Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 8501284 DvMF_2017 sulfate transporter (RefSeq)
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Miya:8501284 Length = 730 Score = 244 bits (622), Expect = 1e-68 Identities = 172/549 (31%), Positives = 290/549 (52%), Gaps = 58/549 (10%) Query: 24 YTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVS 83 Y+ D++A +TV ++A+P +MA A+ +GV P+YGLY A V IV AL G SR+ V+ Sbjct: 120 YSMQVLRADVLAALTVAVVALPQSMAYAVIAGVHPKYGLYAAIVPVIVAALWGASRYLVA 179 Query: 84 GPTAAFVVILY-----------PVS---QQFGLAGLLVATLLSGIFLILMGLARFGRLIE 129 GPT A ++L+ P+S ++ +A + +L+G+ +LMGLAR G L+ Sbjct: 180 GPTNAIAMLLFATMAETVVNGVPLSALPEETRMAYVFGVAILAGLLQVLMGLARLGELVH 239 Query: 130 YIPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIG 189 +I SV +GFT+G + I Q+K+ LG+ + + P +++ V + LP N G Sbjct: 240 FISHSVMVGFTAGAAVLIAVGQLKNLLGVSIGNAPT-FVELVLSTLRHLPRTNPWALGTG 298 Query: 190 IVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNG 249 + + + + R+ RLP A+ A ++L V +G+ Sbjct: 299 LFAMAVALGIARVHRRLPAAFLAVAASGVAAWALDLGAHGVKVVGA-------------- 344 Query: 250 IPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHK 309 IP LP LP P+++ +R L A ++A+LG +E+L A L G G + Sbjct: 345 IPAGLPPFSLP-PAPDAQV------MRDLFMPALAIALLGVVEALSIAKTLAGARGEQVD 397 Query: 310 ANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAP 369 + E V QGL NI A F GI + + RSA N AGA + + + ++ +LA+L+LAP Sbjct: 398 GSREFVAQGLANIAAGLFSGIPGSGSFTRSAVNFVAGARTRFAGALSGVITLLAVLLLAP 457 Query: 370 LLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISV 429 L +++P++A+A +L+++AW M + H + L+ A + D V+L+ + T+L D+ A+ V Sbjct: 458 LAAYIPIAALAGILMIIAWGMVDKHGIALALK-ATRADRTVLLVTFAATLLLDLEKAVFV 516 Query: 430 GIVLASLLFMRRIAR--MTRL----APVVVDVP-----DDVLVLRVIGPLFFAAAEGLFT 478 G++L+ +LF+R+++ +TR+ +P + +P ++ V + G LFF A + Sbjct: 517 GVLLSLVLFLRKVSHPLVTRMDTCDSPELQGLPAGPCCPNLAVYSIEGTLFFGAVD---- 572 Query: 479 DLESRLE-----GKRIVILKWDAVPVLDAGGLDAFQRFVKRLP-EGCELRVCNVEFQPLR 532 +LE RL G R VIL V +DA G+ AFQ+F+++ G L + V+ Sbjct: 573 ELEQRLYEYEDFGHRAVILHLRQVHWVDATGVHAFQQFLRKCQRRGVALVLSGVKPAVRA 632 Query: 533 TMARAGIQP 541 R+G+ P Sbjct: 633 VFERSGLVP 641 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: 821 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 559 Length of database: 730 Length adjustment: 38 Effective length of query: 521 Effective length of database: 692 Effective search space: 360532 Effective search space used: 360532 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: 54 (25.4 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