Align Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter (characterized)
to candidate WP_085545458.1 B9Y55_RS11270 dicarboxylate/amino acid:cation symporter
Query= SwissProt::O59010 (425 letters) >NCBI__GCF_900177735.1:WP_085545458.1 Length = 400 Score = 343 bits (880), Expect = 5e-99 Identities = 197/411 (47%), Positives = 265/411 (64%), Gaps = 24/411 (5%) Query: 11 PVLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGA 70 P++ +I IG +LG G LG + V+P G +F+ LLKML++P+VF+SLVVG Sbjct: 9 PLIWRITIGFVLGIAAGAFLG------PKVSIVEPVGKVFITLLKMLIVPLVFSSLVVGV 62 Query: 71 ASIS-PARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPP 129 +SI P LGR+GVK ++ YL+T+A A+ +G+ M F PG+G+ + G + + AP Sbjct: 63 SSIGEPKTLGRIGVKTILIYLMTTAVAIVIGLGMGHFFQPGSGMAIE-GVEAAAGRAAPA 121 Query: 130 LVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAING 189 L ++++ + P NP ALA G +L I FA+ GIA L + + V + + Sbjct: 122 LSEVIIGMFPDNPVQALAQGHMLQIIVFALFFGIA-AMLAGDKGKPV-------ISFMES 173 Query: 190 LAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFV 249 +AE MYK+ + VM AP GVFALIA +++ G+ V+ AKV AVY+G + ++VY Sbjct: 174 MAETMYKVTDLVMNLAPYGVFALIAVTVSKYGLSVLAPFAKVIGAVYLGCIVHAIVVYSG 233 Query: 250 LLKIYGI-DPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKE-MGISEGIYSFTLPLGA 307 L+ + PI F K ++A LTAFVTRSSS TLPVTM +E MGISE I SF LPLGA Sbjct: 234 LVAVVTKKSPIWFFKGIQEASLTAFVTRSSSATLPVTMTCTQENMGISEKISSFVLPLGA 293 Query: 308 TINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVL 367 TINMDGTALYQGVC FIA A G L++G Q+ I++TA LAS+GTAGVPGAG IML +V+ Sbjct: 294 TINMDGTALYQGVCALFIAQAFGIDLSIGAQVGIIVTATLASVGTAGVPGAGLIMLTLVV 353 Query: 368 ESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEGE 418 GLP+ AM+ GIDA+LDM RT +NVTGD TA++AKTEGE Sbjct: 354 TQAGLPM------EGVAMVAGIDAVLDMARTSLNVTGDACVTAVIAKTEGE 398 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: 509 Number of extensions: 31 Number of successful extensions: 7 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: 400 Length adjustment: 31 Effective length of query: 394 Effective length of database: 369 Effective search space: 145386 Effective search space used: 145386 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: 50 (23.9 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