Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate Echvi_3031 Echvi_3031 Sulfate permease and related transporters (MFS superfamily)
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__Cola:Echvi_3031 Length = 512 Score = 410 bits (1055), Expect = e-119 Identities = 216/475 (45%), Positives = 304/475 (64%), Gaps = 13/475 (2%) Query: 22 RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81 + +VL+G VALAL+PEA+AFS IA V P VGLY++F I LITA LGGRPGMIS ATGA+ Sbjct: 17 KDEVLSGFTVALALVPEAVAFSFIAQVSPLVGLYSAFFIGLITAILGGRPGMISGATGAI 76 Query: 82 ALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFM 141 A+++ LV HG++YLFAA VL G++QV+ G KL + ++ VP VM GFVN LA++IF Sbjct: 77 AVVVVALVVTHGVEYLFAAVVLMGIIQVLVGVLKLGKLIRLVPHPVMYGFVNGLAVIIFT 136 Query: 142 AQLPQFVGAN-------------WQMYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVV 188 +Q QF W M A+V + II LP V K +PSAL AI+V++ + Sbjct: 137 SQFEQFKIETSPGVKEWISGPPLWIMLALVVLTMVIIKFLPKVTKIIPSALAAILVISGI 196 Query: 189 AVVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQL 248 + D +TVGDM ++ LP F P VPL +ET II P + ++ VGL+ESLLT L Sbjct: 197 VIFGNIDTRTVGDMASISGGLPEFHLPMVPLNWETFMIILPYSAIMAGVGLIESLLTLTL 256 Query: 249 IDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAF 308 +DE T+T + N E QGVAN+ TGFFGGM GCAMIGQS+INV +GGR R+S +A Sbjct: 257 VDEITETRGNGNKECIAQGVANVTTGFFGGMGGCAMIGQSLINVNAGGRNRISGIIAACG 316 Query: 309 LMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVF 368 L+ IL + IPMAALV +M +VAI TF+W SL+ P + +VM+ + VTVF Sbjct: 317 LLTFILFFSSYIEMIPMAALVGLMFMVAIGTFEWASLKIFKKVPASDVLVMIVVMLVTVF 376 Query: 369 THDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFD 428 H+L+L VL+GV+++AL FA + S++ + + +G + Y + G LFF S F +FD Sbjct: 377 LHNLALAVLVGVIIAALVFAWENSKMIRARKRVDENGVKHYEIYGPLFFASAQAFGEKFD 436 Query: 429 FTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVER 483 + ++ID +++ D S + A+ KV ++ + G +V +R L+ +S TL+E+ Sbjct: 437 PVNDPDEIIIDFAESRIVDHSGIDAVHKVTERYDKAGKTVYIRHLSTSSKTLLEK 491 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: 535 Number of extensions: 21 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: 512 Length adjustment: 34 Effective length of query: 465 Effective length of database: 478 Effective search space: 222270 Effective search space used: 222270 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