Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 299 bits (766), Expect = 1e-85 Identities = 167/478 (34%), Positives = 271/478 (56%), Gaps = 3/478 (0%) Query: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 T ++ R I K + GV AL + F G+ L GENG+GKSTL+KI+SG T G+V Sbjct: 7 TAFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTV 66 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENI-YLGQLPHKGGIVNRSLLNYE 123 I GQE + + AGV +I+Q+ L P ++VAENI + QL + + + Sbjct: 67 QIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDI 126 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 A L +G+ ID D ++ L + Q Q+V I +ALA A++I DEPT++L+ +E+ L Sbjct: 127 ARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQ 186 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 +IR L++EG +++VSH++ E+ +S+ + V ++G+ V + D +L M GR Sbjct: 187 GIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAE-GPASEFDTQSLTYHMTGR 245 Query: 244 DIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMF 303 D+ ++ + + +++ + G + IS +R+GE++G+ GL+G GR+ + K +F Sbjct: 246 DVPEVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALF 305 Query: 304 GGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKH 363 G AG + +D P+ + P A A + PEDR EG+ S+ N+ + H Sbjct: 306 GLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAH 365 Query: 364 VLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILL 423 GG + G + +D +R L +K P E + +LSGGNQQ+ L RWLS +V++L Sbjct: 366 TSGGFLDMTGLAKEASDW-LRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLIL 424 Query: 424 DEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481 + P+ G+DVG+K +I+++I LA +G+ V+ S DLPE+L R++VMREG I L Sbjct: 425 NGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDAL 482 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: 560 Number of extensions: 25 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: 498 Length adjustment: 34 Effective length of query: 470 Effective length of database: 464 Effective search space: 218080 Effective search space used: 218080 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