Align Glutamate:sodium symporter, GltS (characterized)
to candidate WP_086510424.1 BZY95_RS13395 sodium:glutamate symporter
Query= TCDB::B1XKD9 (480 letters) >NCBI__GCF_002151265.1:WP_086510424.1 Length = 487 Score = 470 bits (1209), Expect = e-137 Identities = 236/484 (48%), Positives = 325/484 (67%), Gaps = 14/484 (2%) Query: 3 TLRDVFFAFILIALLVLAGRYVKQKVRWIQRLYLPESIVAGVLALLLGPQVLGAIATAIS 62 T+ ++F A +LI+L++LA ++ W++RL+LP S++ G + LLLGP+VLG + T Sbjct: 4 TVGELFIALVLISLVLLASNAIRNVSPWLRRLFLPSSVIGGAILLLLGPEVLGRVVT--- 60 Query: 63 GGTSILSDGLFSEPIRAVWSQSPGIFINIVFAALFLGEAIPRPKDIWTKTAPQVVFGQTL 122 G + GLF E + W+ PG+ IN+VFAALF+G IP + IW + PQVV GQT+ Sbjct: 61 -GPFEEAAGLFPEYVFESWAALPGLLINVVFAALFIGRPIPGLRTIWMRAGPQVVVGQTM 119 Query: 123 AWGQYVVGILVTLLILMPLFGVNPIAACLIEIGFEGGHGTAGGMAETFTELGFEAGADLA 182 AWGQYVVG+ + +LIL P+FG+NP+A LIEIGFEGGHGTA GMA+TF ELGFE GADLA Sbjct: 120 AWGQYVVGLTLAILILAPVFGMNPMAGALIEIGFEGGHGTAAGMADTFAELGFEEGADLA 179 Query: 183 LGIATVGIVGGIVAGTALADWGRRKGHVT-----SFQKAVEDLDGVPELTETESPEVRR- 236 LG+ATVGIV G++ GT + + R+G + A+++ +P+ E P Sbjct: 180 LGLATVGIVSGVLIGTLMINIAARRGVIELESPRKTSDALDEAQAMPQGEENALPPTEEY 239 Query: 237 ---RRAQLMRNLLIDPLSINFGIVGAAIVIGWLILEALVWVESVTWGQT-GFEVISYVPL 292 ++ DPLS++ G+VG AI IGWLIL AL W+E TW + G E++++VPL Sbjct: 240 SEFKKDLAQEEETADPLSLHLGLVGIAIAIGWLILTALQWIEQQTWARNDGLEILAHVPL 299 Query: 293 FPMALIGGIIVQLVMERLGLAPLIIRSLMSNIAGLALDVVVVTALASISLSVIGSNLGVF 352 FP+A+IGG+IVQL + R GL P + M+ IAG ALD +V ALA++SL+ +G + F Sbjct: 300 FPIAMIGGVIVQLSVTRFGLEPHVSSRTMARIAGTALDFTIVAALATLSLTALGEHFIPF 359 Query: 353 TILSVVGITWNVVMFLYFAPRIFPSHWFEKGIGDMGQSMGVTATGILLLRMVDPENRTGA 412 +L++ GI W++ + + APR+ P +WFE+GIGD GQSMGVT TG+LL+RM DP+NR+GA Sbjct: 360 LLLALAGIGWSLFVLIVIAPRVIPENWFERGIGDFGQSMGVTVTGLLLMRMADPKNRSGA 419 Query: 413 FESFAYKQLFFEPIVGGGLFTAAAPALVVRFGLVPVLLLTGGLLIFWLAMGFLIIRQNQQ 472 FESF YKQL FEP+VGGGLFTAA+ L+ +FG VL T L + WL G L + Sbjct: 420 FESFGYKQLMFEPVVGGGLFTAASLPLIAQFGAPTVLGFTLILTVAWLIFGLLYFGRMVP 479 Query: 473 QRRR 476 +R R Sbjct: 480 ERGR 483 Lambda K H 0.327 0.144 0.434 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: 764 Number of extensions: 46 Number of successful extensions: 5 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: 480 Length of database: 487 Length adjustment: 34 Effective length of query: 446 Effective length of database: 453 Effective search space: 202038 Effective search space used: 202038 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 (21.7 bits) S2: 52 (24.6 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