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

GapMind for catabolism of small carbon sources

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

Align propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized)
to candidate AO353_20335 AO353_20335 3-methylcrotonyl-CoA carboxylase

Query= BRENDA::P05165
         (728 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20335
          Length = 649

 Score =  493 bits (1268), Expect = e-143
 Identities = 284/671 (42%), Positives = 396/671 (59%), Gaps = 38/671 (5%)

Query: 66  ILVANRGEIACRVIRTCKKMGIKTVAIHSDVDASSVHVKMADEAVCVGPAPTSKSYLNMD 125
           +LVANRGEIACRV+RT K +G+ TVA+HS  D  + H + AD  V +G +  + SYL +D
Sbjct: 9   LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68

Query: 126 AIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAEDVVFIGPDTHAIQAMGDKIESKLLAK 185
            ++ A K + AQA+HPGYGFLSEN  FAR + A  ++F+GP   AI AMG K  +K L +
Sbjct: 69  KLLAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128

Query: 186 KAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRLS 245
            A V  +PG+ G  +D E     A  IGYPV++KA+AGGGGKGM++  D  +  +    +
Sbjct: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188

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

Query: 306 IFLDAETRRAMGEQAVALARAVKYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECIT 365
             L A+ R+AMGE AV  A+A+ Y  AGTVEFL+DS+  F+F+EMNTRLQVEHPVTE IT
Sbjct: 249 PGLSAQLRKAMGEAAVRAAQAIGYVGAGTVEFLLDSRGEFFFMEMNTRLQVEHPVTEAIT 308

Query: 366 GLDLVQEMIRVAKGYPLRHKQADIRINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPLH 425
           GLDLV   IRVA+G PL   QA + + G A+E R+YAEDP   F LP+ G L+ Y+E   
Sbjct: 309 GLDLVAWQIRVAQGEPLPMTQAQVPLLGHAIEVRLYAEDPSNDF-LPATGHLALYRESAA 367

Query: 426 LPGVRVDSGIQPGSDISIYYDPMISKLITYGSDRTEALKRMADALDNYVIRGVTHNIALL 485
            PG RVDSG++ G  IS +YDPM+ KLI +G DR +A  R+   L+ + I G+  NI  L
Sbjct: 368 GPGRRVDSGVEEGDSISPFYDPMLGKLIAWGVDREQARLRLLSMLEEFAIGGLKTNINFL 427

Query: 486 REVIINSRFVKGDISTKFLSDVYPDGFKGHMLTKSEKNQLLAIASSLFVAF-QLRAQHFQ 544
           R +I +  F   ++ T F+                 ++QLL   + L  AF Q  AQ F 
Sbjct: 428 RRIIGHPAFAAAELDTGFI--------------PRYQDQLLPAPNELSDAFWQAAAQAFA 473

Query: 545 ENSRMPVIKPDI-------ANWELSVKLHDKVHTVVASNNGSVFSVEVDGSKLNVTSTWN 597
           ++    V   D        + +   +     +H      + ++     +      T    
Sbjct: 474 QSQAHHVRADDPGSPWAVGSGFRAGLPAETTLHLSCEDQDRAITLATAE------TRNTE 527

Query: 598 LASPLLSVSVDGTQRTVQCLSREAGGNMSIQFLGTVYKVNILTRLAAELNKFMLEKVTED 657
           L    L V   G +R  + + +     + +Q+ G +  + +   +AA        + +  
Sbjct: 528 LNGEQLLVEHHGLRRQHRAIRQ--AETLYLQWEGELRCIKLYDPIAA-------VEASHS 578

Query: 658 TSSVLRSPMPGVVVAVSVKPGDAVAEGQEICVIEAMKMQNSMTAGKTGTVKSVHCQAGDT 717
               L +PM G +V V V PG  V  G ++ V+EAMKM++S+ A   G VK+++CQ G+ 
Sbjct: 579 HQGGLTAPMNGSIVRVLVTPGQTVETGAQLVVLEAMKMEHSIRAPHAGVVKALYCQEGEM 638

Query: 718 VGEGDLLVELE 728
           V EG  LVELE
Sbjct: 639 VNEGSALVELE 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: 1016
Number of extensions: 37
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 728
Length of database: 649
Length adjustment: 39
Effective length of query: 689
Effective length of database: 610
Effective search space:   420290
Effective search space used:   420290
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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