gaps = 6/227 (2%) Query: 283 VSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLRSPRDAIAAGVL 342 V F + GE+ L G GAG++ L+++LSG E++ G + + + + +R+PRDA G+ Sbjct: 28 VRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFIDGQAIDIRTPRDARKYGIA 87 Query: 343 LCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAG 402 + ++ +P +V EN+ + P+ S G L R R +K + P A Sbjct: 88 IIHQELNT---VPDMTVAENLFLGQEPT-SFAGILDRKRMHREAKEKLNRINADIDPQA- 142 Query: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIV 462 + LS G QQ + R +S KVL+LDEPT + ++Y++I + DG+ ++ Sbjct: 143 -PLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRLIAQMRQDGVGMVY 201 Query: 463 VSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQRV 509 +S + EV +++R+ V +G G + + ++++++ + RQ V Sbjct: 202 ISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVGRQIV 248 Lambda K H 0.320 0.138 0.391 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: 680 Number of extensions: 27 Number of successful extensions: 9 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: 514 Length of database: 510 Length adjustment: 35 Effective length of query: 479 Effective length of database: 475 Effective search space: 227525 Effective search space used: 227525 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