GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dauA in Pseudomonas fluorescens FW300-N2E2

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate Pf6N2E2_4131 Sulfate permease

Query= SwissProt::P0AFR2
         (559 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4131 Sulfate permease
          Length = 522

 Score =  212 bits (539), Expect = 3e-59
 Identities = 158/510 (30%), Positives = 253/510 (49%), Gaps = 51/510 (10%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W  + T A   RDL+ G++  I+A+P ++A A+ +G+ P+YGLY A V  ++  L G S 
Sbjct: 15  WLPRQTRASVGRDLVVGLSGAILALPQSIAYALIAGLPPEYGLYAAIVPVLIACLWGSSW 74

Query: 80  FSVSGPTAAFVVILY--------PVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYI 131
             + GPTAA  ++LY        P SQ + +  +L+ T+L+GIF  L+GL RFG L+ ++
Sbjct: 75  HLICGPTAAISIVLYATVSPLAVPASQDY-ITLILLLTVLAGIFQWLLGLLRFGALVNFV 133

Query: 132 PVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHY------LQKVGALFMALPTINVGD 185
             SV LGFT G  + I   Q+ + LGL + +           +  +GA+      + +G 
Sbjct: 134 SHSVVLGFTLGAAVVIALGQLPNLLGLDLPNEATALRGLLMLVSHIGAVDKPSLLLGLGT 193

Query: 186 AAIGIVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGS 245
             +G+V   +L  WP L       L  L+    V+ +   + GHVA + +          
Sbjct: 194 LVLGVVLKRLLPRWPSL-------LITLVISSLVVWLWPAMFGHVALVSAF--------- 237

Query: 246 QGNGIPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTG 305
               +P   P   LP DL         + I  LLP A ++ MLG + SL  A  L   +G
Sbjct: 238 -AGRLPPFTP---LPLDL---------ELILRLLPGAVAVGMLGLVTSLSIARSLSVRSG 284

Query: 306 TKHKANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALL 365
               AN E+  QGL NI+  FF G  +  +  RS  +  AGA SP++ V  ++ V L  +
Sbjct: 285 QLLDANQEVRAQGLSNIVGGFFSGSLSAGSFTRSGLSYEAGACSPLAGVFSALWVALFAV 344

Query: 366 VLAPLLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVI 425
             A L++ +P+ AMA  +L++AW + + H+ +  L    + + +VM L    T+L ++  
Sbjct: 345 AGANLIAHIPIPAMAGSILLIAWGLVD-HRGIRALYRVSRAEFVVMGLTCLATLLLELQT 403

Query: 426 AISVGIVLASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLE 485
           AI  G VLASL F  +     R+         +  +LRV G +FF A+  L   L+ RL+
Sbjct: 404 AIYAG-VLASLFFYLKRTSQPRVQHF---REGEAEILRVGGSIFFGASHYLQARLQ-RLQ 458

Query: 486 GKRIVILKWDAVPVLDAGGLDAFQRFVKRL 515
            +R+VI     +  +D  G++   +  +RL
Sbjct: 459 AQRVVI-DAQQINFIDYSGVEMLHQEARRL 487


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: 664
Number of extensions: 42
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: 522
Length adjustment: 35
Effective length of query: 524
Effective length of database: 487
Effective search space:   255188
Effective search space used:   255188
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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