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 alpha chain, mitochondrial; PCCase subunit alpha; Propanoyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.3 (characterized)
to candidate PfGW456L13_2588 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

Query= SwissProt::P0DTA4
         (730 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2588
          Length = 651

 Score =  489 bits (1259), Expect = e-142
 Identities = 284/665 (42%), Positives = 399/665 (60%), Gaps = 24/665 (3%)

Query: 66  ILIANRGEIACRVIKTCKKMGIKTVAVHSDVDASSVHVTMADEAVCVGPAPTSKSYLNMD 125
           +L+ANRGEIACRV++T K +G+ TVAVHS  D  + H   AD  V +G +    SYL +D
Sbjct: 9   LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAVDSYLQID 68

Query: 126 AIMEAVRTTRAQAVHPGYGFLSENKEFAKCLAAEGVIFIGPDTHAIQAMGDKIESKLLAK 185
            ++ A + + AQA+HPGYGFLSEN  FA+ + A G+IF+GP   AI AMG K  +K L +
Sbjct: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128

Query: 186 KAKVNTIPGFDGVVKDADEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRFS 245
            A V  +PG+ G  +D +        IGYPV++KA+AGGGGKGM++  D  +  +    +
Sbjct: 129 TAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188

Query: 246 SQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEEAPS 305
            +EA SSFGD R+L+EK++  PRH+EIQV  D+HGN L+LNER+CSIQRR+QKVVEEAP+
Sbjct: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248

Query: 306 IFLDSETRRAMGEQAVALAKAVNYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECIT 365
             L  E RRAMGE AV  A+A+ Y  AGTVEFL+D++  F+F+EMNTRLQVEHPVTE IT
Sbjct: 249 PGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308

Query: 366 GLDLVQEMIRVAKGYPLRHRQADIPINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPIH 425
           GLDLV   IRVA+G  L   Q  +P+ G A+E R+YAEDP   F LP+ GRL  Y+E   
Sbjct: 309 GLDLVAWQIRVARGEALPMTQDQVPLVGHAIEVRLYAEDPGNDF-LPATGRLELYRESAQ 367

Query: 426 LPGVRVDSGIQPGSDISIYYDPMISKLITYGSNRMEALKRMENALDNYVIRGVTHNIALL 485
            PG RVDSG++ G +IS +YDPM+ KLI +G +R +A  R+ + LD + I G+  NI  L
Sbjct: 368 GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNINFL 427

Query: 486 REVIINSRFVEGDINTKFLSDVYPDGFKGHKLTEDERNQLLAIASSLFVASQLRAQRFQE 545
           R +I +  F   +++T F+               D+  Q    A+  F  SQ  A R  +
Sbjct: 428 RRIIGHPAFATAELDTGFIPRYQEQLLPTPAELSDDFWQ---AAAQAFAQSQPHATRADD 484

Query: 546 PENSRVPIIKPQVANWELSIRLHDEVHTVTASNSGPTFSVEVDGSKLNVTSTWNLASPLL 605
           P +       P  A   L   L  E+ T+  S  G   ++ +    +N  S   L    L
Sbjct: 485 PSS-------PWAAPNGLRAGLPREI-TLHLSCEGQDRALTL--GDINAHSA-RLKGEQL 533

Query: 606 SVSIDGTQRTIQCLSRDAGGNMSIQFLGTVYKVHILTKLAAELNKFMLEKAAEDTSSILH 665
               +G +R  + + R  G  + +Q+ G + ++     ++A        +A+      L 
Sbjct: 534 LTEHEGVRRQHRAIRR--GDYVYLQWDGELRRIESYDPISA-------VEASHSHQGGLT 584

Query: 666 SPMPGVVVAVSVKPGDLVAEGQEICVIEAMKMQNSMTAGKTGKVKSVHCKAGDTVGEGDL 725
           +PM G +V V V+ G  V  G ++ V+EAMKM++S+ A   G +K+++C+ G+ V EG  
Sbjct: 585 APMNGSIVRVLVEAGQSVEAGAQLVVLEAMKMEHSIRAPHAGVIKALYCQEGEMVSEGSA 644

Query: 726 LVELE 730
           LVELE
Sbjct: 645 LVELE 649


Lambda     K      H
   0.318    0.134    0.385 

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: 1033
Number of extensions: 43
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: 730
Length of database: 651
Length adjustment: 39
Effective length of query: 691
Effective length of database: 612
Effective search space:   422892
Effective search space used:   422892
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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