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

GapMind for catabolism of small carbon sources

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

Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate Pf1N1B4_3984 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

Query= BRENDA::Q19842
         (724 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3984
          Length = 651

 Score =  494 bits (1272), Expect = e-144
 Identities = 291/691 (42%), Positives = 411/691 (59%), Gaps = 58/691 (8%)

Query: 47  PKFDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKS 106
           P    +L+ANRGEIACRV++TA+A+G+ TVAVHS  D ++ H + AD  V +G +  A S
Sbjct: 4   PVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADS 63

Query: 107 YLRADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHS 166
           YL+ D+++ A + +GAQA+HPGYGFLSEN  FA  +E AG  F+GP + AI  MG K  +
Sbjct: 64  YLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAA 123

Query: 167 KKIATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQARE 226
           K +   A V ++PGY GE  D +        IGYPV++KA+AGGGGKGM+V  +  Q  E
Sbjct: 124 KALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183

Query: 227 GYRLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVI 286
               +++EA SSFGD RMLVEK++  PRH+E+QV  D+HGN L+LNER+CSIQRR+QKV+
Sbjct: 184 ALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243

Query: 287 EEAPSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEHPI 346
           EEAP+  + PE+RR MGE AV+ A+A+GY  AGTVEFL+D++  F+F+EMNTRLQVEHP+
Sbjct: 244 EEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPV 303

Query: 347 TECITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLSRY 406
           TE ITG+D+V   +RV+ G  LP+TQ+QVPL G A E R+YAEDP   F LP+ GRL+ Y
Sbjct: 304 TEAITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDF-LPATGRLALY 362

Query: 407 VEPKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGVTH 466
            E     G R DSG+ EG EIS +YDP++ KL+  G++REQA  R+   LD + I G+  
Sbjct: 363 RESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKT 422

Query: 467 NIPLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALNARKLARA 526
           NI  LR I+    F   ++ T ++P  Y E      L P   D+   F  A        A
Sbjct: 423 NINFLRRIIGHPAFAAAELDTGFIPR-YQE-----QLLPAPSDLSDEFWQA--------A 468

Query: 527 NQFLNQNKQRSTHVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSANKAQVRIGGKT 586
            Q   Q++  +T     S  +   +         PTE  + +   E            + 
Sbjct: 469 AQAFAQSQSSTTRADDLSSPWGIGNGF---RAGLPTEITLHLSCEEQD----------RA 515

Query: 587 VTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLPEQAVKYLQYM 646
           +T+ GD +     ++ ++ GE++ T+            + G   + + +      YLQ+ 
Sbjct: 516 LTL-GDAD----AHTAQLKGEYLLTE------------HNGLRRQHRAIRRGDTLYLQWD 558

Query: 647 KEKAKVD----LSTV---------VLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQN 693
            E  +++    +S V         + +PM G+I  V V+ G  V  G +LVV+EAMKM++
Sbjct: 559 GELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEAGAQLVVLEAMKMEH 618

Query: 694 SLHAGKTGRVKAVNVKVGATVDEGEVLVELE 724
           S+ A   G +KA+  + G  V EG  LVELE
Sbjct: 619 SIRAPHAGIIKALYCQEGEMVSEGSALVELE 649


Lambda     K      H
   0.316    0.133    0.378 

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: 1088
Number of extensions: 36
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 724
Length of database: 651
Length adjustment: 39
Effective length of query: 685
Effective length of database: 612
Effective search space:   419220
Effective search space used:   419220
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 (21.6 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, or view the source code.

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