Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 5207981 Shew_0497 putative sulfate transporter YchM (RefSeq)
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__PV4:5207981 Length = 565 Score = 503 bits (1294), Expect = e-146 Identities = 260/528 (49%), Positives = 378/528 (71%), Gaps = 12/528 (2%) Query: 32 DLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTAAFVV 91 +++AG+TVG+IA+PL+MALAI SGV PQ+GLYTA +AGIVIAL GGS+ ++SGPTAAFVV Sbjct: 21 NILAGLTVGVIALPLSMALAIASGVPPQHGLYTAMIAGIVIALCGGSKVNISGPTAAFVV 80 Query: 92 ILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGIGITIGTMQ 151 IL P+ QQFGL GLL++ L++G+ L+LMGL + G+LIE +P VT+GFT+GIG+ I T Q Sbjct: 81 ILLPIVQQFGLGGLLLSGLMAGVILLLMGLGKLGKLIEIVPYPVTVGFTAGIGVVIATFQ 140 Query: 152 IKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRLGIRLPGHLP 211 IKDF GL++A EHYL+K+ + AL +I+ + IG +TL +L+ WP+L ++P HL Sbjct: 141 IKDFFGLEVAAGGEHYLEKLSYILQALTSISWQETLIGALTLAVLLAWPKLKSKVPAHLA 200 Query: 212 ALLAGCAVMGIV-NLLGG-HVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSE-- 267 ALL G + ++ ++GG VATIGS+FHY L DG G+GIP ++P PW+LP ++ Sbjct: 201 ALLVGALIAWVMTQMIGGFSVATIGSRFHYEL-DGLLGSGIPPIMPSFEWPWNLPGADGQ 259 Query: 268 -FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPF 326 ++++ +R LLP+A ++A+LGA+ESLLCAVV DGM+G KH N EL+GQGLGNI+ P Sbjct: 260 PIGMSFELVRELLPSAITIAILGALESLLCAVVADGMSGKKHNPNDELIGQGLGNILVPL 319 Query: 327 FGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAALLLMV 386 FGGI ATAAIAR+AANV+AG + P+++V+H + ++ +L+LAPLLS++P+++MAALLL+V Sbjct: 320 FGGIPATAAIARTAANVKAGGSMPLASVVHGLFILAGILLLAPLLSYIPMASMAALLLVV 379 Query: 387 AWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRIARMT 446 AWNMSEA V L+ AP+DD+++++LC +LTVLFDM IA++VG+ LA++LF+RR +T Sbjct: 380 AWNMSEAKHFVRTLKVAPRDDVLILVLCFALTVLFDMTIAVAVGMGLAAMLFIRRSISLT 439 Query: 447 RLAPV-----VVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVILKWDAVPVLD 501 V +VP+ V+V + GPLFF +A + R+VIL V +LD Sbjct: 440 DARAVETNHQAYEVPESVVVYDINGPLFFGSAHKALKTIALVRPDVRVVILDMSEVTLLD 499 Query: 502 AGGLDAFQRFVKRLP-EGCELRVCNVEFQPLRTMARAGIQPIPGRLAF 548 + A + + L + L + N++ + L + RAGI+ G++ + Sbjct: 500 MSAIVAMESIAQDLSGKQVALIINNLQPRMLLKLRRAGIRKRRGQVEY 547 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: 761 Number of extensions: 33 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: 565 Length adjustment: 36 Effective length of query: 523 Effective length of database: 529 Effective search space: 276667 Effective search space used: 276667 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