Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= SwissProt::P0AER5 (224 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 79.0 bits (193), Expect = 1e-19 Identities = 55/197 (27%), Positives = 100/197 (50%), Gaps = 16/197 (8%) Query: 38 GTMLAVMRLSSFAPVAWFAKAYVN------VFRSIPLVMVLL------WFYLIVPGFLQN 85 G ++ ++ ++ V+W A+ + ++ +I +V VL+ W + PG ++ Sbjct: 178 GWLVVILAIALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRG 237 Query: 86 VLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLI 145 L LS + + ++ + A+ +EIIR GI S+ GQ AA ALG+T Q++ I Sbjct: 238 GLRLS----LEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQI 293 Query: 146 ILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVY 205 ++PQA R +VP L +Q + +++SL + D + TA T + G VE+ L Y Sbjct: 294 VVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTY 353 Query: 206 FVISLSASLLVSYLKRR 222 I+ S ++ L++R Sbjct: 354 LAINAVISAGMNGLQQR 370 Score = 33.1 bits (74), Expect = 7e-06 Identities = 17/65 (26%), Positives = 38/65 (58%), Gaps = 1/65 (1%) Query: 16 LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVM-VLLW 74 L+ GLV +L++ +++ + GT+ V S + ++ YV V R+ PL++ +++W Sbjct: 82 LVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVW 141 Query: 75 FYLIV 79 ++ I+ Sbjct: 142 YFPIL 146 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: 230 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 224 Length of database: 377 Length adjustment: 26 Effective length of query: 198 Effective length of database: 351 Effective search space: 69498 Effective search space used: 69498 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: 48 (23.1 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