GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Pseudomonas fluorescens FW300-N2C3

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate AO356_11320 AO356_11320 SulP family inorganic anion transporter

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_11320
          Length = 522

 Score =  212 bits (539), Expect = 3e-59
 Identities = 159/506 (31%), Positives = 253/506 (50%), Gaps = 43/506 (8%)

Query: 20  WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79
           W  + T     RDLI G++  I+A+P ++A A+ +G+ P+YGLY A V  ++  L G S 
Sbjct: 15  WLPRQTRQSVGRDLIVGLSGAILALPQSIAYALIAGLPPEYGLYAAIVPVLIACLWGSSW 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 PVSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMA--LPTINVGDAAIG 189
             SV LGFT G  + I   Q+ + LGL +   P       G L +   +  ++     +G
Sbjct: 134 SHSVVLGFTLGAAVVIALGQLPNLLGLDL---PNEATALKGLLMLVSHIEAVDKPSLLLG 190

Query: 190 IVTLGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNG 249
           + TL + V   RL  R P  L  L+    V+ +   + GHVA + +              
Sbjct: 191 LGTLLLGVVLKRLLPRWPSLLITLIISSLVVWLWPAMFGHVALVSAF------------- 237

Query: 250 IPQLLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHK 309
             +L P  +LP DL         + I  LLP A ++ MLG + SL  A  L   +G    
Sbjct: 238 AGRLPPLTLLPLDL---------ELILRLLPGAVAVGMLGLVTSLSIARSLSVRSGQLLD 288

Query: 310 ANSELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAP 369
           AN E+  QGL N++  FF G  +  +  RS  +  AGA SP++ V  ++ V L  +  A 
Sbjct: 289 ANQEVRAQGLSNLVGGFFSGSLSAGSFTRSGLSYEAGACSPLAGVFSALWVALFAVAGAK 348

Query: 370 LLSWLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISV 429
           L++ +P+ AMA  +L++AW + + H+ +  L    + + +VM L    T+L ++  AI  
Sbjct: 349 LIAHIPIPAMAGSILLIAWGLVD-HRGIRALYRVSRAEFMVMSLTCLATLLLELQTAIYA 407

Query: 430 GIVLASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRI 489
           G VLASL F  +     R+         +  +LRV G +FF A+  L   L+ RL+ +R+
Sbjct: 408 G-VLASLFFYLKRTSQPRVQHF---REGEAEILRVGGSIFFGASHYLQVRLQ-RLQAQRV 462

Query: 490 VILKWDAVPVLDAGGLDAFQRFVKRL 515
           VI     +  +D  G++   +  +RL
Sbjct: 463 VI-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: 656
Number of extensions: 40
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:

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