GapMind for catabolism of small carbon sources

 

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

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate AO353_19305 AO353_19305 3-methylcrotonyl-CoA carboxylase

Query= metacyc::MONOMER-13589
         (666 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19305
          Length = 653

 Score =  492 bits (1266), Expect = e-143
 Identities = 278/671 (41%), Positives = 398/671 (59%), Gaps = 29/671 (4%)

Query: 3   KKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYIV 62
           +KILIANRGEIACR+ +TA+ +G +TVAV+SDAD +ALHV MADEA++IGP    QSY+ 
Sbjct: 5   RKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVRMADEAVNIGPAAVAQSYLN 64

Query: 63  IDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKKL 122
              I++A   SGA+A+HPGYGFLSE  +FA A   AG+ FIGP   AIE MG K  SK  
Sbjct: 65  SAAIIDAALRSGADAIHPGYGFLSENAEFATACAQAGITFIGPDPAAIELMGSKRLSKIA 124

Query: 123 AKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGFE 182
              AGV  + GY G   D     + +  IGYP+MIKASAGGGG+GMR+  +  E+     
Sbjct: 125 MLAAGVPCIGGYQGAEQDDATLSREAERIGYPLMIKASAGGGGRGMRLVHTADELLAQIR 184

Query: 183 SSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEEA 242
           ++++EA ++FG D + +E+ + +PRH+EIQ+  D+HGN +YL ER+CSIQRR+QKVIEEA
Sbjct: 185 TARSEALHAFGSDELILEQALIEPRHVEIQLFGDQHGNLIYLGERDCSIQRRHQKVIEEA 244

Query: 243 PSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTEL 302
           P P +    R AMGE A    +AV Y  AGTVEF++D +  FYFLEMNTRLQVEHPVTE+
Sbjct: 245 PCPVMTAELRDAMGEAALKAGRAVNYVGAGTVEFLLDARGQFYFLEMNTRLQVEHPVTEM 304

Query: 303 ITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRPPV 362
           ITG+DLV   + VAAG  LP +Q  +++ G AME RLYAEDP ++FLP  GR+ R+ P +
Sbjct: 305 ITGLDLVAWQLDVAAGLPLPLRQEQVELKGHAMEVRLYAEDPAQDFLPQTGRIMRWEPAL 364

Query: 363 ESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGIGH 422
                   VR D G+ EG ++S +YDP++ K+  +  TRE A  ++  A+    + G+  
Sbjct: 365 -----ADGVRIDHGLLEGQQVSPFYDPLLGKIIAYGATREEARRKLLRAVQDSALLGLQT 419

Query: 423 NLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAM-NRVAEIR 481
           N   +  +++HP+F+ GD  T FIA+ + D         PT   +A A A    + A   
Sbjct: 420 NQRLLAGLLEHPQFIAGDFNTGFIAQHFAD-HPSLHSHAPTAEELAIATALFYQQSAGAH 478

Query: 482 RTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSDWTPGQP 541
              ++G  NN   +  +   + L G+ +   + A  +G  V    G +L+          
Sbjct: 479 PPGLAGWRNN--ANAPLLQQIGLNGDRWSTEVTALPDGQLVIQVAGETLQ---------- 526

Query: 542 LASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPDTSKY-- 599
           L  L ++ R   +++  I   +  +L    L +  R        LL  + L P +S+   
Sbjct: 527 LKLLDINARSANLEINGIRRRYAYQLAAGQLWLFTRPGS----LLLQDQTLAPVSSQVGT 582

Query: 600 ----LLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGAS 655
               L  PM G +V + V+EG  V +GQ L  +EAMKME+ L+A   G +K++  +PG  
Sbjct: 583 STGTLKAPMDGAIVDVLVSEGSSVTKGQLLLVLEAMKMEHPLKAGIDGVIKRLQVSPGDQ 642

Query: 656 LRVDDVIMEFE 666
           ++   +++E E
Sbjct: 643 VKNRQILLEVE 653


Lambda     K      H
   0.318    0.134    0.386 

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: 1001
Number of extensions: 40
Number of successful extensions: 3
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: 666
Length of database: 653
Length adjustment: 38
Effective length of query: 628
Effective length of database: 615
Effective search space:   386220
Effective search space used:   386220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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