Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_061533332.1 CAter10_RS10280 amino acid ABC transporter permease
Query= SwissProt::P0AER5 (224 letters) >NCBI__GCF_001584165.1:WP_061533332.1 Length = 250 Score = 131 bits (330), Expect = 1e-35 Identities = 84/239 (35%), Positives = 126/239 (52%), Gaps = 20/239 (8%) Query: 4 FDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFA----------PVA 53 F W I LP ++G ++TLK+ V VV G G +L V R++ V Sbjct: 5 FQWQIIGEYLPLFIEGTLMTLKVAVICVVTGTFLGLLLGVGRVAEARHGAMKYFLRYAVQ 64 Query: 54 WFAKAYVNVFRSIPL-VMVLLWFYLIVPGFLQNVLGLSPKNDIR---------LISAMVA 103 W + YV+ FR PL V +LL + ++P + GL DI +SA++A Sbjct: 65 WPVRFYVSFFRGTPLFVQILLIHFALMPLLINPNGGLLLSGDIAREVRSQYGAFLSAVLA 124 Query: 104 FSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGI 163 ++ AY SEI RAGIQSI RGQS A+ +LGMT+ Q+++ ++LPQAFR M+P L I Sbjct: 125 ITLNSGAYVSEIFRAGIQSIDRGQSEASRSLGMTYLQTLRKVVLPQAFRRMLPPLGNNAI 184 Query: 164 VLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222 + +D+SL + LA+ A T+ E L +Y+ I+L S+ V +L++R Sbjct: 185 AIVKDSSLASAIGLAELAYAARTVSGAYARYWEPYLTISLIYWGITLLLSVFVQHLEKR 243 Lambda K H 0.330 0.140 0.412 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: 144 Number of extensions: 10 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: 224 Length of database: 250 Length adjustment: 23 Effective length of query: 201 Effective length of database: 227 Effective search space: 45627 Effective search space used: 45627 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 (21.9 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