Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 308 bits (790), Expect = 2e-88 Identities = 178/498 (35%), Positives = 293/498 (58%), Gaps = 13/498 (2%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 L I KTFPGVKAL+ ++ G++HAL+GENGAGKSTL+K+L G Y + G++ Sbjct: 16 LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSS--GDLQ 73 Query: 66 YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125 R F++ DS G+ +IHQEL LVP +++AEN+FLG+ AS G+I+ + Sbjct: 74 IGEQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQAL 133 Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185 LK + + P+ + + +G++QLVEIAKALS+ ++ DEPT+SL+ + + L+ + Sbjct: 134 ACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAI 193 Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGRD 245 + R++G + ++H++ EV ++ + +TV +DG V+T + ++ D ++ MVGRD Sbjct: 194 IGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFE-DMSALTHDQLVTCMVGRD 252 Query: 246 LEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTE 305 ++D Y R P G L+V + ++ KGE++G+ GL+GAGRTE Sbjct: 253 IQDIYDYRSRPRGAVALKVDGL-------LGPGLREPVSFEAHKGEILGLFGLVGAGRTE 305 Query: 306 FAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNT 365 + G + G + + G+ + + + R AI AG+ EDRK G++ ++ N Sbjct: 306 LFRMLSGLT--RNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENI 363 Query: 366 TL-ANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424 + A A + ++ + E A L++++ Q+ + LSGGNQQK +L +WL Sbjct: 364 NISARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLS 423 Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484 VL+LDEPTRGID+GAK EIY II+ LAA G V+++SS++ E++G DRI V+ EG Sbjct: 424 MPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEG 483 Query: 485 RIVAELPKGEASQESIMR 502 + EL + +A++ ++++ Sbjct: 484 AMRGELTREQANESNLLQ 501 Lambda K H 0.316 0.135 0.374 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: 590 Number of extensions: 29 Number of successful extensions: 9 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: 512 Length of database: 514 Length adjustment: 35 Effective length of query: 477 Effective length of database: 479 Effective search space: 228483 Effective search space used: 228483 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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