Alignments for a candidate for pimF in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Pseudomonas simiae WCS417

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF1489 PS417_07575 multifunctional fatty acid oxidation complex subunit alpha

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



>FitnessBrowser__WCS417:GFF1489
          Length = 715

 Score =  350 bits (898), Expect = e-100
 Identities = 232/696 (33%), Positives = 356/696 (51%), Gaps = 41/696 (5%)

Query: 23  VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPPQPP------- 75
           VN  +      + + V+   AD +V+ +++      FI GADITEF    + P       
Sbjct: 29  VNKFNRLTLNELRQAVDTIKADASVKGVIVSSGKDVFIVGADITEFVDNFKLPDAELVAG 88

Query: 76  --ALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133
               N + +  E+   PT+AAI+G ALGGGLE+ L   FRV    AK+GLPEVKLG+ PG
Sbjct: 89  NLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADFRVMSATAKIGLPEVKLGIYPG 148

Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE---------NLVAGAVAF 184
            GGT RLPR +G + A++ I  G    A +ALK G V+ VV          NL+ GA++ 
Sbjct: 149 FGGTVRLPRLIGADNAIEWIAAGKENKAEDALKVGAVDAVVAPDKLAEAALNLIKGAISG 208

Query: 185 AKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAID 244
                A+++P    + +  KL A +   S  T       +      AP      I  A +
Sbjct: 209 EFDYKAKRQP----KLEKLKLNAIEQMMSFETAKGFVAGQAGPNYPAPVEAIKTIQKAAN 264

Query: 245 LPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAG 304
              ++ L+ E  GF+KL  +  +++    F  ++E  K     D    + V + A++GAG
Sbjct: 265 FGRDKALEVEAAGFVKLAKTSAAQSLIGLFLNDQELKKKAKAYDEIA-KDVKQAAVLGAG 323

Query: 305 TMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALIT 364
            MGGGIA   A+ G P+ + +  E  +++GL    K       +G +     A+ +  I 
Sbjct: 324 IMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTAAKMAEVLNGIR 383

Query: 365 GLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKR 424
             +   +    DL++EAV E   VK+ V   V+A  K   +LASNTS +SI  +A   KR
Sbjct: 384 PTLSYGDFGHVDLVVEAVVENPKVKQAVLAEVEAQVKDDTILASNTSTISISLLAKALKR 443

Query: 425 PQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRM 484
           P++ +GMHFF+P ++M L E++RG K++  A+ T V+ AKK+ K P+VV  C GF+ NR+
Sbjct: 444 PENFVGMHFFNPVHMMPLVEVIRGEKSSELAVATTVAYAKKMGKNPIVVNDCPGFLVNRV 503

Query: 485 LAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR---------K 535
           L        KL+  G    ++D V+ KFG PMGP  + D+ G+D G   R         +
Sbjct: 504 LFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEGFPDR 563

Query: 536 DRGIKSEIADALCEAGRFGQKTGKGYYKYE---QGSRAPMPDPEVETLINDTLAKLGLKR 592
            +  +    DAL EA R GQK GKG+Y YE   +G +  + DP V    ++ LA +  ++
Sbjct: 564 MKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQKKVADPSV----HEVLAPVIYEQ 619

Query: 593 RDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVG 652
           R+++DE+I+  M+  +  E  R LE+ I    ++ D+  +YG G+P +RGG + Y DS+G
Sbjct: 620 REVSDEDIINWMMIALCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGALRYIDSIG 679

Query: 653 LKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           +         YA     P   P   L  +A  G++F
Sbjct: 680 VAEFVALADKYADL--GPLYHPTAKLREMAKNGQSF 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: 1000
Number of extensions: 62
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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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
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