Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Ac3H11_3820 Sulfate permease
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3820 Length = 553 Score = 342 bits (877), Expect = 2e-98 Identities = 212/572 (37%), Positives = 320/572 (55%), Gaps = 58/572 (10%) Query: 15 LIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIAL 74 LIDA Y +R+ D+ AG+TVGI+A+PLAMA AI SG+ P+ GL+TA +AG +I+ Sbjct: 11 LIDAL--RGYDKSRWLADVGAGVTVGIVALPLAMAFAIASGLKPEAGLWTAIIAGFLISA 68 Query: 75 TGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVS 134 GG+ + GP AF+VI+Y + +++G+A LL++T +G+ L+L+GL R G L+ ++PVS Sbjct: 69 LGGTNVQIGGPAGAFIVIVYGIVERYGVANLLISTACAGVLLVLLGLFRLGTLVRFVPVS 128 Query: 135 VTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLG 194 + +GFT+GI + I Q+KD+LGL + +P ++ +VG L L + N +G + Sbjct: 129 IVIGFTNGIAVLIALSQVKDWLGLSIERMPGNFFSQVGTLAQHLGSFNPYAFGLGAACVA 188 Query: 195 ILVFWPRL--------------GIRLPGHLPALLAGCAVMGIVN-LLGGHVATIGSQFHY 239 L WP+L +R +PA + + ++ L V TIGS+F Sbjct: 189 GLFLWPKLTMKESPVMRVLEQHTVRSFARVPAPVVALVTLSLLAWALQLPVETIGSRF-- 246 Query: 240 VLADGSQGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVV 299 GIPQ LP LP +W+++R L+ ++A+LGAIESLLCA V Sbjct: 247 --------GGIPQALPVFALP--------DFSWETVRLLVTPTLTIALLGAIESLLCARV 290 Query: 300 LDGMT----GTKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVI 355 D + KH N ELV QGL NI+ PFFGG+ AT IAR+ N+R+GATSP++ ++ Sbjct: 291 ADQLATDPHHKKHDPNQELVAQGLANIVVPFFGGMPATGTIARTVTNIRSGATSPVAGMM 350 Query: 356 HSILVILALLVLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCM 415 H++ + + +LV APL +PL+ +A +LL VAWNM E H+ V L+H ++ML Sbjct: 351 HALTLAVIVLVAAPLALHIPLAVLAGILLFVAWNMGEWHEFV-RLKHFSNHYRLLMLGTF 409 Query: 416 SLTVLFDMVIAISVGIVLASLLFMRRIARMTRLA----PVVVDVP-DDVLVLRVIGPLFF 470 LTV+FD+ +A+ VG+ +A LF+RR++ + R+ P P R+ G LFF Sbjct: 410 FLTVVFDLTVAVEVGLFMACALFVRRMSALFRVERQPDPEAATAPRHPAATWRLHGALFF 469 Query: 471 AAAEGLFTDLESRLEGK--RIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVE 527 AA L T +++ G V+L + LD GLDA + +K + G LR+ ++ Sbjct: 470 GAAAKLDTIIQAVEAGPPGLDVVLDASELVALDTTGLDALAQVLKAVAARGGRLRIEHLH 529 Query: 528 FQPLRTMARAGIQPIPGRLAFFPNRRAAMADL 559 QP + R+G F R AA DL Sbjct: 530 EQPRSLIERSG----------FAARLAAQHDL 551 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: 674 Number of extensions: 31 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