Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate YP_004144338.1 Mesci_5190 sodium:dicarboxylate symporter
Query= CharProtDB::CH_014038 (428 letters) >NCBI__GCF_000185905.1:YP_004144338.1 Length = 442 Score = 527 bits (1357), Expect = e-154 Identities = 259/415 (62%), Positives = 327/415 (78%) Query: 6 FKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65 + LY QVL AI +GILLGHFYP +GE MKPLGD F+KL+KMIIAPVIF TV TGIAGM Sbjct: 18 YAQLYVQVLVAITVGILLGHFYPSVGESMKPLGDAFIKLVKMIIAPVIFLTVTTGIAGMS 77 Query: 66 SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAK 125 ++ VGR A+LYF ST+ALIIGL++ NVVQPGAG N+DPATLDA V YA +A Sbjct: 78 DLQKVGRVAGKAMLYFLTFSTLALIIGLVVANVVQPGAGFNIDPATLDASTVNTYAAKAH 137 Query: 126 DQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185 DQ + F+M++IP++++GAFA G+ILQVL F+VLFG AL +G KG+ + N +++ + I Sbjct: 138 DQSVTGFLMNIIPSTIVGAFADGDILQVLFFSVLFGIALALVGDKGEPVLNFLQALTTPI 197 Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245 F +++++M+ APIGAFGAMAFTIGKYG+G ++ L L+ FY+T LFV +VLG++ + Sbjct: 198 FKLVSVLMKAAPIGAFGAMAFTIGKYGIGAVINLAMLVGTFYVTSFLFVFIVLGAVCRYN 257 Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305 GFSI IRYI+EELL+VLGTSSSE+ALP +++KMEK G ++SVVGLVIPTGYSFNLDGT Sbjct: 258 GFSILALIRYIKEELLLVLGTSSSEAALPSLMEKMEKAGAKRSVVGLVIPTGYSFNLDGT 317 Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365 +IY+T+AA+FIAQATN + + QI LL+V +LSSKGAAG+TG+GFI LAATLS V +P Sbjct: 318 NIYMTLAALFIAQATNIHLSMGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVVPAVP 377 Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPD 420 VAG+ALILG+DRFMSE RALTN VGN VAT+VVA+W ELD KL L A D Sbjct: 378 VAGMALILGVDRFMSECRALTNFVGNAVATLVVARWEGELDEAKLARALAGTADD 432 Lambda K H 0.327 0.142 0.401 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: 611 Number of extensions: 28 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: 428 Length of database: 442 Length adjustment: 32 Effective length of query: 396 Effective length of database: 410 Effective search space: 162360 Effective search space used: 162360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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