Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 359 bits (922), Expect = e-103 Identities = 196/491 (39%), Positives = 308/491 (62%), Gaps = 5/491 (1%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L GI K+FPGVKAL +++ +HALMGENGAGKSTLLK L G Y +G+++ Sbjct: 14 LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 G+E+ F AL G+++++QEL+LV + +V +N++LG+ P KG V++ + E Sbjct: 74 GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133 Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187 L +DIDP + LS+ Q QM+EIAKA + NAKI+ DEPTSSL+ +E+++LF +IR Sbjct: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193 Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247 +L++ G I+Y+SH+MEEIF L D +TV +DG+++ T + + D ++ MVGR + Sbjct: 194 KLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIAT-EPLAGLTMDKIIAMMVGRSLNQ 252 Query: 248 IYGWQPRSYGE---ERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFG 304 + + GE E L +++ P +R +S + GEI+G+ GLVGA R+++++ +FG Sbjct: 253 RFPDKENKPGEVILEVRNLTSLRQPSIR-DVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 Query: 305 GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364 + +AG + + + I+ + AI G L E+R++ GI + N IS R + Sbjct: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371 Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424 +++N +++ I S+ +KTPG I +LSGGNQQK I+GRWL + ++++LD Sbjct: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484 EPTRGIDVGAK EIY +I LA +G ++ SS++PE+LG+ DRI+VM G ++G + + Sbjct: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 Query: 485 QADERQALSLA 495 + + L LA Sbjct: 492 TTTQNEILRLA 502 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: 626 Number of extensions: 29 Number of successful extensions: 6 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: 506 Length adjustment: 34 Effective length of query: 470 Effective length of database: 472 Effective search space: 221840 Effective search space used: 221840 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