Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 340 bits (872), Expect = 7e-98 Identities = 192/503 (38%), Positives = 298/503 (59%), Gaps = 13/503 (2%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTT--GS 63 P L +GI KTFPGVKAL D++ G++HAL+GENGAGKSTL+K+LSG Y + G Sbjct: 4 PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGE 63 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYE 123 + GQ +F + G+ II+QEL LVP +++ EN++LG G+++ Sbjct: 64 IRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAATLR 123 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 A L+ +G+ P+T + + +G+ Q+VEIAKAL++ K++ DEPT+SL+ + D L Sbjct: 124 ARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDALL 183 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQV-DHDALVQAMVG 242 ++ + + G + +SH++ EI ++D +T+ +DG V+T + V D +++ MVG Sbjct: 184 ELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMVG 243 Query: 243 RDIGDIYGWQPRSYGEERLRLDAVKA-----PGVRT--PISLAVRSGEIVGLFGLVGAGR 295 R + D Y + G+ + A PG R ++L VR GE+VG+ GL+GAGR Sbjct: 244 RALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGAGR 303 Query: 296 SELMKGMFGGT--QITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRD 353 +E +FG + + GQ ++D + ID+ S A+A G+ EDRK G++ + +R Sbjct: 304 TEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDIRH 363 Query: 354 NINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRW 413 N+ + A + V VI++ E A+ R L I+ Q +NLSGGNQQK +L +W Sbjct: 364 NVTL-ANLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLSKW 422 Query: 414 LSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMR 473 L + +V++LDEPTRGIDVGAK+EIY +I L A+G V+ SS++PE+LGVADRI VM Sbjct: 423 LFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYVMN 482 Query: 474 EGEIAGELLHEQADERQALSLAM 496 GE+ E+ +A + + + M Sbjct: 483 AGEMVAEMPAAEASQEKIMGAIM 505 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: 690 Number of extensions: 38 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: 504 Length of database: 518 Length adjustment: 35 Effective length of query: 469 Effective length of database: 483 Effective search space: 226527 Effective search space used: 226527 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