Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate BPHYT_RS22120 BPHYT_RS22120 sulfate transporter
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__BFirm:BPHYT_RS22120 Length = 482 Score = 372 bits (956), Expect = e-107 Identities = 207/477 (43%), Positives = 294/477 (61%), Gaps = 14/477 (2%) Query: 22 RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81 + +VLAG+ + AL+PE IAF+++A ++P +GLY +F I ITA GGRPGMIS A G+M Sbjct: 5 KSNVLAGLTSSFALVPECIAFALVAHLNPLMGLYGAFSICAITALFGGRPGMISGAAGSM 64 Query: 82 ALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFM 141 A+++ LV HG QYL A +L+G+L V+FG +L + ++ VP VM+GFVN LAI+I M Sbjct: 65 AVVIVALVVQHGAQYLLATVILSGILMVLFGALRLGKLIRMVPHPVMLGFVNGLAIIIAM 124 Query: 142 AQLPQF-----VGANWQ-------MYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVA 189 AQL F G W M +VA +AI+YLLP + +A P ALVAIV + + Sbjct: 125 AQLAHFRQSTPQGEQWLHGSALLLMCGLVALTMAIVYLLPRLTRAAPPALVAIVGVGLFT 184 Query: 190 VVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLI 249 +T+GDM + LP P VPL +TL ++ P A+ +++VGLLE+LLT L Sbjct: 185 QWLHVPTRTLGDMAHIAGGLPGLHMPDVPLNLDTLHVVLPYAVLMAVVGLLETLLTFNLT 244 Query: 250 DERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFL 309 DE T+T N E G ANI +G FGGM GCAMIGQ+MIN+ SGGR RLS V+G + Sbjct: 245 DEITETRGQPNRECLALGAANIASGLFGGMGGCAMIGQTMINLNSGGRSRLSGIVSGVMI 304 Query: 310 MVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFT 369 ++ IL L PL+ +IP+AALV VM VVA TF WGSLR L P+ + +V++A +TVF+ Sbjct: 305 LMYILFLSPLIERIPLAALVGVMFVVAQQTFAWGSLRVLGKVPRNDALVIVAVTIITVFS 364 Query: 370 HDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDF 429 DL++ VL G+V++A FA + ++ V++ G +TY RG LFF ST F FD Sbjct: 365 -DLAIAVLCGIVIAAFNFAWQHAREIH-AHVEDRAGDKTYAPRGTLFFASTTRFHELFDP 422 Query: 430 THPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLAV 486 RV +D D D SA+ AL ++ ++ + G + ++ L+ + L+ R + Sbjct: 423 VKDPARVTVDCRDLLLADHSALAALQGLVERYRKAGKELRMKNLSDRNKRLLSRAGI 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: 478 Number of extensions: 16 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: 482 Length adjustment: 34 Effective length of query: 465 Effective length of database: 448 Effective search space: 208320 Effective search space used: 208320 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