Align Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter (characterized)
to candidate WP_057508795.1 ABB28_RS11690 dicarboxylate/amino acid:cation symporter
Query= SwissProt::O59010 (425 letters) >NCBI__GCF_001431535.1:WP_057508795.1 Length = 443 Score = 249 bits (636), Expect = 1e-70 Identities = 148/443 (33%), Positives = 246/443 (55%), Gaps = 39/443 (8%) Query: 1 MGLYRKYIEYPVLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMP 60 M L ++ P Q+++ G +LGA+ G ++G A +T+ P GDL+V L+KM+ +P Sbjct: 1 MKLVSAWLRIPFWQRVVAGFVLGALAGWLMG-----PAAETWFGPLGDLYVTLIKMIAVP 55 Query: 61 IVFASLVVGAASISPAR-LGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGG 119 +VF +++ +S+ + + + + +++++T+A AV +G+++ + PG G Sbjct: 56 LVFFAVINAISSLHGQKSVAALSGRTFLWFVITAALAVGIGLLVGTVMQPGTGGLQLAMA 115 Query: 120 QQFQPKQAPPLVKILLDIVPTNPFGALAN-----------------GQVLPTIFFAIILG 162 + P++ P +V++LLD+VP+N F AL+ G +LP IFFA ++G Sbjct: 116 HNYVPREVPSVVQVLLDVVPSNVFYALSGIGTRVNAAGETVLAAGRGSILPVIFFAGLVG 175 Query: 163 IAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGV 222 AI L EKV ++ + + ++E M ++ V++ PIG F LIA ++ G Sbjct: 176 FAIVKL----GEKVGQARQL----VGQMSEIMIQVTRFVLEVTPIGTFGLIAGLVGSYGF 227 Query: 223 KVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKKAKDAMLTAFVTRSSSGTL 282 + + L A+Y+ L I++VY LL +G++P+ F + A M AFV+ SS + Sbjct: 228 EKLLPLGNFVLALYIACALHIVVVYSALLLSHGLNPLKFFRGAAPGMQVAFVSSSSFAAM 287 Query: 283 PVTMR-VAKEMGISEGIYSFTLPLGATINMDGT-ALYQGVCTFFIANALGSHLTVGQQLT 340 PV +R + +G+++ SF +PLGA+I MDG A+Y +C FI+ G ++ Q L Sbjct: 288 PVALRSITHNLGVNKDYGSFAVPLGASIKMDGCGAIYPALCAVFISQYSGVPMSPEQYLI 347 Query: 341 IVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDMGRTMV 400 +++ +VL S GTAGVPG +M +VL + GLPL + YA ID ILDM RTM Sbjct: 348 VLIASVLGSFGTAGVPGTAVVMATVVLSAAGLPL--ETIGYLYA----IDRILDMMRTMT 401 Query: 401 NVTGDLTGTAIVAKTEGELEKGV 423 NVTG + +VAK G L++ V Sbjct: 402 NVTGQMLVPVLVAKETGLLDQSV 424 Lambda K H 0.325 0.141 0.396 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: 485 Number of extensions: 36 Number of successful extensions: 8 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: 425 Length of database: 443 Length adjustment: 32 Effective length of query: 393 Effective length of database: 411 Effective search space: 161523 Effective search space used: 161523 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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