Alignments for a candidate for pccA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Pseudomonas fluorescens FW300-N2C3

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate AO356_02930 AO356_02930 3-methylcrotonyl-CoA carboxylase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_02930
          Length = 656

 Score =  484 bits (1247), Expect = e-141
 Identities = 299/671 (44%), Positives = 408/671 (60%), Gaps = 30/671 (4%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61
           F KILIANRGEIACR+ +TA+ +G +TVAV+SEAD DAL V MADEAV IG A  ++SYL
Sbjct: 4   FSKILIANRGEIACRIQRTAQALGYRTVAVFSEADADALHVRMADEAVLIGAAPVQQSYL 63

Query: 62  VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121
               I+ A +++GA+A+HPGYGFLSENA F+    + G+ FIGP   +I  MG K  +K 
Sbjct: 64  DPRVILEAARRSGADAIHPGYGFLSENARFAHACAQAGLVFIGPSPEAIELMGSKRRAKI 123

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

Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241
            S  +EA + FG D + +E+ +++PRH+E+Q+ GD HG  ++L ERDCSIQRRHQK+IEE
Sbjct: 184 RSARSEALHGFGSDELILEQALIDPRHVEVQIFGDHHGQLIHLGERDCSIQRRHQKIIEE 243

Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301
           AP P +  ++R+AMGE A+    AVNY  AGTVEF+++ A   FYFLEMNTRLQVEHPVT
Sbjct: 244 APCPVMTADLRRAMGEAALTAGHAVNYVGAGTVEFLLA-ADGRFYFLEMNTRLQVEHPVT 302

Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361
           E ITGLDLV   + VA G+ LPL Q  V ++G A++ R+ AEDP   FLP TG LV ++P
Sbjct: 303 ESITGLDLVAWQLDVATGKPLPLCQEQVTLSGHALQVRLYAEDPAADFLPQTGCLVGWEP 362

Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421
           P   DG VRVD G+  G  I+ +YDSM+ KLIVHGA+R++A  ++  A+   V+ G+ SN
Sbjct: 363 PIR-DG-VRVDHGLLQGQAITPFYDSMLGKLIVHGATRDEARRKLLRAVEDCVLLGVQSN 420

Query: 422 IPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPA--LLIGVAAFVHRRYIDR 479
               A L+ H RF  G F+TGFI++ +     A+++P +     L I  AAF    Y   
Sbjct: 421 QRLLAGLLAHPRFIDGDFNTGFISQHFAN--HAALLPLEPSVEQLAIATAAF----YQAS 474

Query: 480 AAQVSGQLPGHERKVGDE-WVVIRNGERHPVVAKPIE--GGYLVTYNGEKYE--LLSDWR 534
            A+ +  L G    +G      I  GER  V++   E  G   +  +G   E  LL    
Sbjct: 475 QARHAPGLGGWRNSIGTALHYRIGVGERDWVLSLETETDGTLNIRSDGRLIELRLLDVDA 534

Query: 535 QGQSL-FNGTCNGEEFTLQVERHRMTYQLFHW-GTRADMMVMSARAAELLALMPEKAAPD 592
           QG +L  +G   G+     +E H +      W  TR   + +  R    LA +  KA+  
Sbjct: 535 QGATLVIDGI--GQRHAWHLEGHDL------WLSTRPGGLHLQDRT---LAPVASKASAG 583

Query: 593 LSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSS 652
            S  LL+PM G + EV V+ G  V+ G+ L V+EAMKME+ LKA  D  V+++  T G  
Sbjct: 584 AST-LLAPMDGAIVEVLVSEGSPVRQGQLLMVLEAMKMEHPLKAGSDGVVRQLQATRGDQ 642

Query: 653 LSVDEIIIEFE 663
           +   ++++  E
Sbjct: 643 VRKRQVLLRIE 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: 968
Number of extensions: 44
Number of successful extensions: 4
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: 663
Length of database: 656
Length adjustment: 38
Effective length of query: 625
Effective length of database: 618
Effective search space:   386250
Effective search space used:   386250
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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