Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_03659 H281DRAFT_03659 amino acid ABC transporter substrate-binding protein, PAAT family
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__Burk376:H281DRAFT_03659 Length = 284 Score = 222 bits (566), Expect = 6e-63 Identities = 115/238 (48%), Positives = 159/238 (66%), Gaps = 6/238 (2%) Query: 21 ADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVEQEFDGLIPALK 80 A+ L++GI+ +YPP SKAPDGS+ GFD D+GN +C ++ +C WVE EF G+IPAL+ Sbjct: 50 AESNTLRLGIDPSYPPMDSKAPDGSLKGFDVDLGNEICRRIQARCQWVELEFSGMIPALQ 109 Query: 81 VRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTAVSENLAELKGKNIGVQRGS 140 RKIDAILSSM+IT+ R++ + FT+K + +RL+ + G+ ++ L L GK IGVQ G+ Sbjct: 110 ARKIDAILSSMAITQKREQQILFTSKLFQFKSRLIARQGSPLAAGLQALSGKQIGVQSGT 169 Query: 141 IHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGFLKTDAGKGFAF 200 E +A PLGA + Y SQ+E++ D+ GRLDG + + D GFL+T AGKGFAF Sbjct: 170 QFEGYALTHWVPLGAHVVAYKSQDEVFADLQNGRLDGALLGSVEADFGFLRTPAGKGFAF 229 Query: 201 VGPAFTDVKYFGD-GVGIAVRKGD-ALKDKINTAIAAIRENGKYKQIQDKYFAFDIYG 256 VG + GD G GI +RK + A++ IN AIAA+ ++G Y QI KYF FD YG Sbjct: 230 VGEPLS----MGDRGTGIGLRKDETAIQASINAAIAAMLKDGTYAQIAKKYFDFDPYG 283 Lambda K H 0.318 0.138 0.394 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: 240 Number of extensions: 10 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: 257 Length of database: 284 Length adjustment: 25 Effective length of query: 232 Effective length of database: 259 Effective search space: 60088 Effective search space used: 60088 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 (21.7 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