Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 327 bits (839), Expect = 5e-94 Identities = 189/480 (39%), Positives = 289/480 (60%), Gaps = 9/480 (1%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L RG+GK F AL + AG+VHALMG+NGAGKSTL+K+L+G P GSV ++ Sbjct: 13 LQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVELD 72 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGI--VNRSLLNYEAG 125 G+ ++ S A G+ +YQE++L P ++VAEN+Y G+ P + + ++ + A Sbjct: 73 GRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGAR 132 Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185 L+ L +++D D PL + QMV IA+AL +A+++ DEPTSSL E+ LFRV Sbjct: 133 SLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRV 192 Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245 I +LR+ G IL+V+H +++++A+SD ITV +DG V + + + ALV AMVGRD+ Sbjct: 193 IAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYA-VADLPPAALVNAMVGRDL 251 Query: 246 GDIYGWQ----PRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301 + G P + + G P+ L VR GE++GL GL+G+GR+EL + Sbjct: 252 PTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELARL 311 Query: 302 MFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361 +FG + G++ I + ++++ P+ A+ G+ LCPE+RK +GI+ SVR+NI ++ + Sbjct: 312 LFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLALQA 371 Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421 + G ++ ++ A +++L IK E + LSGGNQQK +L RWL E +++ Sbjct: 372 RQGWRG--MSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPRLL 429 Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481 +LDEPTRGIDV AK E+ + A G+AVLF S++ E+ DRI VMRE AGEL Sbjct: 430 ILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAGEL 489 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: 653 Number of extensions: 35 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: 504 Length of database: 505 Length adjustment: 34 Effective length of query: 470 Effective length of database: 471 Effective search space: 221370 Effective search space used: 221370 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 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