Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate HSERO_RS01545 HSERO_RS01545 sulfate transporter
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__HerbieS:HSERO_RS01545 Length = 496 Score = 379 bits (974), Expect = e-109 Identities = 209/474 (44%), Positives = 293/474 (61%), Gaps = 13/474 (2%) Query: 22 RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81 R++VLAG+ + AL+PE IAF+++A ++P +GLY +F I ITA GGRPGMIS A G+M Sbjct: 17 RQNVLAGLTTSFALVPECIAFALVAQLNPLMGLYGAFFICTITALFGGRPGMISGAAGSM 76 Query: 82 ALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFM 141 A+++ LV HG QY A VL+G++ + FG +L + ++ VP VM+GFVN LAI+I + Sbjct: 77 AVVIVALVVQHGAQYFLATVVLSGLIMLAFGALRLGKLVRMVPHPVMLGFVNGLAIVIAL 136 Query: 142 AQLPQFV------------GANWQMYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVA 189 +QL F A W M A+ A + I++LLP V KA+P AL AI+ + +V Sbjct: 137 SQLEHFRIATAAGTQWLQGSALWVMIALTLATMLIVWLLPRVTKAVPPALAAILGVGLVT 196 Query: 190 VVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLI 249 +G +T+ DM + LP P VPLT ETL II P A+ +++VGLLE+LLT L Sbjct: 197 YASGLHTRTLADMAQIAGGLPPLHLPSVPLTLETLRIIGPYAVLMAIVGLLETLLTFNLT 256 Query: 250 DERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFL 309 DE T T N E G ANIV+G FGGM GCAMIGQ+MIN+ SGGR RLS VAG + Sbjct: 257 DEITATRGQPNRECLALGAANIVSGLFGGMGGCAMIGQTMINLGSGGRSRLSGVVAGVMI 316 Query: 310 MVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFT 369 ++ IL L P + +IP+AAL VM VVA TF WGSLR L P+ + +V++A +TV T Sbjct: 317 LLFILFLSPAIERIPLAALAGVMFVVAQETFAWGSLRVLGKVPRSDALVIIAVTVITVLT 376 Query: 370 HDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDF 429 DL++ VL G+V++AL FA + ++ + DE DG+RTY G LFF ST FL FD Sbjct: 377 -DLAVAVLCGIVIAALNFAWQHAREVRSDVRDEDDGSRTYLPHGTLFFASTTHFLALFDT 435 Query: 430 THPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVER 483 + + V +D D SA+ A+ + ++ R G + + L+ + L++R Sbjct: 436 GNDPQEVTLDCRHLRLADHSAIAAVQTLAERYTRMGKQLRVVALSQRCSQLLQR 489 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: 512 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: 496 Length adjustment: 34 Effective length of query: 465 Effective length of database: 462 Effective search space: 214830 Effective search space used: 214830 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