Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate WP_200770547.1 BUQ81_RS04135 dicarboxylate/amino acid:cation symporter
Query= uniprot:A1S570 (437 letters) >NCBI__GCF_900141795.1:WP_200770547.1 Length = 422 Score = 286 bits (732), Expect = 9e-82 Identities = 160/415 (38%), Positives = 252/415 (60%), Gaps = 18/415 (4%) Query: 8 KIGLTGKILIGMGAGILIGLLLRN--FFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVP 65 K+ L +IL+ + +L+G L G W+ Y IGT+F+N+LKM+VVP Sbjct: 2 KLALHWQILLALALAVLMGWLTGTDATILGVHWIAIY------DFIGTLFLNALKMVVVP 55 Query: 66 LVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNAS-----L 120 LV +++ G S++ GRLG KTL +YL T+AIA+++ I+ L+QPG + + Sbjct: 56 LVMAAIITGMASIARQGGFGRLGLKTLGYYLMTSAIAILIGITLVNLIQPGVSDNPPPQI 115 Query: 121 ASESM---QYSAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERG 177 A+++ + ++ +A+V + ++P+N ++A +E ML +I F+++FG+ + I Sbjct: 116 AADTQLQQKLEGRDIGDIAEVFLRMIPTNIVEAAAETQMLGLIFFSLLFGYFMMKIQTPY 175 Query: 178 RRVAALF-DDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVL 236 R F + EV+M++ +M+ AP GVF L+ G + ++ +F+ V++ L Sbjct: 176 RDTLYNFWQGVFEVMMQITEWVMKFAPLGVFGLVAASVARTGFDQFANLALFFITVVLAL 235 Query: 237 LFHGFVVYPTLLKLFSGL-SPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADN 295 H FVV P +L+ G+ +P + M L AFST+SS +TLPVT+E E G N Sbjct: 236 GIHFFVVMPLILRFIGGVRNPWKHYKVMLPAILTAFSTSSSASTLPVTIECVERGAGVPN 295 Query: 296 KVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVP 355 +++ F LPLGAT+NMDGTA+ + VA +FIAQ+FG+ L +T M+++ A L SIG AG+P Sbjct: 296 RISGFVLPLGATVNMDGTALYEAVAALFIAQLFGVHLDVTQQFMIIVIALLTSIGVAGIP 355 Query: 356 GVGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEG 410 LV ++++L VGLP E I L+L VDR+LDM+RT VN+ D+V VVIA+SEG Sbjct: 356 SASLVAISIILVSVGLPAEAIGLLLVVDRLLDMMRTTVNIFSDSVGAVVIARSEG 410 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: 381 Number of extensions: 13 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: 437 Length of database: 422 Length adjustment: 32 Effective length of query: 405 Effective length of database: 390 Effective search space: 157950 Effective search space used: 157950 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 Apr 09 2024. 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