GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudomonas fluorescens FW300-N1B4

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Pf1N1B4_225 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

Query= reanno::PS:Dsui_0516
         (663 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_225
          Length = 653

 Score =  502 bits (1293), Expect = e-146
 Identities = 299/674 (44%), Positives = 406/674 (60%), Gaps = 36/674 (5%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61
           F KILIANRGEIACR+ +TA+ +G +TVAV+S+AD DAL V+MADEAV IGPA  ++SYL
Sbjct: 4   FSKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVQMADEAVNIGPAPVQQSYL 63

Query: 62  VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121
               II A ++TGA+A+HPGYGFLSENAEF+R  ++ GI FIGP   +I  MG K  SK 
Sbjct: 64  NIQAIIDAARRTGADAIHPGYGFLSENAEFARACQQAGIIFIGPSPEAIELMGSKRLSKL 123

Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181
             I+A V  I GY  +          A++IGYP+MIKASAGGGG+G+R+ ++  E  E  
Sbjct: 124 AMIKAGVPCIKGYQGSEQDDATLSREAERIGYPLMIKASAGGGGRGMRLVHSAGELLEQL 183

Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241
            +  +EA++ FG D + +E+ +++PRH+E+QV GD HGN +YL ERDCSIQRRHQK+IEE
Sbjct: 184 RTARSEAQHGFGSDELILEQALIDPRHVEVQVFGDQHGNLIYLGERDCSIQRRHQKIIEE 243

Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301
           AP P +  ++R+AMGE A+   RAVNY  AGTVEF++  A  +FYFLEMNTRLQVEHPVT
Sbjct: 244 APCPVMTADLRQAMGEAALKAGRAVNYVGAGTVEFLLD-ARGQFYFLEMNTRLQVEHPVT 302

Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361
           ELITGLDLV     VA G  LPL Q  VQ+NG AME R+ AEDP +GFLP TGR+  ++P
Sbjct: 303 ELITGLDLVAWQFHVAEGLPLPLQQEQVQLNGHAMEVRLYAEDPAQGFLPQTGRIAAWEP 362

Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421
              + G VR+D G+ +G  +S +YD M+ KLI HGA+RE+A  ++  A+   V+ G+ SN
Sbjct: 363 --ALPGGVRIDHGLIEGQSVSPFYDPMLGKLIAHGATREEARRKLLRAVQDSVLLGVQSN 420

Query: 422 IPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRAA 481
               A L++H +F SG F TGFI   +       + PH   A  + +AA +  +   +A 
Sbjct: 421 QRLLACLLEHPQFISGKFSTGFIPTHFAD--HPCLHPHVPSAEELAIAAALFYQASAQAH 478

Query: 482 QV-------SGQLPGHERKVG---DEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLS 531
           +        +  +P H R +G    +W V  N E      KP    Y         EL  
Sbjct: 479 RTPLAGWRNNASVPLHYR-IGLEDQDWPVELNAE----PGKP----YRAQIGARTLELKV 529

Query: 532 DWRQGQSLFNGTCNGEEFTLQVE--RHRMTYQLFHWGTRADMMVMSARAAELLALMPEKA 589
                       C+G   TL+++  R R  Y+L            S R  +    +    
Sbjct: 530 I----------QCDGRWATLEIDGIRQRHAYRLKAGQLWLFTRPGSLRLVDRTQALVSGQ 579

Query: 590 APDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTA 649
           A   S  L +PM G + +V V+ G  V  G+ L V+EAMKME+ LK+  D  +K++ V  
Sbjct: 580 ASVSSGTLKAPMDGAIVDVLVSEGSPVSKGQLLVVLEAMKMEHPLKSGIDGVLKRLQVRV 639

Query: 650 GSSLSVDEIIIEFE 663
           G  +   +I++E E
Sbjct: 640 GDQVKNRQILLEVE 653


Lambda     K      H
   0.319    0.135    0.391 

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: 1067
Number of extensions: 51
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 663
Length of database: 653
Length adjustment: 38
Effective length of query: 625
Effective length of database: 615
Effective search space:   384375
Effective search space used:   384375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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