GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_10315 AO353_10315 sulfate
           transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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