Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate GFF3437 PS417_17595 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__WCS417:GFF3437 Length = 233 Score = 231 bits (589), Expect = 9e-66 Identities = 112/224 (50%), Positives = 159/224 (70%), Gaps = 1/224 (0%) Query: 2 LKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPD 61 L GYG ++ GAW+TL+LA ++AL++ LGLI A +LS +WL LY+T+IR +PD Sbjct: 7 LHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPD 66 Query: 62 LVLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIP 121 LVLILLIFY Q LN ++ + G+D Y +++P AG+ TLGFI+GAY +E FRGA +++P Sbjct: 67 LVLILLIFYSLQLWLNDLSEVFGWD-YFEIDPFTAGVITLGFIYGAYFTENFRGAILSVP 125 Query: 122 KGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKA 181 GQ EA AYG+S +Q F VL PQ++R A+PG NNWLVL K+TAL+S++GL D++ A Sbjct: 126 VGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAA 185 Query: 182 KQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVR 225 + A T EP F + MYLVIT++S L+ LE+RY++G++ Sbjct: 186 QNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIK 229 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: 206 Number of extensions: 12 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: 233 Length adjustment: 23 Effective length of query: 206 Effective length of database: 210 Effective search space: 43260 Effective search space used: 43260 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