Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate BWI76_RS19240 BWI76_RS19240 ABC transporter substrate-binding protein
Query= CharProtDB::CH_003045 (260 letters) >FitnessBrowser__Koxy:BWI76_RS19240 Length = 257 Score = 234 bits (597), Expect = 1e-66 Identities = 116/255 (45%), Positives = 167/255 (65%), Gaps = 2/255 (0%) Query: 6 LALSLLIGLGATAASYAALP-QTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQ 64 + L+ L+ A +A AA T+ G D Y PF GE GFDID+ N +C +++ Sbjct: 3 IRLAALLACMALSAPLAAQQFDTISFGVDGGYPPFDVLAPSGEITGFDIDIANALCTQLK 62 Query: 65 VKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPI 124 KC +V F+++I +L A K DAII+SL+ITD+R++E+ F+D+ Y + ++L+A KGSP+ Sbjct: 63 AKCVFVKQPFESMIAALNAHKFDAIIASLNITDERKKEVDFTDRYYRSAAQLVARKGSPL 122 Query: 125 QPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDE 184 P SLKGK VGV GST EA+A NW GV +V YANQD +Y DL +GR+DAALQD Sbjct: 123 LPDAASLKGKTVGVQTGSTHEAFAKANWANHGVKIVGYANQDNVYLDLLSGRIDAALQDN 182 Query: 185 VAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGT 244 + A+ GF+ P G+++AFAGP ++D D G+ + KD+ L+ A + A+ +R DGT Sbjct: 183 IQAATGFIDTPRGQKFAFAGPVIQDGGISSD-VGIAVNKDNPALRDALNGAIKAIRADGT 241 Query: 245 YDKMAKKYFDFNVYG 259 YD + KKYF F++YG Sbjct: 242 YDAIQKKYFSFDIYG 256 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: 232 Number of extensions: 12 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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