Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate H281DRAFT_01715 H281DRAFT_01715 sulfate permease, SulP family
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Burk376:H281DRAFT_01715 Length = 553 Score = 228 bits (582), Expect = 4e-64 Identities = 169/544 (31%), Positives = 262/544 (48%), Gaps = 57/544 (10%) Query: 32 DLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTAAFVV 91 D+ G+ G++A+PLA+A + SG+ P GLY A V GIV AL GG+ ++GPT + Sbjct: 20 DIFGGVAAGVVALPLALAFGVASGLGPVAGLYGAIVTGIVAALFGGTPVQITGPTGPMTL 79 Query: 92 ILYPV-SQQFGLAGLLVATLLSGIFL------ILMGLARFGRLIEYIPVSVTLGFTSGIG 144 ++ V + +G L+ GIF+ I GL R G I Y+P V GF SGIG Sbjct: 80 VVAGVLAANMHSSGSANLPLVVGIFVVAGFMQIAFGLLRIGSYIRYVPYPVISGFMSGIG 139 Query: 145 ITIGTMQIKDFLGLQMAHVPEHYLQKV-GALFMALPTINVGDAAIGIVTLGILVFWPRLG 203 + I T Q+ G A+ P + L + I A+ T+ I + PR Sbjct: 140 VIIITQQVFPMFG---ANAPGSDPWSILSQLHLLGGNIKWSAVALSASTIAIALLLPRFT 196 Query: 204 IRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLP-WD 262 +P L AL+ ++ L V IG IP LP L +P +D Sbjct: 197 KVIPASLVALIVLTITAVMLKL---DVPVIGE--------------IPSGLPTLTMPAFD 239 Query: 263 LPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNI 322 L + +L+PAA +++LGAI+SLL A+V D +T T+H +N EL+GQGLGNI Sbjct: 240 LHR---------LPSLVPAALQLSLLGAIDSLLTALVADNLTRTRHDSNRELIGQGLGNI 290 Query: 323 IAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAAL 382 A GG+ A R+ NV AG + +S VIH + + LL L+ LL +P + +A L Sbjct: 291 AAAVIGGLPGAGATMRTVVNVDAGGRTRLSGVIHGLFLAAVLLGLSGLLQHVPRAILAGL 350 Query: 383 LLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRI 442 L+ V + + LL+ + D +MLL ++LTV D++IA++ G+V+AS +F++++ Sbjct: 351 LVTVGIGIIDRRSFRHLLK-LSRSDAFLMLLVLALTVFTDLIIAVATGLVVASFVFVKKV 409 Query: 443 ARMTRLAPVVVDVPDD---------------VLVLRVIGPLFFAAAEGLFTDLESRLEGK 487 +T ++ V D+ +L+ V GP+FF A Sbjct: 410 GDITEQRTMLTPVADEPWADELTIPAGLRDRLLIKHVDGPIFFGFASKFLDIARQATLLS 469 Query: 488 RIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGIQP--IPG 544 R+++L+ D + +D G+ A + RL G + V V + R + P +P Sbjct: 470 RLLVLRMDRISYMDQTGVYALDDALVRLNAAGVRVLVVGVSVSQRDLLERLQVIPAVVPE 529 Query: 545 RLAF 548 R F Sbjct: 530 RDIF 533 Lambda K H 0.328 0.142 0.425 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: 709 Number of extensions: 41 Number of successful extensions: 5 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: 559 Length of database: 553 Length adjustment: 36 Effective length of query: 523 Effective length of database: 517 Effective search space: 270391 Effective search space used: 270391 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: 53 (25.0 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