Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_013092024.1 BC1002_RS21105 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >NCBI__GCF_000092885.1:WP_013092024.1 Length = 509 Score = 367 bits (941), Expect = e-106 Identities = 202/495 (40%), Positives = 312/495 (63%), Gaps = 5/495 (1%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 + P L R K+F V+AL+D + G+VHAL+GENGAGKSTL+KIL+G + P G Sbjct: 7 AVPRLELRHASKSFGRVRALSDGDLVLWPGEVHALLGENGAGKSTLVKILAGVHQPDAGE 66 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLP-HKGGIVNRSLLNY 122 +++NG+ F+ A +AG+A+IYQE L ++++AENI++G+ P + G + ++ Sbjct: 67 LLVNGEPRRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRFGRIQYDAMHR 126 Query: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182 E L LG+D+ D ++ LSI Q++EIAKAL+ NA ++ DEPT++LS E++ L Sbjct: 127 EVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNASVLIMDEPTAALSLPEVERL 186 Query: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQ-QVDHDALVQAMV 241 F ++R+LR+ IL+++HR++E+FAL+ +T+ +DG K F + + DA+V MV Sbjct: 187 FAIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDG--AKVFDALTADLSTDAIVAKMV 244 Query: 242 GRDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301 GRD+ Y + G+ RL + + GV +S VR+GEIV L GLVGAGRSE+ + Sbjct: 245 GRDLETFYPKADCTPGDVRLSVRGLTRIGVFKDVSFDVRAGEIVALAGLVGAGRSEVARA 304 Query: 302 MFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361 +FG + AG+V++ + +D KP+ A+ AG+ L PEDR+ +G+ S+ N +++ Sbjct: 305 IFGIDTLDAGEVWLAGKRLDTGKPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLG 364 Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421 + V G +I+ E A L +K + LSGGNQQK +LG+WL+ KV+ Sbjct: 365 RLVRHG-LISTRSETQLAHKWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVL 423 Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481 ++DEPTRGIDVGAK E+Y+ + L G+AVL SS+LPEVLG+ADR++VM EG I+ E+ Sbjct: 424 IIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISAEI 483 Query: 482 LHEQADERQALSLAM 496 A+E + + A+ Sbjct: 484 ARADANEERIMGAAL 498 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: 692 Number of extensions: 36 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: 509 Length adjustment: 34 Effective length of query: 470 Effective length of database: 475 Effective search space: 223250 Effective search space used: 223250 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 24 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