Align Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate (characterized)
to candidate WP_011781846.1 MVAN_RS23590 C4-dicarboxylate transporter DctA
Query= TCDB::Q1J1H5 (442 letters) >NCBI__GCF_000015305.1:WP_011781846.1 Length = 461 Score = 394 bits (1013), Expect = e-114 Identities = 213/412 (51%), Positives = 283/412 (68%), Gaps = 6/412 (1%) Query: 8 LYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAHMRDTK 67 LY+ V++A+V G+ VG L P G+ + LG F+ LIKM+IAP+IF T+V GI +R Sbjct: 24 LYIAVIVAVVAGVAVGILAPEVGKSVGVLGTMFVALIKMMIAPVIFCTIVLGIGSVRKAA 83 Query: 68 KVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSA--ISKYTQAAGE 125 VG+VGG A +YF V++TFAL IGLVV N+L PG G+ V+ A K +A G Sbjct: 84 TVGKVGGLAFLYFLVMSTFALAIGLVVGNLLHPGSGLQVSDTAAGKGAELADKAHEAGG- 142 Query: 126 QSVADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEAVNSAVF 185 + DF+ IIP T+ S+ TEG +LQ L I++L GFAL LGT G+ +L GIE + VF Sbjct: 143 --LLDFVQGIIPTTMFSSLTEGSVLQALFIALLVGFALQGLGTAGEPILRGIEHLQKLVF 200 Query: 186 VILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGLIARF-A 244 +L ++ LAPIGAFGA+A +G+ G + QL LM+ FY TC +FVF VLG + R + Sbjct: 201 KVLVMILWLAPIGAFGAIANVVGQTGWAAVGQLMALMLGFYLTCAIFVFGVLGALLRVVS 260 Query: 245 GFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSFNLDGT 304 G SI K +R++ E LL++ TSSSESALPRLI K+E+ G +RS VG+VVP GYSFNLDGT Sbjct: 261 GVSIFKLVRYLAREYLLIVSTSSSESALPRLIAKMEHLGVDRSTVGVVVPTGYSFNLDGT 320 Query: 305 SIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSAVGHVP 364 +IYLTMA+LFIA A LSLG+Q+G+L +++ SKGAAGVTG+G TLA L A Sbjct: 321 AIYLTMASLFIAGALGDPLSLGEQIGLLVFMIVASKGAAGVTGAGLATLAGGLQAHRPDL 380 Query: 365 VAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGE 416 + G+ LI+GIDRFMSEARALTNF GN VATL++ + +D +++ VL G+ Sbjct: 381 LDGVGLIVGIDRFMSEARALTNFSGNAVATLLVGSWTRTIDRDKVNSVLAGD 432 Lambda K H 0.325 0.142 0.398 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: 552 Number of extensions: 28 Number of successful extensions: 3 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: 442 Length of database: 461 Length adjustment: 33 Effective length of query: 409 Effective length of database: 428 Effective search space: 175052 Effective search space used: 175052 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