Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate Ac3H11_4900 Putative amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_16280 (223 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4900 Length = 217 Score = 99.4 bits (246), Expect = 5e-26 Identities = 64/203 (31%), Positives = 108/203 (53%), Gaps = 15/203 (7%) Query: 22 TLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPLLLVITWFYLAVPFV 81 T+ L+++ +GG ++G LL ++RLS + + GAYV F+ PLL+ + Y + Sbjct: 20 TVSLSLIAFIGGGLVGLLLLVLRLSKVRGVDRAVGAYVQVFQGTPLLMQLFLAYFGIA-- 77 Query: 82 LRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAKALGMGYGQMMR 141 + G T +T+ VA ++ +AY EI R V SIPKGQ AA++L +G+ +R Sbjct: 78 ---LFGIKT--SPWTAAAVALTLYTSAYLTEIWRGCVASIPKGQWEAAQSLAFNFGEQLR 132 Query: 142 LIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATRASGDIIGRA--NEFLIIA 199 ++LPQA R P + + + + T+L +G V+ A G +I A FL+ A Sbjct: 133 HVVLPQALRIAVPPTVGFLVQVIKGTALASVIGFVELTKA----GSMISNATYKPFLVYA 188 Query: 200 --GLVYFTISFAASRLVKRLQKR 220 L+YF + F S + + L+++ Sbjct: 189 CVALLYFVLCFPVSLVAQSLERK 211 Lambda K H 0.331 0.143 0.425 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: 127 Number of extensions: 7 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: 223 Length of database: 217 Length adjustment: 22 Effective length of query: 201 Effective length of database: 195 Effective search space: 39195 Effective search space used: 39195 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 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