Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate Pf1N1B4_1205 Sulfate permease
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1205 Length = 461 Score = 372 bits (955), Expect = e-107 Identities = 198/460 (43%), Positives = 294/460 (63%), Gaps = 9/460 (1%) Query: 36 IPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAMALLMTGLVKDHGIQ 95 +PE IAF+++A ++P +GLY +FII +TA GGRPGM+S A G+MA+++ LV HG+Q Sbjct: 1 MPECIAFALVAHLNPLMGLYGAFIICTLTALFGGRPGMVSGAAGSMAVVIVALVVQHGVQ 60 Query: 96 YLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFMAQLPQFV-GANW-- 152 YL A +L G++ + FG +L + ++ VP VM+GFVN LAI+I +AQL F G W Sbjct: 61 YLLATVLLGGLIMLAFGLLRLGKLVRMVPHPVMLGFVNGLAIVIALAQLEHFKSGDGWLS 120 Query: 153 -----QMYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVAVVTGADVKTVGDMGTLPT 207 M +VA +AI+YL+P + +A+P ALVAI+ + + + G +T+GDM + Sbjct: 121 GAPLYMMVGLVALTMAIVYLMPRLTRAVPPALVAILGVGLAVYLLGLPTRTLGDMAHIAG 180 Query: 208 ALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLIDERTDTTSDKNVESRGQG 267 +LP F P +P + ETL II P A+ ++LVGLLE+LLT L DE T++ + E G Sbjct: 181 SLPGFALPDIPWSLETLRIIAPYAILMALVGLLETLLTLNLTDEITESRGYPDRECVALG 240 Query: 268 VANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLMVLILALQPLLVQIPMAA 327 AN+V+G FGGM GCAMIGQ+MIN++SGGRGRLS VAG +++ +L L PL+ +IP+AA Sbjct: 241 AANMVSGVFGGMGGCAMIGQTMINLSSGGRGRLSGAVAGIMILLFVLFLSPLIERIPLAA 300 Query: 328 LVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFTHDLSLGVLIGVVLSALFF 387 LV VM VV+ TF W SLR + P + +V++A +TVFT DL++ VL G++++AL F Sbjct: 301 LVGVMFVVSQQTFAWASLRVINKVPLNDVLVIIAVTVITVFT-DLAIAVLCGIIIAALNF 359 Query: 388 ARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFTHPARRVVIDLSDAHFWD 447 A + ++ E DG++ YR+ G LFF ST FL+QFD + +V +D F D Sbjct: 360 AWQQARELYADSYQESDGSKLYRLHGTLFFASTTPFLNQFDPANDPAQVTLDCRHLSFVD 419 Query: 448 GSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLAVH 487 SA+ AL + ++ + G + + L+ L++R + H Sbjct: 420 YSAIAALRTLRERYTKAGKQLRVLHLSERCKKLLKRASEH 459 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: 474 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: 461 Length adjustment: 34 Effective length of query: 465 Effective length of database: 427 Effective search space: 198555 Effective search space used: 198555 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: 51 (24.3 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