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 RR42_RS19790 RR42_RS19790 C4-dicarboxylate ABC transporter
Query= TCDB::Q1J1H5 (442 letters) >FitnessBrowser__Cup4G11:RR42_RS19790 Length = 473 Score = 457 bits (1175), Expect = e-133 Identities = 234/418 (55%), Positives = 306/418 (73%), Gaps = 3/418 (0%) Query: 3 KIFRSLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAH 62 + FRSL+ QVL+A+VLG +G LFP F LKPLGD FIKLIKMLI PI+F VV+GI Sbjct: 23 RFFRSLFGQVLVALVLGTALGLLFPEFAAKLKPLGDAFIKLIKMLIGPIVFCVVVAGICG 82 Query: 63 MRDTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSAISKYTQA 122 + KKVGRVG KA++YFEVVTT AL +G+ +A I PG GMNVNPA+LD SA+S Y Sbjct: 83 AGELKKVGRVGIKAVLYFEVVTTIALALGIALAYIFHPGTGMNVNPASLDASAMSAYVDT 142 Query: 123 AGEQSVA---DFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKVLAGIEA 179 A + A DFLL +IP+T++ AF GD+LQVLL+S+LFG AL+ +G GQ ++ I+ Sbjct: 143 AQKVKSAGMVDFLLKLIPSTVMGAFASGDVLQVLLVSILFGCALSLVGERGQPLVTIIDT 202 Query: 180 VNSAVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGL 239 + +F ++GF+++LAP+G GA+AFT+GKYG+G+L QL YL++ FY LFV VVLG Sbjct: 203 FSHTLFKMMGFIIKLAPLGVLGAVAFTVGKYGIGSLKQLGYLVLVFYGAVALFVMVVLGT 262 Query: 240 IARFAGFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSF 299 + R GFS+ K IR+++ ELL+VLGT+SS+S LP+++ KLE+ G +SVVGLV+P GYSF Sbjct: 263 VMRLCGFSVFKLIRYLRAELLVVLGTASSDSVLPQVMKKLEFLGIKKSVVGLVIPTGYSF 322 Query: 300 NLDGTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSA 359 NLD SIYLT+A +FIAQATNT L+LG LGIL V L+TSKGA G+ GS + LAATLSA Sbjct: 323 NLDAFSIYLTLAAVFIAQATNTPLALGDLLGILAVALVTSKGAHGIPGSAIVILAATLSA 382 Query: 360 VGHVPVAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGEV 417 +P GL L+L +D F+ ARA+ N +GN VAT+V+A EK +D R VLNG + Sbjct: 383 HPAIPAIGLVLVLSVDWFIGIARAVGNLIGNCVATVVVAAWEKDIDRARAHDVLNGRI 440 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: 611 Number of extensions: 29 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: 473 Length adjustment: 33 Effective length of query: 409 Effective length of database: 440 Effective search space: 179960 Effective search space used: 179960 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