Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate H281DRAFT_03659 H281DRAFT_03659 amino acid ABC transporter substrate-binding protein, PAAT family
Query= CharProtDB::CH_003045 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_03659 Length = 284 Score = 242 bits (617), Expect = 7e-69 Identities = 122/257 (47%), Positives = 173/257 (67%), Gaps = 9/257 (3%) Query: 5 VLALSLLIGLGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQ 64 + +L+ +GA YAA T+R+G D +Y P SK G GFD+DLGNE+C+R+Q Sbjct: 36 IFGAALMFSVGA----YAAESNTLRLGIDPSYPPMDSKAPDGSLKGFDVDLGNEICRRIQ 91 Query: 65 VKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPI 124 +C WV +F +IP+L+A+KIDAI+SS++IT KR+Q+I F+ KL+ SRLIA +GSP+ Sbjct: 92 ARCQWVELEFSGMIPALQARKIDAILSSMAITQKREQQILFTSKLFQFKSRLIARQGSPL 151 Query: 125 QPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDE 184 L++L GK +GV G+ E YA +W G VVAY +QD +++DL GRLD AL Sbjct: 152 AAGLQALSGKQIGVQSGTQFEGYALTHWVPLGAHVVAYKSQDEVFADLQNGRLDGALLGS 211 Query: 185 VAASEGFLKQPAGKEYAFAGPSVKDKKYFGD-GTGVGLRKDDTELKAAFDKALTELRQDG 243 V A GFL+ PAGK +AF G + GD GTG+GLRKD+T ++A+ + A+ + +DG Sbjct: 212 VEADFGFLRTPAGKGFAFVGEPLS----MGDRGTGIGLRKDETAIQASINAAIAAMLKDG 267 Query: 244 TYDKMAKKYFDFNVYGD 260 TY ++AKKYFDF+ YG+ Sbjct: 268 TYAQIAKKYFDFDPYGN 284 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: 236 Number of extensions: 16 Number of successful extensions: 2 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: 284 Length adjustment: 25 Effective length of query: 235 Effective length of database: 259 Effective search space: 60865 Effective search space used: 60865 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