Alignments for a candidate for pccA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Pseudomonas fluorescens GW456-L13

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate PfGW456L13_2284 Geranyl-CoA carboxylase biotin-containing subunit

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2284
          Length = 653

 Score =  491 bits (1263), Expect = e-143
 Identities = 299/671 (44%), Positives = 405/671 (60%), Gaps = 32/671 (4%)

Query: 3   KKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYLV 62
           KKILIANRGEIACR+ +TA+ +G +TVAV+S+AD DAL V +ADEAV IGPA  ++SYL 
Sbjct: 5   KKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVRIADEAVNIGPAPVQQSYLN 64

Query: 63  ADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKKL 122
              I+ A ++TGA+A+HPGYGFLSENA F+    + GI FIGP   +I  MG K  SK  
Sbjct: 65  IQAILDAARRTGADAIHPGYGFLSENAGFALACRDAGITFIGPSPEAIELMGSKRLSKIA 124

Query: 123 AIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGFS 182
            IEA V  I GY  A          A++IGYP+MIKASAGGGG+G+R+ ++ ++  E   
Sbjct: 125 MIEAGVPCINGYQGAGQDDATLGREAERIGYPLMIKASAGGGGRGMRLVHDASDLLEQIR 184

Query: 183 SCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEEA 242
           +  +EA N FG   + +E+ ++EPRH+E+Q+ GD HGN +YL ERDCS+QRRHQKVIEEA
Sbjct: 185 TARSEALNGFGSGELILEQALVEPRHVEVQLFGDRHGNLIYLGERDCSVQRRHQKVIEEA 244

Query: 243 PSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVTE 302
           P P +  E+R+AMGE A+   RAV Y  AGTVEF++  A  +FYFLEMNTRLQVEHPVTE
Sbjct: 245 PCPVMTAELRQAMGEAALKAGRAVKYVGAGTVEFLLD-ARGQFYFLEMNTRLQVEHPVTE 303

Query: 303 LITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQPP 362
           LITGLDLV   + +A G+ LPL Q  VQ+ G AME R+ AEDP +GFLP TGR+V ++P 
Sbjct: 304 LITGLDLVAWQLSIAEGQPLPLRQEQVQLTGHAMEVRLYAEDPAQGFLPQTGRVVAWEPA 363

Query: 363 AEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSNI 422
            + DG VR+D G+ +G  IS +YD M+ KLI HGA+RE+A  ++  A+   V+ G+ SN 
Sbjct: 364 LQ-DG-VRIDHGLIEGQVISPFYDPMLGKLIAHGATREEARRKLLRAVQDSVLLGLKSNQ 421

Query: 423 PFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPA---LLIGVAAFVHRRYIDR 479
              A+L++H +F SG F TGFIA+ +    D + +  + P    L I  A F        
Sbjct: 422 RLLASLLEHPQFASGDFSTGFIAQHFT---DHTCLHPETPGAHHLAIAAALFYQAAAQAH 478

Query: 480 AAQVSG-----QLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWR 534
            A + G      +P H R +G E       +  PV  + I G  L     E+   L    
Sbjct: 479 LAPLGGWRNNASVPLHYR-IGLE------DQDWPVALQAIPGEPLRIQVAERSLELKIIH 531

Query: 535 QGQSLFNGTCNGEEFTLQVE--RHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPD 592
                     +G   TL++E  R R  Y+L     R      S +  +   +     A  
Sbjct: 532 S---------DGRWATLEIEGVRQRHAYRLEAGRLRLFTRPGSLQFVDRTQVQVTGQASV 582

Query: 593 LSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSS 652
            S  L +PM G + +V V  G +V  G+ L V+EAMKME+ LK+  D  +K++ V  G  
Sbjct: 583 SSGTLKAPMDGAIVDVLVNEGSQVTKGQLLVVLEAMKMEHPLKSGIDGVLKRLQVKVGDQ 642

Query: 653 LSVDEIIIEFE 663
           +   +I++E E
Sbjct: 643 VKNRQILLEVE 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: 1073
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources