Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate H281DRAFT_01715 H281DRAFT_01715 sulfate permease, SulP family
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__Burk376:H281DRAFT_01715 Length = 553 Score = 243 bits (619), Expect = 2e-68 Identities = 158/511 (30%), Positives = 257/511 (50%), Gaps = 52/511 (10%) Query: 22 RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81 R D+ G+ + +P A+AF + +G+ P GLY + + ++ A GG P I+ TG M Sbjct: 18 RGDIFGGVAAGVVALPLALAFGVASGLGPVAGLYGAIVTGIVAALFGGTPVQITGPTGPM 77 Query: 82 ALLMTGLVKDH-------GIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNA 134 L++ G++ + + + V+ G +Q+ FG ++ Y+++VP V+ GF++ Sbjct: 78 TLVVAGVLAANMHSSGSANLPLVVGIFVVAGFMQIAFGLLRIGSYIRYVPYPVISGFMSG 137 Query: 135 LAILIFMAQLPQFVGAN---------------------WQMYAMVAAGLAIIYLLPLVFK 173 + ++I Q+ GAN W A+ A+ +AI LLP K Sbjct: 138 IGVIIITQQVFPMFGANAPGSDPWSILSQLHLLGGNIKWSAVALSASTIAIALLLPRFTK 197 Query: 174 AMPSALVAIVVLTVVAVVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALT 233 +P++LVA++VLT+ AV+ DV +G+ +P+ LP P L L + P AL Sbjct: 198 VIPASLVALIVLTITAVMLKLDVPVIGE---IPSGLPTLTMPAFDL--HRLPSLVPAALQ 252 Query: 234 LSLVGLLESLLTAQLIDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVT 293 LSL+G ++SLLTA + D T T D N E GQG+ NI GG+ G ++++NV Sbjct: 253 LSLLGAIDSLLTALVADNLTRTRHDSNRELIGQGLGNIAAAVIGGLPGAGATMRTVVNVD 312 Query: 294 SGGRGRLSTFVAGAFLMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPK 353 +GGR RLS + G FL ++L L LL +P A L +++ V I D S R L + Sbjct: 313 AGGRTRLSGVIHGLFLAAVLLGLSGLLQHVPRAILAGLLVTVGIGIIDRRSFRHLLKLSR 372 Query: 354 GETVVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQLSQ----VTPV------DEV 403 + +ML +A+TVFT DL + V G+V+++ F +KV +++ +TPV DE+ Sbjct: 373 SDAFLMLLVLALTVFT-DLIIAVATGLVVASFVFVKKVGDITEQRTMLTPVADEPWADEL 431 Query: 404 -------DGTRTYRVRGQLFFVSTHDFLH-QFDFTHPARRVVIDLSDAHFWDGSAVGALD 455 D V G +FF FL T +R +V+ + + D + V ALD Sbjct: 432 TIPAGLRDRLLIKHVDGPIFFGFASKFLDIARQATLLSRLLVLRMDRISYMDQTGVYALD 491 Query: 456 KVMLKFMRQGTSVELRGLNAASATLVERLAV 486 +++ G V + G++ + L+ERL V Sbjct: 492 DALVRLNAAGVRVLVVGVSVSQRDLLERLQV 522 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: 546 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 499 Length of database: 553 Length adjustment: 35 Effective length of query: 464 Effective length of database: 518 Effective search space: 240352 Effective search space used: 240352 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