Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate PfGW456L13_5136 Sulfate permease
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5136 Length = 481 Score = 377 bits (967), Expect = e-109 Identities = 204/476 (42%), Positives = 300/476 (63%), Gaps = 10/476 (2%) Query: 22 RKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAM 81 R DVLAG+ + AL+PE IAF+++A ++P +GLY +FII +TA GGRPGM+S A G+M Sbjct: 7 RADVLAGLTTSFALLPECIAFALVAHLNPLMGLYGAFIICTLTALFGGRPGMVSGAAGSM 66 Query: 82 ALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFM 141 A+++ LV HG+QYL A +L G++ + FG KL + ++ VP VM+GFVN LAI+I + Sbjct: 67 AVVIVALVVQHGVQYLLATVLLGGLIMIAFGLLKLGKLVRMVPYPVMLGFVNGLAIVIAL 126 Query: 142 AQLPQFV-GANW-------QMYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVAVVTG 193 AQL F G W M +VA +A++Y++P + + +P ALVAI+ + + + G Sbjct: 127 AQLEHFKNGEAWLSGTPLYMMLGLVAVTMAVVYVMPRLTRTVPPALVAILGVGLAVYLLG 186 Query: 194 ADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLIDERT 253 +T+GDM + LP P + +TL II P A+ ++LVGLLE+LLT L DE T Sbjct: 187 LPTRTLGDMAHIAGGLPTLALPDIAWNLDTLRIIAPYAIVMALVGLLETLLTLNLTDEFT 246 Query: 254 DTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLMVLI 313 ++ + E G AN+V+G FGGM GCAMIGQ++IN++SGGRGRLS VAG +++ I Sbjct: 247 ESRGYPDRECVALGAANLVSGAFGGMGGCAMIGQTVINLSSGGRGRLSGVVAGVSILLFI 306 Query: 314 LALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFTHDLS 373 L L PL+ +IP+AALV VM VV+ TF W SLR L P + +V++A +TVFT DL+ Sbjct: 307 LFLSPLIERIPLAALVGVMFVVSQQTFAWASLRVLNKVPLNDVLVIIAVTVITVFT-DLA 365 Query: 374 LGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFTHPA 433 + VL G++++AL FA + ++ E DG++ YRV G LFF ST FL+QFD + Sbjct: 366 MAVLCGIIIAALNFAWQQARQLYADSHLETDGSKLYRVHGTLFFASTTPFLNQFDPANDP 425 Query: 434 RRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERLAV-HD 488 +V +D F D SA+ AL + ++ + G + + L+ L++R + HD Sbjct: 426 AQVTLDCQHLSFVDYSAIAALGTLRERYTKAGKHLRVLHLSERCKKLLKRARMQHD 481 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: 472 Number of extensions: 12 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: 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