Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 200106 SO0922 proton/glutamate symporter (NCBI ptt file)
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__MR1:200106 Length = 424 Score = 367 bits (942), Expect = e-106 Identities = 190/406 (46%), Positives = 270/406 (66%), Gaps = 13/406 (3%) Query: 14 KILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFISLVC 73 +I +GM GIL+G+ L + IGT+F+N++KML+VPLVF SL+ Sbjct: 8 QIFVGMVLGILVGVTLGE------------QASYLKPIGTLFVNTIKMLIVPLVFCSLIV 55 Query: 74 GTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG-NASLASESMQYSAKEA 132 G S+ + +K+GR+G K+ +FYL TTAIA+ + + ++QPG L +AKE Sbjct: 56 GVTSMEDTAKMGRIGFKSFSFYLCTTAIAISLGLVVGYVIQPGAGVPLLQHEAVNTAKEV 115 Query: 133 PSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDLNEVIM 192 PS+ LI+IVP+NP+ AL+ G +LQ+I+FAV G A+ IG+ G+ +F+ L E + Sbjct: 116 PSVMQTLIDIVPTNPVAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMY 175 Query: 193 RVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPTLLKLFS 252 ++ ++M+LAPYGVF LM +A G++ L +IK + V + + H Y +L+LF+ Sbjct: 176 KLTDMVMKLAPYGVFGLMAWVAGEYGIDMLWPLIKVIIAVYIGCIIHVLGFYSIVLRLFA 235 Query: 253 GLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGATINMDG 312 L+PL F + + + AF+T+SS TLP +M+ + LG + K++SF LPLG TINMDG Sbjct: 236 KLNPLHFFKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDG 295 Query: 313 TAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLP 372 TA+ QGV +F+AQ FGIDLT DY +++TATLASIGTAGVPG GLVML +VL+ VGLP Sbjct: 296 TALYQGVTALFVAQAFGIDLTWVDYLTIILTATLASIGTAGVPGAGLVMLTLVLSTVGLP 355 Query: 373 VEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFN 418 +EG+ALI G+DR+LDM RT VNV+GD VAT VIAKSE L+ +N Sbjct: 356 LEGVALIAGIDRILDMARTVVNVSGDLVATTVIAKSENELDVEHYN 401 Lambda K H 0.325 0.139 0.388 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: 422 Number of extensions: 13 Number of successful extensions: 2 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: 437 Length of database: 424 Length adjustment: 32 Effective length of query: 405 Effective length of database: 392 Effective search space: 158760 Effective search space used: 158760 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 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