GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimF in Pseudomonas fluorescens FW300-N2E2

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Pf6N2E2_2290 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

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



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2290 Enoyl-CoA hydratase
           (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA
           isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase
           (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC
           5.1.2.3)
          Length = 715

 Score =  340 bits (873), Expect = 1e-97
 Identities = 223/689 (32%), Positives = 349/689 (50%), Gaps = 27/689 (3%)

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

Query: 78  ----NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133
               N + +  E+   PT+ AI+G ALGGGLE+ L   +RV    AK+GLPEVKLG+ PG
Sbjct: 89  NLEANRIFSDFEDLNVPTVVAINGIALGGGLEMCLAADYRVMSTTAKIGLPEVKLGIYPG 148

Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE--NLVAGAVAFAKKVLA- 190
            GGT RLPR +G + A++ I  G    A +ALK G V+ VVE   L   A+   K+ ++ 
Sbjct: 149 FGGTVRLPRLIGADNAIEWIAAGKENRAEDALKVGAVDAVVEPGKLQEAALETIKRAISG 208

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

Query: 249 EGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGG 308
           + L+ E  GF+KL  +  +++    F  ++E  K     D    R V + A++GAG MGG
Sbjct: 269 KALEVEAAGFVKLAKTSAAQSLIGLFLNDQELKKKAKAYDEIA-RDVKQAAVLGAGIMGG 327

Query: 309 GIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVG 368
           GIA   A+ G P+ + +  E  +++GL    K       +G +     A+ +  I   + 
Sbjct: 328 GIAYQSASKGTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTAAKMAEVLNGIRPTLS 387

Query: 369 LENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDV 428
             +    DL++EAV E+  VK+ V   V+   K   +LASNTS +SI  +A   KRP++ 
Sbjct: 388 YGDFGHVDLVVEAVVESPKVKQAVLAEVEDKVKEDTILASNTSTISISLLAKALKRPENF 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 VGMHFFNPVHMMPLVEVIRGEKSSEHAVATTVAYAKKMGKNPIVVNDCPGFLVNRVLFPY 507

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

Query: 540 KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEE 599
           +    D L EA R GQK GKG+Y YE   R        ++ + + L  +  ++R++TDE+
Sbjct: 568 RRSAVDVLYEAKRLGQKNGKGFYAYETDKRGKQ-KKVADSSVLEVLKPIVYEQREVTDED 626

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

Query: 660 LSAYAKATNDPSLEPAPLLARLAAEGKTF 688
              YA         P   L  +A  G++F
Sbjct: 687 ADQYADL--GALYHPTAKLREMAKNGQSF 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: 970
Number of extensions: 61
Number of successful extensions: 6
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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