Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate Dsui_1250 Dsui_1250 sulfate permease-like transporter, MFS superfamily
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__PS:Dsui_1250 Length = 555 Score = 250 bits (638), Expect = 1e-70 Identities = 162/517 (31%), Positives = 268/517 (51%), Gaps = 45/517 (8%) Query: 10 LRQYQREWFANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGG 69 L Y R F +DV AG+ V + +P A+AF+I +GVDP G++ + + I A LGG Sbjct: 12 LPDYDRAQFG---RDVSAGLTVGVLALPLAMAFAIASGVDPAAGIWTAIVAGFIIAALGG 68 Query: 70 RPGMISAATGAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMV 129 I TGA +++ G+V +G+ L AT+L G++ + G A+L ++F+P +V++ Sbjct: 69 SRVQIGGPTGAFIVIVYGIVAQYGLANLLIATMLAGLILIGMGLARLGALIRFIPVTVVI 128 Query: 130 GFVNALAILIFMAQLPQFVGANWQ-----------------------MYAMVAAGLAIIY 166 GF N +A+LIF++Q+ +F+G + + A+ +A L ++ Sbjct: 129 GFTNGIAVLIFISQIKEFLGLDMEALPAEFFAKMKVLAANLPNTDLPTLALASASLVLLV 188 Query: 167 L--------LPLVFKAMPSALVAIVVLTVVAVVTGADVKTVGD-MGTLPTALPHFQFPQV 217 L LPL+ K +P L ++ TV + V+T+G G +P +LP F FP+ Sbjct: 189 LWNKKVAGKLPLLGK-LPGPLAVLIAGTVAQSLLEFPVETIGSRFGGIPQSLPAFAFPE- 246 Query: 218 PLTFETLAIIFPVALTLSLVGLLESLLTAQLIDERTDTTSDKNVESRGQGVANIVTGFFG 277 LT TL + A+T++L+G +ESLL+A++ D + D D N E QGVAN+V G Sbjct: 247 -LTLSTLRNLISPAITIALLGAIESLLSARVADSQIDDRHDPNQELLAQGVANVVAPLVG 305 Query: 278 GMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLMVLILALQPLLVQIPMAALVAVMMVVAI 337 G A I ++ NV +GGR ++ V L+ ++L PL +P+A L A++MVVA Sbjct: 306 GFAATGAIARTSTNVRAGGRTPVAGMVHALTLLAVVLVAAPLASDVPLATLSAILMVVAW 365 Query: 338 STFDWGSLRTLTVFPKGETVVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQLSQV 397 + +W + L + ++L+T +TV DL+L V IG+VL++LFF ++S+L++V Sbjct: 366 NMGEWHEFKELPRYSMNYRAILLSTFFITV-VFDLTLAVEIGMVLASLFFIYRMSELTKV 424 Query: 398 TPVDEVD-----GTRTYRVRGQLFFVSTHDFLHQFD-FTHPARRVVIDLSDAHFWDGSAV 451 P+ D Y + G LFF + D + +++DL D + + Sbjct: 425 APLSLPDWAAGQPVAAYSLYGSLFFGAVGKLQTLLDQHAQGTQVLILDLHQVINLDTTGL 484 Query: 452 GALDKVMLKFMRQGTSVELRGLNAASATLVERLAVHD 488 L+ + ++G + L GLNA +LV R D Sbjct: 485 DTLEALQRMLAKRGGCLILAGLNAQPGSLVSRSGFAD 521 Lambda K H 0.328 0.140 0.407 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: 598 Number of extensions: 32 Number of successful extensions: 5 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: 499 Length of database: 555 Length adjustment: 35 Effective length of query: 464 Effective length of database: 520 Effective search space: 241280 Effective search space used: 241280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 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