Align C4-dicarboxylate transport protein 2 (characterized)
to candidate WP_057508795.1 ABB28_RS11690 dicarboxylate/amino acid:cation symporter
Query= SwissProt::Q9I4F5 (436 letters) >NCBI__GCF_001431535.1:WP_057508795.1 Length = 443 Score = 204 bits (519), Expect = 4e-57 Identities = 129/423 (30%), Positives = 209/423 (49%), Gaps = 30/423 (7%) Query: 5 PFYKSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVTGIAG 64 PF++ + ++ G +G P P GD +V LIKM P++F V+ I+ Sbjct: 11 PFWQRVVAGFVLGALAGWLMG---PAAETWFGPLGDLYVTLIKMIAVPLVFFAVINAISS 67 Query: 65 MQSMKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAAYAAA 124 + KSV G L+F + + +A+ IGL+V V+QPG G L + Y Sbjct: 68 LHGQKSVAALSGRTFLWFVITAALAVGIGLLVGTVMQPGTG------GLQLAMAHNYVPR 121 Query: 125 GEKQSTVDFLMNVIP-----------------GTVVGAFANGDILQVLFFSVLFGYALHR 167 E S V L++V+P G V A G IL V+FF+ L G+A+ + Sbjct: 122 -EVPSVVQVLLDVVPSNVFYALSGIGTRVNAAGETVLAAGRGSILPVIFFAGLVGFAIVK 180 Query: 168 LGSYGKPVFEFIERVSHVMFNIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCF 227 LG + + ++S +M + +++V PIG FG +A +G+YG L+ LG +L Sbjct: 181 LGEKVGQARQLVGQMSEIMIQVTRFVLEVTPIGTFGLIAGLVGSYGFEKLLPLGNFVLAL 240 Query: 228 YITCILFVLIVLGGIARAHGFSILRFIRYIREELLIVLGTSSSESALPRMIDKM-EKLGC 286 YI C L +++V + +HG + L+F R + + +SSS +A+P + + LG Sbjct: 241 YIACALHIVVVYSALLLSHGLNPLKFFRGAAPGMQVAFVSSSSFAAMPVALRSITHNLGV 300 Query: 287 NKSVVGLVIPTGYSFNLDGT-SIYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAA 345 NK +P G S +DG +IY + AVFI+Q + PM + +L+ ++ S G A Sbjct: 301 NKDYGSFAVPLGASIKMDGCGAIYPALCAVFISQYSGVPMSPEQYLIVLIASVLGSFGTA 360 Query: 346 GVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNGVATVVVSKWCKQ 405 GV G+ ++ LSA G LP+ + + IDR + R +TN+ G + V+V+K Sbjct: 361 GVPGTAVVMATVVLSAAG-LPLETIGYLYAIDRILDMMRTMTNVTGQMLVPVLVAKETGL 419 Query: 406 LDE 408 LD+ Sbjct: 420 LDQ 422 Lambda K H 0.325 0.140 0.406 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: 535 Number of extensions: 33 Number of successful extensions: 5 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: 436 Length of database: 443 Length adjustment: 32 Effective length of query: 404 Effective length of database: 411 Effective search space: 166044 Effective search space used: 166044 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