Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 236 bits (602), Expect = 1e-66 Identities = 161/494 (32%), Positives = 251/494 (50%), Gaps = 25/494 (5%) Query: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 TP L GI K F + A DIS + G+V AL+GENGAGKSTL+ IL G+Y G+V Sbjct: 3 TPILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTV 62 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124 ++GQ + AAL AG+ +++Q L ++V +NI LG P ++ + Sbjct: 63 EVDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKV 122 Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184 + G+ + P + LS+G+ Q VEI KAL R A+++ DEPT+ L+ E + LF Sbjct: 123 LALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFS 182 Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244 + +L EG ++++SH+++E+ +SD I V + G+ V Q + L + MVGR Sbjct: 183 TLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAE-LAELMVGRV 241 Query: 245 I-------------GDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLV 291 + G P E + A + +SL VR+GEIVG+ G+ Sbjct: 242 VAMPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVS 301 Query: 292 GAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSV 351 G G++ L + G + + G++ + +P+ KP I AG+ PEDR A G++ +V Sbjct: 302 GNGQAALAELASGMLEASEGRITLAGKPMS-AKPRAWIGAGVARVPEDRHAIGVVGDLAV 360 Query: 352 RDNI---NISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKA 408 +N +S R G VI + A + +++T G + +SGGN QK Sbjct: 361 WENAVSEQLSEPRFSRWG--VIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKL 418 Query: 409 ILGRWLS-----EEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVL 463 ILGR LS ++++ +PT G+D+GA + + A +G AVL S DL E+ Sbjct: 419 ILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELH 478 Query: 464 GVADRIVVMREGEI 477 +ADRI VM G + Sbjct: 479 ALADRIAVMHAGHL 492 Score = 80.9 bits (198), Expect = 1e-19 Identities = 66/233 (28%), Positives = 110/233 (47%), Gaps = 23/233 (9%) Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGM- 333 ISL ++ GE++ L G GAG+S L+ +FG AG V +D QP+ +P A+ AG+ Sbjct: 24 ISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAGIG 83 Query: 334 MLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGA 393 M+ A+ + SV DNI + + W+ H R + Sbjct: 84 MVHQHFTLADNL----SVLDNIMLGTQPL-----------WQWRLDGHAARGKVLALAER 128 Query: 394 EQLIMN-------LSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALA 446 L + LS G +Q+ + + L +V++LDEPT + +++ + L Sbjct: 129 FGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLI 188 Query: 447 AQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAMPKV 499 A+G++V+F S L EVL V+DRI V+R G++ Q + + L + +V Sbjct: 189 AEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRV 241 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: 663 Number of extensions: 37 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: 504 Length of database: 530 Length adjustment: 35 Effective length of query: 469 Effective length of database: 495 Effective search space: 232155 Effective search space used: 232155 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