Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate AO356_07795 AO356_07795 sulfate transporter
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07795 Length = 481 Score = 374 bits (961), Expect = e-108 Identities = 202/479 (42%), Positives = 301/479 (62%), Gaps = 10/479 (2%) Query: 19 ANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAAT 78 A R D LAG+ + AL+PE IAF+++A ++P +GLY +FI+ +TA GGRPGM+S A Sbjct: 4 ARLRADTLAGLTTSFALLPECIAFALVAHLNPLMGLYGAFILCTLTALFGGRPGMVSGAA 63 Query: 79 GAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAIL 138 G+MA+++ LV HG+QYL A +L G++ + FG +L + ++ VP VM+GFVN LAI+ Sbjct: 64 GSMAVVIVALVVQHGVQYLLATVLLGGLIMMAFGLLRLGKLVRMVPHPVMLGFVNGLAIV 123 Query: 139 IFMAQLPQFV-GANWQ-------MYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVAV 190 I +AQL F G W M +VA +AI+YLLP + +++P ALVAI+ + + Sbjct: 124 IALAQLEHFKNGEAWLSGPPLYLMAGLVALTMAIVYLLPRLTRSVPPALVAILGVGLAVD 183 Query: 191 VTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLID 250 + G +T+GDM + LP F P +P ETL I+ P A+ +++VGLLE+LLT L D Sbjct: 184 LLGLPTRTLGDMAHIAGGLPTFALPDIPWNLETLQIVAPYAVIMAMVGLLETLLTLNLTD 243 Query: 251 ERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLM 310 E T++ + E G AN+ +G GGM GCAMIGQ+MIN++SGGRGRLS VAG ++ Sbjct: 244 EITESRGYPDRECVALGAANMASGLLGGMGGCAMIGQTMINLSSGGRGRLSGVVAGVMVL 303 Query: 311 VLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFTH 370 + +L L PL+ +IP+AALV VM VV+ TF W SLR + P + +V++A +TVFT Sbjct: 304 LFVLFLSPLIERIPLAALVGVMFVVSQQTFAWASLRVVNKVPANDVLVIIAVTVITVFT- 362 Query: 371 DLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFT 430 DL++ VL G++++AL FA + ++ +E DG++ YR+ G LFF S+ FL+QFD Sbjct: 363 DLAVAVLCGIIIAALNFAWQQARELYADTHEEADGSKLYRLHGTLFFASSTPFLNQFDPA 422 Query: 431 HPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLAV-HD 488 + V +D F D SAV AL + ++ + G + + L+ +++R V HD Sbjct: 423 NDPALVTLDCRHLRFVDYSAVAALKTLRERYSKAGKHLRVFHLSERCKQMLKRAGVQHD 481 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: 492 Number of extensions: 13 Number of successful extensions: 3 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: 481 Length adjustment: 34 Effective length of query: 465 Effective length of database: 447 Effective search space: 207855 Effective search space used: 207855 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