Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 6936893 Sama_1067 putative sulfate transporter YchM (RefSeq)
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__SB2B:6936893 Length = 572 Score = 585 bits (1507), Expect = e-171 Identities = 310/559 (55%), Positives = 400/559 (71%), Gaps = 11/559 (1%) Query: 9 VMPFRALIDACWKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVA 68 ++P AL + E+Y+ A DL+AGITVG+IAIPLAMALAI SGVAPQYGLYTA +A Sbjct: 10 LIPAFALRQSLLGERYSRAELLADLLAGITVGVIAIPLAMALAIASGVAPQYGLYTAIIA 69 Query: 69 GIVIALTGGSRFSVSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLI 128 GI+IA++GGS+ SVSGPTAAFVV+L P+S Q+GL GLL+AT++SG+ L+LM L R GRLI Sbjct: 70 GIIIAISGGSKLSVSGPTAAFVVLLAPISAQYGLGGLLLATVMSGVILLLMSLMRLGRLI 129 Query: 129 EYIPVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAI 188 +YIP VTLGFT GI I I +QIKD L + +PE + KV LF A+P + Sbjct: 130 QYIPEPVTLGFTGGIAIVIAMLQIKDMFALPVEALPEDFWHKVSTLFHAMPHAQWPSILV 189 Query: 189 GIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGN 248 +TL +LVFWP+ +LP HLPA+LAG + LG V TIGS+F + L DG+ Sbjct: 190 AAITLSVLVFWPKFTQKLPPHLPAILAGTLCALALGGLGFDVETIGSRFSFTLDDGTLMA 249 Query: 249 GIPQLLPQLVLPWDLP---NSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTG 305 GIP +LP +LPW+LP TL W ++ LLP+A ++AMLGAIESLLCAVV+DGMTG Sbjct: 250 GIPSVLPSFLLPWELPGVGGEPLTLNWQLVQNLLPSAMAIAMLGAIESLLCAVVVDGMTG 309 Query: 306 TKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALL 365 +H ANSEL GQGLGN+IAPFFG I ATAAIARSAANVRAGA SP++AV H++ V+LAL+ Sbjct: 310 NRHSANSELFGQGLGNLIAPFFGAIPATAAIARSAANVRAGAKSPLAAVFHALTVLLALV 369 Query: 366 VLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVI 425 +LAP+L+++P++ MAALLL+VAW+MSEA K + L+R A D+ V+L C+ LTV FDMVI Sbjct: 370 LLAPVLAYIPMATMAALLLVVAWHMSEAKKSLHLIRRAHVSDVAVLLTCLMLTVAFDMVI 429 Query: 426 AISVGIVLASLLFMRRIARMTRLAPVVVDVPDD-----VLVLRVIGPLFFAAAEGLFTDL 480 AI VGIVLASLL M ++A TRL V +D D + R+ GPLFFAAA+ LF++L Sbjct: 430 AIGVGIVLASLLLMGQLAASTRL--VALDCGSDAGSPNIEAFRIDGPLFFAAADNLFSEL 487 Query: 481 ESRLEGKRIVILKWDAVPVLDAGGLDAFQRFVK-RLPEGCELRVCNVEFQPLRTMARAGI 539 R G I++L W V +LDAGGL A +R V +G E+R+ +V FQ LR + +AG+ Sbjct: 488 MHRQNGAPILVLDWQNVSLLDAGGLSALERTVAWAQKQGREIRIVSVPFQALRALVKAGV 547 Query: 540 QPIPGRLAFFPNRRAAMAD 558 Q PG L+F+P+ AA+ D Sbjct: 548 QEKPGVLSFYPDMTAALQD 566 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: 777 Number of extensions: 34 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: 572 Length adjustment: 36 Effective length of query: 523 Effective length of database: 536 Effective search space: 280328 Effective search space used: 280328 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