Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate H281DRAFT_01522 H281DRAFT_01522 amino acid ABC transporter substrate-binding protein, PAAT family
Query= CharProtDB::CH_003045 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_01522 Length = 260 Score = 286 bits (733), Expect = 2e-82 Identities = 136/259 (52%), Positives = 184/259 (71%) Query: 1 MKKTVLALSLLIGLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMC 60 +KK + AL++ + + ++A T+R G D +Y PF SK + G+ +GFDIDLGNE+C Sbjct: 1 VKKLLAALTVALLATVSIGAHAKDWSTIRFGVDASYPPFESKGSDGKLVGFDIDLGNEIC 60 Query: 61 KRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAK 120 R++ KC WV +DFD +IP+LKAKK D ++SS+S+T +R +++AFS KL+ +RL+A K Sbjct: 61 ARLKAKCVWVENDFDGMIPALKAKKFDGVLSSMSMTPQRAEQVAFSSKLFNTPTRLVAKK 120 Query: 121 GSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAA 180 GS I PT ESLKGK VGV QG+ QE YA W KG VV Y NQD +Y+DL +GRLDAA Sbjct: 121 GSGILPTAESLKGKTVGVEQGTIQETYAKTYWEPKGAKVVPYQNQDQVYADLLSGRLDAA 180 Query: 181 LQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELR 240 LQD V A GFLK P G + F G ++ D K G+G G+G+RK+DT+LKA DKA+ ++ Sbjct: 181 LQDAVQAEIGFLKTPRGAGFDFVGKNLDDPKILGNGAGIGMRKEDTDLKAKVDKAIADII 240 Query: 241 QDGTYDKMAKKYFDFNVYG 259 +DGTY K+ KKYFDF+VYG Sbjct: 241 KDGTYKKLEKKYFDFDVYG 259 Lambda K H 0.315 0.132 0.374 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: 275 Number of extensions: 10 Number of successful extensions: 1 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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