Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate 3607284 Dshi_0699 TRAP C4-dicarboxylate transport system permease DctM subunit (RefSeq)
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Dino:3607284 Length = 437 Score = 221 bits (564), Expect = 3e-62 Identities = 139/444 (31%), Positives = 229/444 (51%), Gaps = 16/444 (3%) Query: 5 DWLGPM-MFVGALVFL-GCGYPVAFSLGGVAILFA--IIGAALGSFDPIFLSAMPQRIFG 60 DW + + +GA+V L G PVA + IL A +G G + + G Sbjct: 2 DWFEALALLLGAIVALMALGMPVALAFLAANILGAWVFMGGERG------IVQLLNNGLG 55 Query: 61 IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTG 120 + L+ IP F+ +G + +G+ ++ + +LG L G L+ +L GT + +G Sbjct: 56 ALTTYALVPIPLFLLMGEIFFHTGLGGRMFTAIDRLLGRLPGRLSYVTVLGGTGFSTLSG 115 Query: 121 VVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGD 180 + +G + +P M GY ++ G I+ +G L IIPPS + ++LA + VG Sbjct: 116 SSMGSTALLGSLMVPEMNARGYKSHMSIGPILGTGGLAIIIPPSALAVLLATLAQIDVGA 175 Query: 181 LFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVL 240 L I ++PGLM+AG + + I P APA ++G + +++ ++P + + Sbjct: 176 LLIAGVIPGLMLAGFYIATIWIQTRRDPSAAPAYEVAEVSLGAK--LGLLLRDVVPMVGV 233 Query: 241 ILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILL 300 +++++ + FGI +P+EA A G++G I LA + L +AL L++T M +I+ Sbjct: 234 MVVIVSLMIFGIVTPSEAAAFGALGVIILAAAFRCLTVEALRRSVVGALKVTLMAYMIVF 293 Query: 301 GSTAFS--LVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLP 358 GS FS L F G G + I L + +LG F++ I + +P Sbjct: 294 GSATFSQLLAFSGASGG--LIGWATGFDLDPIWMLLAMFGVLLVLGMFMEQISIMLLTVP 351 Query: 359 LFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPF 418 +F P+A++L DLIW+ +I+ L+ SF TPPFG LF ++GVAP S T +IY A+PF Sbjct: 352 IFFPLAQSLGFDLIWFALIMLLALEISFTTPPFGLLLFVMKGVAPPSTTMREIYLAAIPF 411 Query: 419 IGLQVLVLLLIIIFPALINWLPSL 442 I +L++ L+I+FP L WLP L Sbjct: 412 IACSLLLVALLILFPPLATWLPGL 435 Lambda K H 0.331 0.148 0.443 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: 569 Number of extensions: 36 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: 445 Length of database: 437 Length adjustment: 32 Effective length of query: 413 Effective length of database: 405 Effective search space: 167265 Effective search space used: 167265 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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