GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Pseudomonas putida KT2440

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate PP_2136 PP_2136 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__Putida:PP_2136
          Length = 715

 Score =  362 bits (929), Expect = e-104
 Identities = 234/689 (33%), Positives = 358/689 (51%), Gaps = 27/689 (3%)

Query: 23  VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFG---KPPQPPAL-- 77
           VN  +      + + V+A  AD +V+ +++      FI GADITEF    K P+   +  
Sbjct: 29  VNKFNRLTLNELRQAVDAIRADASVKGVIVRSGKDVFIVGADITEFVDNFKLPEAELVAG 88

Query: 78  ----NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133
               N +  A E+   PT+AAI+G ALGGGLE+ L   +RV    A++GLPEVKLG+ PG
Sbjct: 89  NLEANRIFNAFEDLEVPTVAAINGIALGGGLEMCLAADYRVMSTSARIGLPEVKLGIYPG 148

Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVAGAVAFAKKVLA- 190
            GGT RLPR +G + A++ I  G    A +ALK G V+ VV  E L+AGA+   K+ ++ 
Sbjct: 149 FGGTVRLPRLIGSDNAIEWIAAGKENRAEDALKVGAVDAVVAPELLLAGALDLIKRAISG 208

Query: 191 --EKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFE 248
             + +  R+ + +  KL A +   +  T       +      AP     +I  A +   +
Sbjct: 209 ELDYKAKRQPKLEKLKLNAIEQMMAFETAKGFVAGQAGPNYPAPVEAIKSIQKAANFGRD 268

Query: 249 EGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGG 308
           + L+ E  GF KL  +  +++    F  ++E  +     D      V + A++GAG MGG
Sbjct: 269 KALEVEAAGFAKLAKTSVAESLIGLFLNDQELKRKAKAHDEIA-HDVKQAAVLGAGIMGG 327

Query: 309 GIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVG 368
           GIA   A  G P+ + +  EE ++ GL    K       +G L P   A+ +  I   + 
Sbjct: 328 GIAYQSAVKGTPILMKDIREEAIQLGLNEASKLLGNRVEKGRLTPAKMAEALNAIRPTLS 387

Query: 369 LENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDV 428
             +  + D+++EAV E   VK+ V   V+   K  A+LASNTS +SI+ +A   KRP++ 
Sbjct: 388 YGDFANVDIVVEAVVENPKVKQAVLAEVEGQVKDDAILASNTSTISINLLAKALKRPENF 447

Query: 429 LGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAAR 488
           +GMHFF+P ++M L E++RG K++  A+ T V+ AKK+ K P+VV  C GF+ NR+L   
Sbjct: 448 VGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVAYAKKMGKNPIVVNDCPGFLVNRVLFPY 507

Query: 489 SKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR---------KDRGI 539
                KL+  G    ++D V+ KFG PMGP  + D+ G+D G   R         + +  
Sbjct: 508 FGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEGFPDRMKDE 567

Query: 540 KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEE 599
           +    DAL EA R GQK GKG+Y YE   R   P    +  + D L  +  ++R++TDE+
Sbjct: 568 RRSAVDALYEANRLGQKNGKGFYAYETDKRG-KPKKVFDATVLDVLKPIVFEQREVTDED 626

Query: 600 ILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAER 659
           I+  M+ P+  E  R LE+ I    ++ D+  +YG G+P +RGG + Y DS+G+      
Sbjct: 627 IINWMMVPLCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGALRYIDSIGVAEFVAL 686

Query: 660 LSAYAKATNDPSLEPAPLLARLAAEGKTF 688
              YA     P   P   L  +A  G+ F
Sbjct: 687 ADQYADL--GPLYHPTAKLREMAKNGQRF 713


Lambda     K      H
   0.317    0.134    0.383 

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: 1011
Number of extensions: 64
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: 699
Length of database: 715
Length adjustment: 39
Effective length of query: 660
Effective length of database: 676
Effective search space:   446160
Effective search space used:   446160
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: 55 (25.8 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