Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate WP_054558634.1 I595_RS06915 dicarboxylate/amino acid:cation symporter
Query= uniprot:A1S570 (437 letters) >NCBI__GCF_001306415.1:WP_054558634.1 Length = 437 Score = 294 bits (753), Expect = 3e-84 Identities = 170/427 (39%), Positives = 257/427 (60%), Gaps = 30/427 (7%) Query: 8 KIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLV 67 K+ L +ILIGM AG+L G + G ++V D+I +GTIF+ LK++ +PL+ Sbjct: 3 KLELHWQILIGMIAGVLFGFAMNQLDWGEQFVADWIRP-----LGTIFVKLLKLIAIPLI 57 Query: 68 FISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG----------- 116 SLV G L + SK +G +T+A Y+ TT +A+ + + ++QPG Sbjct: 58 LASLVKGVSDLKDISKFRSIGLRTMAIYMGTTLVAITIGLVLVNVIQPGVAIPADTISKL 117 Query: 117 ------NASLASESMQYSAKEAPSLADVLINIVPSNPMKALSEGN-MLQIIIFAVIFGFA 169 ++ + S+ + S ++ L +VP N + A+S+ + MLQ+I F + G + Sbjct: 118 VDTYSGDSGVTSKLAEASMQKERGPLQFLEEMVPDNAVYAMSDNSLMLQVIFFTIFLGIS 177 Query: 170 ISHIGE-RGRRVAALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLG-METLESVIK 227 + +G+ R + + F+ LN+V++++V LIM AP VFAL+ + ++ + L +++K Sbjct: 178 MLLVGQKRAKPLKKFFNSLNDVVLKMVDLIMLTAPVAVFALLASVVVSSSDPDLLLALLK 237 Query: 228 YFMLVLVVLLFHGFVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEAS 287 Y +VL+ LL + Y ++ F+G PL F+ K+ QL AFST+SS ATLPVTME Sbjct: 238 YAGVVLLGLLLM-VLFYCVIISFFTGYHPLKFLIKISPAQLLAFSTSSSAATLPVTMERV 296 Query: 288 EHRLGADNKVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLA 347 E +G D +V+SF LP+GAT+NMDGT++ QGVA VFI+Q DLT D +V TA LA Sbjct: 297 EEHIGVDAEVSSFVLPVGATVNMDGTSLYQGVAAVFISQALAFDLTFPDQLTIVFTALLA 356 Query: 348 SIGTAGVPGVGLVMLAMVLNQVGLPVE----GIALILGVDRMLDMVRTAVNVTGDTVATV 403 SIG+A VPG G+VML +VL +G P + G+ALI VDR LDM RT VNVTGD++ + Sbjct: 357 SIGSAAVPGAGMVMLVIVLEAIGFPADKLAIGLALIFAVDRPLDMCRTVVNVTGDSMVAI 416 Query: 404 VIAKSEG 410 ++AKS G Sbjct: 417 LVAKSVG 423 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: 378 Number of extensions: 11 Number of successful extensions: 4 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: 437 Length adjustment: 32 Effective length of query: 405 Effective length of database: 405 Effective search space: 164025 Effective search space used: 164025 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