Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Dsui_1250 Dsui_1250 sulfate permease-like transporter, MFS superfamily
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__PS:Dsui_1250 Length = 555 Score = 374 bits (959), Expect = e-108 Identities = 220/530 (41%), Positives = 322/530 (60%), Gaps = 41/530 (7%) Query: 24 YTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVS 83 Y A+F RD+ AG+TVG++A+PLAMA AI SGV P G++TA VAG +IA GGSR + Sbjct: 15 YDRAQFGRDVSAGLTVGVLALPLAMAFAIASGVDPAAGIWTAIVAGFIIAALGGSRVQIG 74 Query: 84 GPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGI 143 GPT AF+VI+Y + Q+GLA LL+AT+L+G+ LI MGLAR G LI +IPV+V +GFT+GI Sbjct: 75 GPTGAFIVIVYGIVAQYGLANLLIATMLAGLILIGMGLARLGALIRFIPVTVVIGFTNGI 134 Query: 144 GITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFW---- 199 + I QIK+FLGL M +P + K+ L LP ++ A+ +L +LV W Sbjct: 135 AVLIFISQIKEFLGLDMEALPAEFFAKMKVLAANLPNTDLPTLALASASLVLLVLWNKKV 194 Query: 200 ----PRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLP 255 P LG +LPG L L+AG +LL V TIGS+F GIPQ LP Sbjct: 195 AGKLPLLG-KLPGPLAVLIAGTVAQ---SLLEFPVETIGSRF----------GGIPQSLP 240 Query: 256 QLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELV 315 P LT ++R L+ A ++A+LGAIESLL A V D +H N EL+ Sbjct: 241 AFAFP--------ELTLSTLRNLISPAITIALLGAIESLLSARVADSQIDDRHDPNQELL 292 Query: 316 GQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLP 375 QG+ N++AP GG AT AIAR++ NVRAG +P++ ++H++ ++ +LV APL S +P Sbjct: 293 AQGVANVVAPLVGGFAATGAIARTSTNVRAGGRTPVAGMVHALTLLAVVLVAAPLASDVP 352 Query: 376 LSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLAS 435 L+ ++A+L++VAWNM E H+ +L R++ + ++L +TV+FD+ +A+ +G+VLAS Sbjct: 353 LATLSAILMVVAWNMGEWHEFKELPRYS-MNYRAILLSTFFITVVFDLTLAVEIGMVLAS 411 Query: 436 LLFMRRIARMTRLAPVVVDVPD-----DVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIV 490 L F+ R++ +T++AP + +PD V + G LFF A L T L+ +G +++ Sbjct: 412 LFFIYRMSELTKVAP--LSLPDWAAGQPVAAYSLYGSLFFGAVGKLQTLLDQHAQGTQVL 469 Query: 491 ILKWDAVPVLDAGGLDAFQRFVKRLPE--GCELRVCNVEFQPLRTMARAG 538 IL V LD GLD + + L + GC L + + QP ++R+G Sbjct: 470 ILDLHQVINLDTTGLDTLEALQRMLAKRGGC-LILAGLNAQPGSLVSRSG 518 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: 690 Number of extensions: 40 Number of successful extensions: 6 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: 555 Length adjustment: 36 Effective length of query: 523 Effective length of database: 519 Effective search space: 271437 Effective search space used: 271437 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