Align lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT (characterized)
to candidate Pf1N1B4_5844 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= CharProtDB::CH_003045 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5844 Length = 259 Score = 236 bits (601), Expect = 5e-67 Identities = 118/260 (45%), Positives = 172/260 (66%), Gaps = 3/260 (1%) Query: 1 MKKTVLALSLLIG-LGATAASYAALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEM 59 MKK V+ +L + L TA + A P +R+G + Y PFS K+ G+ GFD+D+G+ + Sbjct: 1 MKKRVMFGALALSMLSLTAMADDAKP--IRLGIEAGYPPFSMKNPDGKLTGFDVDIGDAL 58 Query: 60 CKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAA 119 C++M+VKCTWV +FD LIP+LK KKIDAI+SS++ITD R++ + F+ K Y +R + Sbjct: 59 CEQMKVKCTWVEQEFDGLIPALKVKKIDAILSSMTITDDRKKNVDFTIKYYHTPARFVMK 118 Query: 120 KGSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDA 179 +G+ ++ L LKGK VGVL+ ST + +A + G+++V Y +Q D+ AGRLDA Sbjct: 119 EGTDVKDPLTELKGKKVGVLRASTHDRFATEVLVPAGINLVRYGSQQEANLDMVAGRLDA 178 Query: 180 ALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTEL 239 L D V +GFLK AGK +AF GP+ +D KYFG G G+ +RK D EL F+ A+TE+ Sbjct: 179 MLADSVNLDDGFLKTDAGKGFAFVGPTYEDAKYFGGGAGIAVRKGDKELADKFNTAITEI 238 Query: 240 RQDGTYDKMAKKYFDFNVYG 259 R +G Y ++ KYF+F+VYG Sbjct: 239 RANGKYKQVQDKYFNFDVYG 258 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: 221 Number of extensions: 7 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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