Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate PP_4112 PP_4112 Sulphate transporter
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__Putida:PP_4112 Length = 486 Score = 373 bits (957), Expect = e-108 Identities = 204/473 (43%), Positives = 298/473 (63%), Gaps = 9/473 (1%) Query: 19 ANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAAT 78 A R D+LAG+ + AL+PE IAF+++A ++P +GLY +FII +TA GGRPGMIS A Sbjct: 10 ARLRADLLAGLTTSFALVPECIAFALVAHLNPLMGLYGAFIICTLTALFGGRPGMISGAA 69 Query: 79 GAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAIL 138 G+MA+++ LV HG+QYL A +L GV+ ++FG +L + ++ VP VM+GFVN LAI+ Sbjct: 70 GSMAVVIVALVVQHGVQYLLATVLLGGVVMILFGLLRLGKLVRLVPYPVMLGFVNGLAIV 129 Query: 139 IFMAQLPQFV-GANWQ-------MYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVAV 190 I MAQL F G +W M +VA +A++Y+LP + +A+P ALVAI+ + +V Sbjct: 130 IAMAQLEHFKDGEHWLSGTPLYLMIGLVALTMAVVYVLPKLTRAVPPALVAILGVGLVVY 189 Query: 191 VTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLID 250 V G +T+GDM + LP P VP ETL II P A+ +++VGLLE+LLT L D Sbjct: 190 VLGLPTRTLGDMAHIAGGLPGLALPDVPWNLETLKIIAPYAVLMAMVGLLETLLTLNLTD 249 Query: 251 ERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLM 310 E T++ + E G AN+V+G GGM GCAMIGQ++IN++S GRGRLS VAG ++ Sbjct: 250 EITESRGFPDRECVALGAANMVSGLCGGMGGCAMIGQTVINLSSNGRGRLSGVVAGVMIL 309 Query: 311 VLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTVFTH 370 + +L L PL+ +IP+AALV VM VVA TF W SLR L P + + ++A VTV T Sbjct: 310 LFVLFLSPLIERIPLAALVGVMFVVAQQTFAWASLRVLHKVPVNDVLAIVAVTVVTVLT- 368 Query: 371 DLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFT 430 DL++ VL G++++AL FA + ++ ++ +G + Y++ G LFF ST FL+QFD Sbjct: 369 DLAMAVLFGIIIAALNFAWQHARELYADTHEDAEGGKCYQLHGTLFFASTTSFLNQFDTA 428 Query: 431 HPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVER 483 +V +D F D SAV AL + ++ + G + + L+ L++R Sbjct: 429 GDPAQVTLDCQHLSFVDYSAVAALKTLRERYAKAGKHLRVVHLSERCKKLLKR 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: 490 Number of extensions: 19 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: 486 Length adjustment: 34 Effective length of query: 465 Effective length of database: 452 Effective search space: 210180 Effective search space used: 210180 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