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 HSERO_RS22690 HSERO_RS22690 C4-dicarboxylate ABC transporter
Query= TCDB::Q1J1H5 (442 letters) >FitnessBrowser__HerbieS:HSERO_RS22690 Length = 444 Score = 453 bits (1166), Expect = e-132 Identities = 235/425 (55%), Positives = 310/425 (72%), Gaps = 3/425 (0%) Query: 3 KIFRSLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAH 62 K+F+SL+ QV++A++ GI++G +P FG+ LKPLGDGFIKLIKM+I I+F VV GI Sbjct: 3 KLFKSLFGQVVLALIGGIIIGLFWPDFGQNLKPLGDGFIKLIKMIIPVIVFCVVVQGICG 62 Query: 63 MRDTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYTQA 122 D KKVG VG KA+IYFEVVTT AL++GLV+A +++PG GMN++P+ LD S++S Y Sbjct: 63 ASDLKKVGSVGVKAIIYFEVVTTIALLLGLVLALVVQPGAGMNIDPSNLDASSLSGYMAN 122 Query: 123 AG---EQSVADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEA 179 AG E A+F++ +IP T VSAFT GD+LQVLLISV FG AL +G G V+A + + Sbjct: 123 AGKVKETGFAEFIMKLIPATAVSAFTSGDVLQVLLISVTFGCALLLIGEKGAPVVALVAS 182 Query: 180 VNSAVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGL 239 ++ A F + F +RLAP+G GA+AFT+GKYG+G+L QLA L++ FY + FV VVLG Sbjct: 183 LSDAFFKCMSFFIRLAPLGVLGAIAFTVGKYGIGSLKQLALLVLLFYGAVIFFVLVVLGG 242 Query: 240 IARFAGFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSF 299 I R +G SI K IR+++EEL++VL T+SS+S LP+++ KLE+ G +S VGLV+P GYSF Sbjct: 243 ILRASGLSIFKLIRYLREELVVVLATTSSDSVLPQIMKKLEHMGIKKSTVGLVIPTGYSF 302 Query: 300 NLDGTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSA 359 NLD SIYLTMA LFIAQATNTHLS+G IL + L+TSKGA GV GS + LAATL+ Sbjct: 303 NLDAFSIYLTMAALFIAQATNTHLSMGDLAAILAIALVTSKGAHGVPGSAIVILAATLTT 362 Query: 360 VGHVPVAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGEVLP 419 + +PV GL L+L ID F+ ARAL N +GN VAT+VIA E+ +D R + VLNGE + Sbjct: 363 IPAIPVVGLVLVLSIDWFIGIARALGNLLGNCVATVVIASWERDIDKVRARAVLNGESVA 422 Query: 420 PATPE 424 P E Sbjct: 423 PLVEE 427 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: 551 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: 444 Length adjustment: 32 Effective length of query: 410 Effective length of database: 412 Effective search space: 168920 Effective search space used: 168920 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 17 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