Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_013460100.1 SULKU_RS06260 sodium-independent anion transporter
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_000183725.1:WP_013460100.1 Length = 555 Score = 359 bits (921), Expect = e-103 Identities = 204/507 (40%), Positives = 315/507 (62%), Gaps = 35/507 (6%) Query: 21 KEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRF 80 ++ Y+ + F D +AG+ V I+A+PLAMA+AI S + P+ GL+TA VAG +I+ GGSR+ Sbjct: 19 RQGYSRSDFIADAVAGLAVAIVALPLAMAIAIASNLPPERGLFTAIVAGFLISAHGGSRY 78 Query: 81 SVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFT 140 + GPTAAF+V + V+ + G GL++AT+++G LI+M R G LI++IP V +GFT Sbjct: 79 QIGGPTAAFIVTVAMVAMKHGYEGLVLATIMAGAILIIMAFLRAGELIKFIPYPVIVGFT 138 Query: 141 SGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWP 200 SGI + I QI+DF GL++ VP ++ K+ L N + ++++G++ Sbjct: 139 SGIALLIAFSQIRDFFGLKITTVPPDFIDKLSIYVAHLHETNFTAVLLALISIGVIYIAK 198 Query: 201 RLGIRLPGHLPAL-LAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVL 259 R+PG + + L+ AV G NL V TI S+F IP +LP V Sbjct: 199 HRFPRIPGPIIVVTLSAFAVWGF-NL---PVETIESRF----------GSIPSMLPSPVW 244 Query: 260 PWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGL 319 P +T++ +R LLP A ++A L AIESLL AVV DGMTGT+HK+N+EL+GQG+ Sbjct: 245 P--------EITFERLRFLLPDAITIATLAAIESLLSAVVADGMTGTRHKSNAELLGQGV 296 Query: 320 GNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAM 379 NI + FGG+ AT AIAR+A N++AGA +P++ ++H+I + L +L+LAPL+ +PL+A+ Sbjct: 297 ANIASGIFGGLPATGAIARTATNIKAGARTPVAGMMHAIWLFLFMLLLAPLIIKVPLAAL 356 Query: 380 AALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFM 439 AA+L++VAWNMSE + +++ H+P+ D IV+++ LTVL D+ AI GI LAS+LF+ Sbjct: 357 AAILMVVAWNMSEIKHIKEIM-HSPRTDRIVLIVTFLLTVLVDLNFAIQAGIALASILFI 415 Query: 440 RRIARMTRLAPVVVD-----------VPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKR 488 ++ + T++ P+ + +P V V + GPLFF AE L L + + Sbjct: 416 DQMMKATQIRPITSEENDPDSTSNKTIPHGVEVYEIQGPLFFGVAEKLVDTLMLFEKPPQ 475 Query: 489 IVILKWDAVPVLDAGGLDAFQRFVKRL 515 + IL+ VP++DA GL + + +RL Sbjct: 476 VFILRMRYVPLIDAAGLHSLEILHERL 502 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: 562 Number of extensions: 20 Number of successful extensions: 4 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 24 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