Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate WP_083492058.1 ABB28_RS15865 dicarboxylate/amino acid:cation symporter
Query= uniprot:A1S570 (437 letters) >NCBI__GCF_001431535.1:WP_083492058.1 Length = 440 Score = 249 bits (635), Expect = 2e-70 Identities = 159/432 (36%), Positives = 243/432 (56%), Gaps = 32/432 (7%) Query: 2 AAAQSSKIGLTGKILIGMGAGILIGLLLRNF-------FGGSEWVQDYITEGFFHVIGTI 54 A+ K+ L K+ IG G+++GL++ ++W+ YIT + Sbjct: 4 ASPAKKKMPLHWKMGIGFAIGLVLGLVVHALGAQTPALMDAAKWLMHYITTP----ASGL 59 Query: 55 FINSLKMLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQ 114 F+N + ML+VPL+F +LV G + + LGR+G KTLA+ + ++IA+ + + L++ Sbjct: 60 FLNLIFMLIVPLIFSALVMGVSEMGDIRALGRIGWKTLAYTIVLSSIAVAIGLVLVNLLK 119 Query: 115 PGNA-------SLASESMQYSAK------EAPSLADVLINIVPSNPMKALSE-GNMLQII 160 PG + +E+++ S + P D+L++IVPSN ++A S G +L ++ Sbjct: 120 PGVGVDPAMANQILAENLERSKEIVAGVGSQPKGMDMLLSIVPSNIVEAASSNGAILSLM 179 Query: 161 IFAVIFGFAISHIGERGRRVAAL---FDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTL 217 FA++FG I + +VA L + + EV M ++ L+++LAPY V M LA Sbjct: 180 FFALMFG--IGMVLTDDEKVAPLRRAIEGIFEVSMTLINLVIRLAPYAVACFMFNLAALF 237 Query: 218 GMETLESVIKYFMLVLVVLLFHGFVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSN 277 G E L + Y +V++ L H V Y + L SG SPL F R ++ + AFSTASSN Sbjct: 238 GFELLIRLGAYVGVVVLALGLHMVVTYGVAVWL-SGRSPLAFFRDTQEATVMAFSTASSN 296 Query: 278 ATLPVTMEASEHRLGADNKVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDY 337 ATLP + ++ +G KV+ F L +GAT N +GTA+ +GV +F+AQ FG+DL+I Sbjct: 297 ATLPTALRVADE-MGLPQKVSRFVLTVGATANQNGTALFEGVTVIFLAQFFGVDLSIGQQ 355 Query: 338 AMVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTG 397 MV+ L IGTAGVP L ++AM+ VG+ GI LILGV+ LDM RTA+NVTG Sbjct: 356 IMVMAVCILGGIGTAGVPSGSLPVVAMICAMVGVNPLGIGLILGVNHFLDMCRTALNVTG 415 Query: 398 DTVATVVIAKSE 409 D T ++AK E Sbjct: 416 DLALTTLVAKGE 427 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: 421 Number of extensions: 25 Number of successful extensions: 6 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: 440 Length adjustment: 32 Effective length of query: 405 Effective length of database: 408 Effective search space: 165240 Effective search space used: 165240 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 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