Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate WP_029151526.1 METMI_RS0106850 dicarboxylate/amino acid:cation symporter
Query= uniprot:A1S570 (437 letters) >NCBI__GCF_000384075.1:WP_029151526.1 Length = 413 Score = 269 bits (688), Expect = 1e-76 Identities = 148/409 (36%), Positives = 239/409 (58%), Gaps = 14/409 (3%) Query: 8 KIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQD--YITEGFFHVIGTIFINSLKMLVVP 65 ++ L ++L+G+ AGIL+GLL + Q Y++ +IG +FI+ LKM++VP Sbjct: 2 RVSLNTQMLLGVSAGILVGLLFAELGPDAALAQSGLYVSG----LIGNLFIDLLKMVLVP 57 Query: 66 LVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNAS----LA 121 LVF S+ G +L ++ ++ TL F+ +T A+++ ++A L +PG Sbjct: 58 LVFTSIAVGIANLRLHQQMHQVWLSTLGFFGLSTTAAIILGLTACNLFEPGRGLSLDVFH 117 Query: 122 SESMQYSAKEAPSLADVLINIVPS---NPMKALSEGNMLQIIIFAVIFGFAISHIGERGR 178 S + AK+ +L D + NP AL++GN+L I++FA+ G A+ G+R R Sbjct: 118 SAMHNFDAKQM-TLTDFIAKFFHGLFVNPFAALADGNVLAIVVFALFLGIALVKGGDRYR 176 Query: 179 RVAALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLF 238 + L + E+ +R+V IM LAP+G+ AL+ +L T M L + K+ +V+ L Sbjct: 177 NILVLLQEGLEITLRMVGWIMHLAPFGIMALLTRLVATQDMGLLAGLAKFVAVVIGTTLV 236 Query: 239 HGFVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVA 298 H VV P +L + + P+ F R R+ + AF+T+SS+ATLPVT+ +E L ++A Sbjct: 237 HSLVVLPLMLYAVTRIKPMAFFRGAREALVTAFATSSSSATLPVTLRCAEQHLHVKPEIA 296 Query: 299 SFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVG 358 F +PLGAT+NMDGTA+ + A +F+A + G++L +V TA +A+IG G+P G Sbjct: 297 GFVVPLGATVNMDGTALYEAAAALFVANLAGVELNFVQQLIVFFTAMIAAIGAPGIPSAG 356 Query: 359 LVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAK 407 +V + MVL VGLP E IA++L +DR+LD RT VNV GD V ++++ + Sbjct: 357 MVTMVMVLQSVGLPAEAIAILLPIDRLLDTFRTMVNVQGDMVGSLIVQR 405 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: 365 Number of extensions: 16 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: 413 Length adjustment: 32 Effective length of query: 405 Effective length of database: 381 Effective search space: 154305 Effective search space used: 154305 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