Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate H281DRAFT_05291 H281DRAFT_05291 amino acid ABC transporter membrane protein 1, PAAT family
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__Burk376:H281DRAFT_05291 Length = 240 Score = 169 bits (429), Expect = 3e-47 Identities = 83/217 (38%), Positives = 138/217 (63%) Query: 3 KGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDL 62 +G+G V+L A +T+ L L+++A+ V G + A +LS +R L +GD+Y+TV RG+P+L Sbjct: 12 EGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRLRTLRVIGDIYTTVFRGVPEL 71 Query: 63 VLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPK 122 ++I L ++GG L+ V G + ++ + P V G +G I GAY +E +R A +A+ + Sbjct: 72 LVIYLFYFGGSTLVTTVGQWFGAEGFVGVPPFVIGALAVGMISGAYQAEVYRSAVLAVSR 131 Query: 123 GQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAK 182 G+ EA + GM + + R+L+PQ++R A+PG N W + K +ALISV GL +++ ++ Sbjct: 132 GELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQ 191 Query: 183 QAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 AA +T + FTFF+ A+YL++TS+S H E R Sbjct: 192 VAAGSTHQYFTFFVVGGALYLLMTSISNRVFNHAEAR 228 Lambda K H 0.329 0.144 0.421 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: 154 Number of extensions: 9 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: 240 Length adjustment: 23 Effective length of query: 206 Effective length of database: 217 Effective search space: 44702 Effective search space used: 44702 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