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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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:

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:

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:

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:

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