Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate AZOBR_RS00680 AZOBR_RS00680 ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >FitnessBrowser__azobra:AZOBR_RS00680 Length = 234 Score = 186 bits (471), Expect = 4e-52 Identities = 93/224 (41%), Positives = 144/224 (64%) Query: 4 GYGAVILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLV 63 G+G +L G +T+ +++S+ VL +V G +G + +LS L + ++Y+TV+RG+P+L+ Sbjct: 11 GWGGQLLGGAAMTVAVSVSAFVLGLVFGSLGASAKLSRNLALTGVAEVYTTVVRGVPELL 70 Query: 64 LILLIFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKG 123 +I L+F+GG + V +FGY+ YI+LN + G+ +G I GAY +E RGA A+P G Sbjct: 71 VIYLLFFGGSGAVMAVGRVFGYEGYIELNAFSIGVLAVGLISGAYSTEVIRGAVQAVPHG 130 Query: 124 QAEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQ 183 Q EA A GMS + + R+LVPQ +R A+PG N W + K TALISV L ++M + Sbjct: 131 QIEAARACGMSRWLILRRILVPQTLRYALPGLGNVWQLTLKDTALISVTALAEIMRVSHV 190 Query: 184 AADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAA 227 AA +TR+PF F+ A +YL++T+VS +A E+ + GVR A Sbjct: 191 AAGSTRQPFLFYTTAAVLYLLLTTVSTVAFERAERYANRGVRRA 234 Lambda K H 0.329 0.144 0.428 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: 162 Number of extensions: 6 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: 229 Length of database: 234 Length adjustment: 23 Effective length of query: 206 Effective length of database: 211 Effective search space: 43466 Effective search space used: 43466 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 46 (22.3 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