Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate 3608674 Dshi_2067 sulphate transporter (RefSeq)
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__Dino:3608674 Length = 534 Score = 403 bits (1036), Expect = e-117 Identities = 215/466 (46%), Positives = 302/466 (64%), Gaps = 14/466 (3%) Query: 22 RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81 R ++L+G+ VALAL+PEA+AF+ +AGV P VGLYA+FI+ LITA +GGRPGMIS ATGA+ Sbjct: 30 RIELLSGLTVALALVPEAVAFAFVAGVHPLVGLYAAFIVGLITALIGGRPGMISGATGAL 89 Query: 82 ALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFM 141 A++M LV +HG++YLFA VL G+LQ++FG KL ++++ VP VM+GFVN LAI+IF+ Sbjct: 90 AVVMVALVAEHGVEYLFATVVLMGILQILFGIFKLGKFIRLVPHPVMLGFVNGLAIVIFL 149 Query: 142 AQLPQFVGAN------WQ-------MYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVV 188 AQL QF N W M +VA +AII+ +P + + +P+ L I ++ V+ Sbjct: 150 AQLTQFKVPNDAGEMVWMTGWPLVIMLGLVALTMAIIWGMPKITRVIPAPLAGIGIVAVL 209 Query: 189 AVVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQL 248 + G DV VGD+ ++ LP P VPL ETL II P A L+ +GL+ESLLT L Sbjct: 210 VIAFGIDVPRVGDLASIAGGLPSLHIPMVPLNMETLQIIAPYAFILAAIGLIESLLTLNL 269 Query: 249 IDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAF 308 + E T + E QGVAN VTGFFGGM GCAMIGQSMINV SGGR R++ A F Sbjct: 270 VGEITGKRGGASQECIAQGVANTVTGFFGGMGGCAMIGQSMINVKSGGRTRIAGVAAALF 329 Query: 309 LMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVF 368 L++ I+A PL+ QIP+AALV VM +V I TF W SL L P + +V++ VTV Sbjct: 330 LLLFIVAASPLIEQIPLAALVGVMFMVVIGTFAWQSLTILRRVPLTDALVIVLVTVVTVL 389 Query: 369 THDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFD 428 T DL++ V++GV++SAL +A + +G + Y+V+G LFF S+ F+ FD Sbjct: 390 T-DLAIAVVVGVIVSALAYAWNNASRIHAKTYTTPEGAKVYQVQGPLFFGSSAGFVELFD 448 Query: 429 FTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLN 474 TH +V++D +D+ D SA+ A++ + K+ G +++LR L+ Sbjct: 449 VTHDPGQVIVDFADSRVVDQSALTAIEAMAAKYADAGKNLQLRHLS 494 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: 607 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: 499 Length of database: 534 Length adjustment: 35 Effective length of query: 464 Effective length of database: 499 Effective search space: 231536 Effective search space used: 231536 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