Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate 6937849 Sama_1990 sulphate transporter (RefSeq)
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__SB2B:6937849 Length = 518 Score = 391 bits (1004), Expect = e-113 Identities = 222/493 (45%), Positives = 306/493 (62%), Gaps = 30/493 (6%) Query: 19 ANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAAT 78 A+ + D+L+G+ VALAL+PEA+AF+ +AGV+P VGLYA+FI+ L+TA +GGRPGMIS AT Sbjct: 10 ASHKADLLSGLTVALALVPEAVAFAFVAGVEPMVGLYAAFIMGLVTAMIGGRPGMISGAT 69 Query: 79 GAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAIL 138 GAMA++M LV HG+QYLFAA VL G+LQV G KL ++++ VP VM+GFVN LAI+ Sbjct: 70 GAMAVVMVALVATHGVQYLFAAVVLAGLLQVAAGIFKLGKFIRIVPYPVMIGFVNGLAIV 129 Query: 139 IFMAQLPQF--VGAN-----------WQMYAMVAAGLAIIYLLPLVFKAMPSALVAIVVL 185 IF+AQL QF G N + M +VA +AII+ LP + A+PS+L AI+ + Sbjct: 130 IFLAQLGQFKVPGDNGELTWLTGDGLYLMLGLVALTMAIIHFLPKLTTAIPSSLAAILTV 189 Query: 186 TVVAVVTGADVKTV---------GDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSL 236 T + V D +TV D T+ LP F P VP T+ETL II P ++ L+ Sbjct: 190 TGLVVFFELDTRTVVDFLKTMSGDDNATIAGTLPTFAIPHVPFTWETLQIILPYSVILAA 249 Query: 237 VGLLESLLTAQLIDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGG 296 VGL+ESLLT ++DE T T N E GQGV NI +GFFG M GCAMIGQSMIN+ SGG Sbjct: 250 VGLIESLLTLTVLDEMTGTRGRGNKECVGQGVGNITSGFFGAMGGCAMIGQSMININSGG 309 Query: 297 RGRLSTFVAGAFLMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGET 356 RGRLS A L+ IL + IP+AALV VM +V + TF+W S + + PK + Sbjct: 310 RGRLSGITAALALLTFILFGAAFIEIIPLAALVGVMFMVVLGTFEWASFKVMRKVPKHDA 369 Query: 357 VVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLF 416 V++ VTVFT DL++ V +GV++SAL FA + ++ V +G++ Y++ G LF Sbjct: 370 FVIVLVTTVTVFT-DLAVAVFVGVIVSALVFAWEHAKHISARTVINANGSKVYQLSGPLF 428 Query: 417 FVSTHDFLHQFDFTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVEL------ 470 F S FL FD + + V++D + D SA+ A+D + ++ G ++ L Sbjct: 429 FGSVSHFLELFDAANDPKDVIVDFGQSRVADHSALDAIDTLAERYNTLGKTLHLVHLSED 488 Query: 471 -RGLNAASATLVE 482 + L A + LVE Sbjct: 489 CKALLAKAGDLVE 501 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: 589 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 499 Length of database: 518 Length adjustment: 34 Effective length of query: 465 Effective length of database: 484 Effective search space: 225060 Effective search space used: 225060 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