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_035946450.1 N798_RS03995 cation:dicarboxylase symporter family transporter
Query= TCDB::Q1J1H5 (442 letters) >NCBI__GCF_000768675.1:WP_035946450.1 Length = 457 Score = 395 bits (1015), Expect = e-114 Identities = 210/410 (51%), Positives = 283/410 (69%), Gaps = 4/410 (0%) Query: 8 LYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAHMRDTK 67 LY+ V+IA+VLGI VG + P FG LK LG F+ LIKM+I+PIIF T+V GI +R Sbjct: 18 LYIAVIIAMVLGIAVGIIAPDFGVKLKWLGTAFVDLIKMMISPIIFCTIVLGIGSVRRAA 77 Query: 68 KVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYTQAAGEQS 127 +VG+VGG AL YF ++T AL +GL+V NI+KPG G+N+ T + +A + ++ Sbjct: 78 QVGKVGGLALGYFLTMSTVALAVGLLVGNIVKPGAGLNL---TDELAASGQKAVGEEHET 134 Query: 128 VADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEAVNSAVFVI 187 DF+L +IP+TLVSA T G +LQ LL+++L GFAL ++G G+ +L GI + VF + Sbjct: 135 TVDFILGLIPDTLVSALTAGSVLQTLLVALLVGFALQKMGRAGEPILGGIRHLERLVFRL 194 Query: 188 LGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLG-LIARFAGF 246 + +M APIGAFGAMA +G G L LA +MVAFY TC LFVFV+LG L+ G Sbjct: 195 MAMIMYAAPIGAFGAMAAVVGATGWQALKSLALIMVAFYVTCFLFVFVILGALLKAVTGI 254 Query: 247 SILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSFNLDGTSI 306 ++ ++++ E LL+L TSSSESALPRLI K+E+AG +R VVG+ VP GYSFNLDGT+I Sbjct: 255 NVFALLKYLSREFLLILSTSSSESALPRLIAKMEHAGVSRPVVGITVPTGYSFNLDGTAI 314 Query: 307 YLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSAVGHVPVA 366 YLTMA+LFIA+A + S+G+Q+ +L +++ SKGAAGVTG+G TLA L + V Sbjct: 315 YLTMASLFIAEALDKPFSIGEQVSLLLFMIIASKGAAGVTGAGLATLAGGLQSHRPDLVD 374 Query: 367 GLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGE 416 G+ I+GIDR MSEARALTNF GN +AT++I LD +L RVL G+ Sbjct: 375 GVGFIVGIDRMMSEARALTNFAGNSIATVLIGHWVGELDRPKLDRVLAGD 424 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: 530 Number of extensions: 30 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: 457 Length adjustment: 33 Effective length of query: 409 Effective length of database: 424 Effective search space: 173416 Effective search space used: 173416 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