Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate 7025413 Shewana3_2568 sulphate transporter (RefSeq)
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__ANA3:7025413 Length = 519 Score = 392 bits (1006), Expect = e-113 Identities = 227/500 (45%), Positives = 309/500 (61%), Gaps = 30/500 (6%) Query: 8 FDLRQYQREWFANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFL 67 FDL +++ ++ + D+L+G+ VALALIPEA+AF+ +A V+P VGLYA+FI+ L+TA + Sbjct: 2 FDLFRHKT---SSHKADILSGLTVALALIPEAVAFAFVANVEPMVGLYAAFIMGLVTALI 58 Query: 68 GGRPGMISAATGAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSV 127 GGRPGMIS ATGAMA++M LV +HG+QYLFAA VL G++Q+ G KL ++++ VP V Sbjct: 59 GGRPGMISGATGAMAVVMVSLVVEHGVQYLFAAVVLAGLIQISAGIFKLGKFIRIVPYPV 118 Query: 128 MVGFVNALAILIFMAQLPQFVGAN------W-------QMYAMVAAGLAIIYLLPLVFKA 174 M+GFVN LAI+IF+AQL QF N W M +VA +AIIY LP + A Sbjct: 119 MIGFVNGLAIVIFLAQLGQFKVKNAAGELVWLPQEPLMLMLGLVALTMAIIYFLPKLTTA 178 Query: 175 MPSALVAIVVLTVVAVVTGADVKTVG-----------DMGTLPTALPHFQFPQVPLTFET 223 +PS+LVAI L+V A+V G D++T + T+ +LP F PQVP ET Sbjct: 179 VPSSLVAI--LSVTAIVVGFDLETRNVLDFLKTMSGDEHATIAGSLPSFAIPQVPFNLET 236 Query: 224 LAIIFPVALTLSLVGLLESLLTAQLIDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCA 283 L II P + L+ VGL+ESLLT +IDE T+T N E GQGV NI +GFFG M GCA Sbjct: 237 LYIILPYSFILAAVGLIESLLTLTVIDEMTNTRGRSNKECIGQGVGNITSGFFGAMGGCA 296 Query: 284 MIGQSMINVTSGGRGRLSTFVAGAFLMVLILALQPLLVQIPMAALVAVMMVVAISTFDWG 343 MIGQSMIN+ SGGRGRLS A L+ IL + IP+AALV VM +V + TF+W Sbjct: 297 MIGQSMININSGGRGRLSGITAAIGLLTFILFGASFIEIIPLAALVGVMFIVVLGTFEWA 356 Query: 344 SLRTLTVFPKGETVVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEV 403 S + + PK + V++ VTVFT DL+ V +GVV+SAL FA + ++ V Sbjct: 357 SFKFMGKIPKHDAFVIVLVTTVTVFT-DLAFAVFVGVVVSALVFAWQHAKHISVKVTSNS 415 Query: 404 DGTRTYRVRGQLFFVSTHDFLHQFDFTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMR 463 G + Y + G LFF S FL FD + + VVID + D SA+ A+D + +++ Sbjct: 416 LGWKVYELNGPLFFGSVASFLELFDASQDPQDVVIDFKHSRVADHSALEAIDTLAERYVA 475 Query: 464 QGTSVELRGLNAASATLVER 483 G + L L+A L+ + Sbjct: 476 LGKKLHLVHLSADCKALLHK 495 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: 557 Number of extensions: 31 Number of successful extensions: 4 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: 519 Length adjustment: 34 Effective length of query: 465 Effective length of database: 485 Effective search space: 225525 Effective search space used: 225525 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