Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_011386051.1 AMB_RS18695 sodium-independent anion transporter
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_000009985.1:WP_011386051.1 Length = 569 Score = 411 bits (1057), Expect = e-119 Identities = 239/559 (42%), Positives = 335/559 (59%), Gaps = 43/559 (7%) Query: 19 CWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGS 78 C KE Y R DLIAG+TV I+A+PLAMAL I SGV P GL+TA VAG +I+ GGS Sbjct: 23 CLKEGYDLPRGRGDLIAGLTVAIVALPLAMALGIASGVTPDRGLFTAIVAGFLISFLGGS 82 Query: 79 RFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLG 138 RF + GPT AFVV++Y + QQ G GL++ATL++G+ L+L GLARFG +I+YIP + G Sbjct: 83 RFQIGGPTGAFVVVVYNIVQQHGYDGLVLATLMAGVMLLLFGLARFGVVIKYIPYPLVTG 142 Query: 139 FTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVF 198 FTSGI + I + Q+KDFLGL+M VP + +K A + T + A+ TL +++ Sbjct: 143 FTSGIAVIIFSSQVKDFLGLRMESVPAEFFEKWVAYGEHIGTTHGPTLAVAAGTLAVILV 202 Query: 199 WPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLV 258 R PG L + G +V +V LG V TIGS+F GIP LP Sbjct: 203 LRRFRPGWPGFLIG-VTGASV--LVWALGMPVETIGSRF----------GGIPSTLPSPQ 249 Query: 259 LPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQG 318 P L+W + LL AF++A L IESLL A+V DGMTG +HK+N EL+ QG Sbjct: 250 FP--------ALSWGKVTALLQPAFTIAFLAGIESLLSAMVADGMTGRRHKSNCELLAQG 301 Query: 319 LGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSA 378 + NI + FGGI AT AIAR+A ++++GA +P++ ++H++ ++L +L+ APL SW+PL + Sbjct: 302 IANIASVLFGGIPATGAIARTATSIKSGAQTPVAGMLHAVFILLFMLLFAPLASWIPLPS 361 Query: 379 MAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLF 438 +AA+L++VAWNMSEA + L+ AP+ D V+L+ LTV+ D+ +AI VG+VLAS+LF Sbjct: 362 LAAVLMVVAWNMSEAPHFIHLM-SAPRSDRAVLLVTFVLTVMVDLTVAIEVGMVLASILF 420 Query: 439 MRRIARMTRL--------------------APVVVDVPDDVLVLRVIGPLFFAAAEGLFT 478 MRR+A +T + A +PD V V ++ GP FF A L Sbjct: 421 MRRMAEVTEIGTGIHLIDEDAEDGGDDHVGAIPTTPIPDGVEVFQISGPFFFGVATRLSE 480 Query: 479 DLESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARA 537 E + R+ IL+ VPV+DA G+ A FV+R G E+ + V+ QP++ M R Sbjct: 481 VFEQTHKPPRVFILRMRLVPVIDASGIQALTEFVRRCRKHGTEVLLSGVQPQPMQVMGRM 540 Query: 538 GIQPIPGRLAFFPNRRAAM 556 G+ G F PN AA+ Sbjct: 541 GLCHEIGEDNFVPNIDAAL 559 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: 748 Number of extensions: 37 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: 569 Length adjustment: 36 Effective length of query: 523 Effective length of database: 533 Effective search space: 278759 Effective search space used: 278759 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