Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate GFF4615 PS417_23615 sulfate transporter
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__WCS417:GFF4615 Length = 481 Score = 387 bits (994), Expect = e-112 Identities = 209/474 (44%), Positives = 299/474 (63%), Gaps = 9/474 (1%) Query: 22 RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81 R D LAG+ + AL+PE IAF+++A ++P +GLY +FII +TA GGRPGM+S A G+M Sbjct: 7 RADALAGLTTSFALLPECIAFALVAHLNPLMGLYGAFIICTLTALFGGRPGMVSGAAGSM 66 Query: 82 ALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFM 141 A+++ LV HG++YL A +L G++ V FG +L + ++ VP VM+GFVN LAI+I + Sbjct: 67 AVVIVALVVQHGVEYLLATVLLGGLIMVAFGLLRLGKLVRMVPHPVMLGFVNGLAIIIAL 126 Query: 142 AQLPQFV-GANWQ-------MYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVAVVTG 193 AQL F G W M +V +AI+YLLP + +A+P ALVAI+ + + + G Sbjct: 127 AQLEHFKSGEQWLSGTPLYVMIGLVLVTMAIVYLLPRITRAVPPALVAILGVGLAVYLLG 186 Query: 194 ADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLIDERT 253 +T+GDM + LP F PQ+P T ETL II P A +++VGLLE+LLT L DE T Sbjct: 187 LPTRTLGDMAHIAGGLPTFSLPQIPWTLETLGIIAPYAFLMAMVGLLETLLTLNLTDEIT 246 Query: 254 DTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLMVLI 313 ++ + ES G AN+V+G FGGM GCAMIGQ++IN++SGGRGRLS AG +++ I Sbjct: 247 ESRGYPDRESVALGAANMVSGLFGGMGGCAMIGQTVINLSSGGRGRLSGVFAGVMILLFI 306 Query: 314 LALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFTHDLS 373 L L P + +IP+AALV VM VV+ TF W SLR + P + +V+LA +TVFT DL+ Sbjct: 307 LFLSPFIERIPLAALVGVMFVVSQQTFAWASLRVINKVPVNDVLVILAVTVITVFT-DLA 365 Query: 374 LGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFTHPA 433 VL G+V++AL FA + ++ E DG++ YRV G LFF ST FL+QFD + Sbjct: 366 TAVLCGIVIAALNFAWQQARELYADEHLEADGSKLYRVHGTLFFASTTPFLNQFDPANDP 425 Query: 434 RRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLAVH 487 +V +D F D SA+ AL + ++ + G + + L+ L++R VH Sbjct: 426 AQVTLDCRHLSFVDYSAIAALMTLRERYTKAGKHLRVLHLSERCKKLLKRAKVH 479 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: 511 Number of extensions: 18 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: 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