Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 372 bits (956), Expect = e-107 Identities = 215/515 (41%), Positives = 325/515 (63%), Gaps = 15/515 (2%) Query: 2 QQSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTT 61 + P L+ I K+F GV AL D+ F+ AG++HALMGENGAGKSTL+K+LSG Y Sbjct: 13 ESDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYE 72 Query: 62 GSVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIV--NRSL 119 G+V ++G+ + FS+ A AG+AII+QEL+LVPE+ VA+NI+LG+ G+ ++ Sbjct: 73 GAVRVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVDRKAS 132 Query: 120 LNYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREI 179 L GL L LG+++DP+ + L +G+ Q+VEIAKAL+ A+I+ DEPTS+LS E Sbjct: 133 LEAARGL-LNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGEC 191 Query: 180 DNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239 LF+++R+L +G I+Y+SHR++E+ LSD +TVF+DGR+V M +D + ++ A Sbjct: 192 RRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWA-RPMAGLDENTIIAA 250 Query: 240 MVGRDIGDIYGWQPRSYGEE---RLRLDAVKAPG------VRTPISLAVRSGEIVGLFGL 290 MVGR++ D + G E +R ++ G V +S VR+GEI+G+ GL Sbjct: 251 MVGRNLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGL 310 Query: 291 VGAGRSELMKGMFGGTQ-ITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVH 349 +GAGR+E+++ +F + + G++ +D ++IR P A G L EDRKA+G+ Sbjct: 311 LGAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHE 370 Query: 350 SVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAI 409 S+RDN+ + + G G E A + +L ++ G Q LSGGNQQK + Sbjct: 371 SIRDNVALPLVGRLARFGLRSFEG-ERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVV 429 Query: 410 LGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRI 469 +G+WL+ +V+LLDEPTRGIDVGAK EIY++I+ LA G+A++ SS+LPE+L +ADRI Sbjct: 430 IGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRI 489 Query: 470 VVMREGEIAGELLHEQADERQALSLAMPKVSQAVA 504 +VM EG G + E+A E + + LA P+ ++ A Sbjct: 490 LVMAEGRQTGLISREEASEERIMQLAAPRSARGRA 524 Lambda K H 0.319 0.136 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: 722 Number of extensions: 41 Number of successful extensions: 11 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: 504 Length of database: 526 Length adjustment: 35 Effective length of query: 469 Effective length of database: 491 Effective search space: 230279 Effective search space used: 230279 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