Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate GFF2619 PGA1_c26600 amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__Phaeo:GFF2619 Length = 273 Score = 96.7 bits (239), Expect = 4e-25 Identities = 75/222 (33%), Positives = 114/222 (51%), Gaps = 14/222 (6%) Query: 7 AVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLA-RLGD-LYSTVIRGIPDLVL 64 + ++ G LT+ + L S LA +LGL G+AL RWL R G Y V+RGIP +VL Sbjct: 47 STLMRGVQLTIFVTLISFFLASLLGL-GLALAAGS-RWLVIRQGARFYIEVVRGIPIIVL 104 Query: 65 ILLIFYGGQDLLNRVAPLLGYDDYIDLNP--------LVAGIGTLGFIFGAYLSETFRGA 116 +L + + L + LG D+I L+P L I L + A++SE FR Sbjct: 105 LLYVAFVLAPALVELRNWLG--DHIGLDPIRTRNFPLLWRAIIALMIAYSAFISEVFRAG 162 Query: 117 FMAIPKGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQD 176 ++ +GQ EA + G+S + F ++ PQ IR +P N+++ L K ++L+SV+G+ D Sbjct: 163 LQSVDEGQIEAAKSLGLSRWHRFRFIVFPQAIRTILPPLGNDFVALVKDSSLVSVLGVAD 222 Query: 177 MMFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEK 218 + K A F + VA +YL +T L LR EK Sbjct: 223 VTQLGKLTAVGNFRYFETYNVVALIYLTLTIGLSLLLRRFEK 264 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: 181 Number of extensions: 11 Number of successful extensions: 3 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: 273 Length adjustment: 24 Effective length of query: 205 Effective length of database: 249 Effective search space: 51045 Effective search space used: 51045 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