Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3432 (229 letters) >NCBI__GCF_001294205.1:WP_053937456.1 Length = 221 Score = 132 bits (332), Expect = 5e-36 Identities = 77/219 (35%), Positives = 119/219 (54%), Gaps = 12/219 (5%) Query: 1 MLKGYGAVILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIP 60 +L+ +L G TL A+ +MV +++G + LRLS I+ L W LY + +RG P Sbjct: 6 LLQSAWPYLLKGTGYTLLFAVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGTP 65 Query: 61 DLVLILLIFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAI 120 LV I +I+YG P G I P+ AGI L GAY+SET RGA + Sbjct: 66 LLVQIFIIYYG--------LPAIG----IQFEPITAGILALSLNTGAYVSETMRGAINGV 113 Query: 121 PKGQAEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFK 180 +GQ EA + GM +Q ++ PQ +RLA+P +N+ + L K T+L+SV+ + ++M Sbjct: 114 DRGQWEAAFSQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELMLA 173 Query: 181 AKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 K+ T +PF ++A AA+Y ++ + R LE+R Sbjct: 174 TKEVISTTFQPFPLYVAAAAIYWCLSLIFEQVQRLLERR 212 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: 133 Number of extensions: 8 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: 229 Length of database: 221 Length adjustment: 22 Effective length of query: 207 Effective length of database: 199 Effective search space: 41193 Effective search space used: 41193 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 24 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