GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dauA in Pseudomonas fluorescens FW300-N2E3

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate AO353_10315 AO353_10315 sulfate transporter

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10315
          Length = 552

 Score =  375 bits (963), Expect = e-108
 Identities = 214/525 (40%), Positives = 322/525 (61%), Gaps = 37/525 (7%)

Query: 31  RDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTAAFV 90
           R++++G+ VG++A+PLAMA AI SGV P+ G+YTA V+G++++L GGSR  ++GPT AFV
Sbjct: 20  RNIVSGVIVGVVALPLAMAFAIASGVKPEQGIYTAIVSGLLVSLFGGSRLQIAGPTGAFV 79

Query: 91  VILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGIGITIGTM 150
           VIL  V+ ++G+ GL +AT+++G  L+L+G+ + G +I++IP  V +GFT+GIG+ I   
Sbjct: 80  VILSGVTAKYGVDGLQIATMMAGAILLLLGITKLGAIIKFIPDPVIVGFTAGIGVIIWVG 139

Query: 151 QIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRL-GIR-LPG 208
           Q KDF GL      EH+ +++  L  ALP+ +V    + + +L +++  P++ GIR +PG
Sbjct: 140 QWKDFFGLPKIS-GEHFHERLWHLVQALPSFHVPTTLLALSSLVLVITAPKIPGIRRVPG 198

Query: 209 HLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSEF 268
            L A++   A+       G  VATIGS F           GIPQ LP++ LP        
Sbjct: 199 PLIAMVVVTALQAFFQFAG--VATIGSAF----------GGIPQGLPEVGLP-------- 238

Query: 269 TLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPFFG 328
            +T   +  L+  AF++AMLGAIESLL AVV DGM GTKH +N EL+GQG+ N++ P FG
Sbjct: 239 AITLPQVIELIGPAFAIAMLGAIESLLSAVVADGMAGTKHDSNQELIGQGIANLVTPLFG 298

Query: 329 GITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAALLLMVAW 388
           G  AT AIAR+A N+R G  SPI+  +H++ +IL +L LAPL S +PL A+AA+L +VA+
Sbjct: 299 GFAATGAIARTATNIRNGGNSPIAGFVHALTLILLILFLAPLASDIPLCALAAILFVVAY 358

Query: 389 NMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRIARMTRL 448
           NMSE      +++ APK D+ ++L+  SLTV  D+ IA+++G++LA L FMRR+A    +
Sbjct: 359 NMSELKHFQRMVKRAPKADVAILLITFSLTVFSDLAIAVNIGVILAMLQFMRRMASSVEV 418

Query: 449 APVV-------------VDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVILKWD 495
             +V             V +P  VLV  + GPLFF AAE     L         +I++  
Sbjct: 419 QQMVEKELEVELRINGHVRLPPGVLVYTIEGPLFFGAAETFERVLAQTHTDPGTLIIRLK 478

Query: 496 AVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGI 539
            VP +D  GL      ++ L      +++C    + L  + +AGI
Sbjct: 479 RVPFMDITGLQTLLEVIEHLRKRSIVVKLCEANEKVLGKLDKAGI 523


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: 662
Number of extensions: 35
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: 552
Length adjustment: 36
Effective length of query: 523
Effective length of database: 516
Effective search space:   269868
Effective search space used:   269868
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.

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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