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_012386365.1 BIND_RS17555 C4-dicarboxylate transporter DctA
Query= TCDB::Q1J1H5 (442 letters) >NCBI__GCF_000019845.1:WP_012386365.1 Length = 439 Score = 449 bits (1155), Expect = e-131 Identities = 218/417 (52%), Positives = 307/417 (73%), Gaps = 1/417 (0%) Query: 4 IFRSLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAHM 63 +F+ LY+QV++A++ G ++GF++PSF GLKPL D FI LI+M++ P+IF TVV GIA M Sbjct: 3 LFKHLYIQVIVAVLCGAILGFVWPSFASGLKPLSDVFINLIRMVLLPVIFGTVVLGIARM 62 Query: 64 RDTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYTQAA 123 + +++GRVG KAL YFE+ +T AL+IG+VV NI++PG G++ +P TLD +IS+YT+A Sbjct: 63 ENMRELGRVGAKALAYFEIASTLALIIGMVVVNIVRPGTGIHADPLTLDAESISQYTKAV 122 Query: 124 GEQS-VADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEAVNS 182 E + + DFL+HI+P+ +V +F G++LQVL S+L G AL + G + + +E++ Sbjct: 123 AEHAGLVDFLVHIVPSNIVESFASGNILQVLFFSLLLGIALAKAGDAARPFVCTLESLLD 182 Query: 183 AVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGLIAR 242 +F I+ VMR AP+GA GAMAFTI KYG+G+LA + ++V YATCLLF + GLIAR Sbjct: 183 GIFHIVSMVMRFAPLGALGAMAFTISKYGLGSLASMGLVLVCVYATCLLFAILSFGLIAR 242 Query: 243 FAGFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSFNLD 302 GFS +F+R+I++E++ V GT SSES LPRL+ KLE AG R+VVGLV+P G +FN Sbjct: 243 LVGFSAFRFLRYIRDEIVTVFGTCSSESVLPRLMQKLEMAGVPRTVVGLVLPGGLTFNAC 302 Query: 303 GTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSAVGH 362 G++IY T+ LFIAQAT+T LS+ QL ILGVL+LTSKG+AGV G+GF+TLAATL A+ Sbjct: 303 GSAIYFTIGALFIAQATDTSLSMVDQLAILGVLMLTSKGSAGVAGAGFVTLAATLGALHK 362 Query: 363 VPVAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGEVLP 419 +PV+GL L+LG+DRFM+EAR++TN + N + +A E LD +L L GE+ P Sbjct: 363 IPVSGLVLLLGVDRFMAEARSVTNTISNAFGAVAVAAWEGVLDREKLAAALRGELEP 419 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: 532 Number of extensions: 25 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: 442 Length of database: 439 Length adjustment: 32 Effective length of query: 410 Effective length of database: 407 Effective search space: 166870 Effective search space used: 166870 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