Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate GFF4056 Psest_4129 Sulfate permease and related transporters (MFS superfamily)
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__psRCH2:GFF4056 Length = 495 Score = 581 bits (1498), Expect = e-170 Identities = 299/494 (60%), Positives = 377/494 (76%), Gaps = 4/494 (0%) Query: 10 LRQYQREWFANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGG 69 L+ ++ WF+N R DVL+G+VVALALIPEAIAFSIIAGVDP+VGLYASF IA++ AF+GG Sbjct: 2 LQSIKQNWFSNIRGDVLSGLVVALALIPEAIAFSIIAGVDPRVGLYASFCIAVVIAFVGG 61 Query: 70 RPGMISAATGAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMV 129 RPGMISAATGAMALLM LV++HG+QYL AAT+L G+LQ+ G+ +L ++FV RSV+ Sbjct: 62 RPGMISAATGAMALLMVTLVREHGLQYLLAATLLCGLLQIGAGYLRLGSLMRFVSRSVVT 121 Query: 130 GFVNALAILIFMAQLPQFVGANWQMYAMVAAGLAIIYLLPLV---FKAMPSALVAIVVLT 186 GFVNALAILIFMAQLP+ W +YAM AAGL IIYL P V K +PS LV I+ +T Sbjct: 122 GFVNALAILIFMAQLPELTNVTWHVYAMTAAGLGIIYLFPYVPKLGKVIPSPLVCILSMT 181 Query: 187 VVAVVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTA 246 VAV G D++TV DMG LP LP F +P+VPLTFETLAIIFP + L++VGLLESL+TA Sbjct: 182 AVAVYFGLDIRTVADMGDLPDTLPVFLWPEVPLTFETLAIIFPYSAALAVVGLLESLMTA 241 Query: 247 QLIDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAG 306 ++D+ TDT+SDKN E +GQGV+NIV+G FGGMAGCAMIGQS+INV SGGR RLST +AG Sbjct: 242 TIVDDLTDTSSDKNRECKGQGVSNIVSGLFGGMAGCAMIGQSVINVKSGGRTRLSTLIAG 301 Query: 307 AFLMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVT 366 L+++++ L + QIPMAALVAVM++V+I TF W SLR L +P +VM+ TV V Sbjct: 302 VVLLLMVVFLSDWVGQIPMAALVAVMIMVSIGTFSWDSLRNLKRYPLSTNIVMVVTVVVV 361 Query: 367 VFTHDLSLGVLIGVVLSALFFARKVSQLSQV-TPVDEVDGTRTYRVRGQLFFVSTHDFLH 425 VFTH+L+ GVL GV+L+A+FFA KV + + +D RTY+V GQ+FF S+ F Sbjct: 362 VFTHNLAYGVLAGVLLAAMFFANKVGHYLHIGSELDATGNQRTYKVIGQVFFSSSDKFTG 421 Query: 426 QFDFTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLA 485 FDF +V IDLS AHFWD +AV ALDKV++KF R+GT VE+ GLN ASAT+V+R Sbjct: 422 AFDFKEALGKVTIDLSRAHFWDITAVAALDKVVIKFRREGTEVEVLGLNEASATIVDRFG 481 Query: 486 VHDKPDALDRMGGH 499 VHDKP+A+D++ H Sbjct: 482 VHDKPEAIDKLMSH 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: 566 Number of extensions: 16 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: 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