Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate SM_b20070 SM_b20070 sulfate permease
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__Smeli:SM_b20070 Length = 495 Score = 588 bits (1517), Expect = e-172 Identities = 307/483 (63%), Positives = 374/483 (77%), Gaps = 1/483 (0%) Query: 10 LRQYQREWFANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGG 69 + Y+REWF+N R DVL+GIVVALALIPEAI FS+IAGVDP+VGL+ASF IA ++AF GG Sbjct: 5 ITSYKREWFSNIRGDVLSGIVVALALIPEAIGFSVIAGVDPKVGLFASFAIACVSAFAGG 64 Query: 70 RPGMISAATGAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMV 129 RPGMISAAT A A+LM LVK+HG++YLFAAT+L G+ Q+ G+ KL R ++FV RSV+ Sbjct: 65 RPGMISAATAATAVLMVTLVKEHGLEYLFAATLLMGLFQIAAGFLKLGRVMRFVSRSVIT 124 Query: 130 GFVNALAILIFMAQLPQFVGANWQMYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVA 189 GFVNALAILIFMAQLP+ +G YAM+AAGL IIYL P V KA+PS LVAI VLT V Sbjct: 125 GFVNALAILIFMAQLPELIGVPHLTYAMIAAGLGIIYLFPYVTKAVPSPLVAIAVLTAVD 184 Query: 190 VVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLI 249 TG DV+TVGD+G LP++LP F PQVPLTFETL IIFP ++ L+ VGLLESLLTAQ++ Sbjct: 185 FWTGMDVRTVGDLGALPSSLPIFALPQVPLTFETLQIIFPYSVALAAVGLLESLLTAQIV 244 Query: 250 DERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFL 309 D+ TDTTS K+ E GQG +NI +G GGM GCAMIGQS+INVTSGGRGRLSTFVAGAFL Sbjct: 245 DDMTDTTSSKSQECIGQGASNIASGLIGGMGGCAMIGQSVINVTSGGRGRLSTFVAGAFL 304 Query: 310 MVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFT 369 + LIL L L+ IPMAALVAVM++V++ TF W S+ L P +VVMLATV TV T Sbjct: 305 LFLILVLDDLVRIIPMAALVAVMIMVSVGTFSWRSILDLRRNPLPSSVVMLATVVTTVGT 364 Query: 370 HDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDG-TRTYRVRGQLFFVSTHDFLHQFD 428 HDL+ GVL+GV+LS +FFA KV++L V + E G RTY V GQ+FF ST F+ FD Sbjct: 365 HDLAKGVLVGVLLSGVFFAGKVARLFHVRSMLEESGKVRTYHVDGQIFFASTEGFIGAFD 424 Query: 429 FTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLAVHD 488 F P +VVID+ +AH WD +AVGALDKV+LK+ R G +VE+ GLNAASA +++R AVHD Sbjct: 425 FAEPLEKVVIDVGEAHLWDITAVGALDKVVLKYRRHGVTVEVIGLNAASAHMLDRFAVHD 484 Query: 489 KPD 491 K + Sbjct: 485 KSE 487 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: 574 Number of extensions: 16 Number of successful extensions: 2 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: 495 Length adjustment: 34 Effective length of query: 465 Effective length of database: 461 Effective search space: 214365 Effective search space used: 214365 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