Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_16280 (223 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 112 bits (280), Expect = 6e-30 Identities = 69/218 (31%), Positives = 126/218 (57%), Gaps = 8/218 (3%) Query: 3 LDFSGVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYF 62 LD + ++ VP + + + +TL + V+ +V ++L +LLA+ R+ +L + ++++F Sbjct: 4 LDIAYMLGLVPVLLSYVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFF 63 Query: 63 RSIPLLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIP 122 R PLL+ + FY +P VL +T I ++ I+ + AAY E +RA + + Sbjct: 64 RGTPLLVQLFLFYYGLPQVLSVLT----QINGVSAAIMGLTLHFAAYMAESIRAAILGVD 119 Query: 123 KGQMGAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNAT 182 + Q AA+++GM GQMMR I+LPQA R P L+ I + + TSL +T+G+ + + AT Sbjct: 120 RSQWEAAQSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGAT 179 Query: 183 R--ASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQ 218 + A+G + FL++A ++Y+ + A S + +RL+ Sbjct: 180 QKEAAGSFL-YFEAFLVVA-VIYWILVEALSLVQRRLE 215 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: 117 Number of extensions: 6 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: 224 Length adjustment: 22 Effective length of query: 201 Effective length of database: 202 Effective search space: 40602 Effective search space used: 40602 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: 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