Alignments for a candidate for pimF in Phyllobacterium leguminum ORS 1419

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Phyllobacterium leguminum ORS 1419

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_110754194.1 C7477_RS16650 3-hydroxyacyl-CoA dehydrogenase

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



>NCBI__GCF_003217235.1:WP_110754194.1
          Length = 740

 Score =  307 bits (786), Expect = 1e-87
 Identities = 226/729 (31%), Positives = 346/729 (47%), Gaps = 51/729 (6%)

Query: 11  DQVAIVTVDSPP--VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADIT-- 66
           D +A+VT D P   +N  +  V   +   V+    D A++  V+     +F  GAD+T  
Sbjct: 14  DGIALVTWDMPDKSMNVFTEEVMDELETIVDRVAGDAAIKGAVITSGKDSFSGGADLTML 73

Query: 67  ---------EFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVAL 108
                    E  K  Q            +  +   LE S KP ++AI+GT +GG  E++L
Sbjct: 74  KRMFQLFQEEKAKDSQKAVELLFKSSGRMGGLFRKLETSGKPWVSAINGTCMGGAFEMSL 133

Query: 109 GCHFRVA--VKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALK 166
            CH RVA      K+ LPEVK+G+ PGAGGTQR+PR    + A+QM+  G  +    A  
Sbjct: 134 ACHARVASDAPGVKMALPEVKVGIFPGAGGTQRVPRLTNQQDALQMMTTGQSLTPQRAKA 193

Query: 167 HGLVEEVVENLVAGAVAFAKKVL-AEKRPLRRLRDDDSKLAAAK----ADRSIFTNAVAA 221
            GL+ E+        V  AKK++    +P++   +   KL  A     A  +++  A A 
Sbjct: 194 MGLITEIAP--AKKLVETAKKLIKGGLKPVQPWDEKGFKLPGAPIYSAAGANLWPAASAI 251

Query: 222 MTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQ-RYAFFAERE 279
           + ++  G   A  A    +   + +PF+ GLK E+  F +++ + ++    R  F + +E
Sbjct: 252 LRRETYGNYPAAAAILKCVYEGLLVPFDTGLKIEQRYFTQILQTLEAGMMIRSLFVSLQE 311

Query: 280 AAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQ 339
             K    P   KP   +++ +IGAG MG GIA   A +GIPV LI+   E  ++G     
Sbjct: 312 LNKGARRPADIKPTKFTKIGVIGAGFMGAGIAYVTAKSGIPVVLIDRDVEAAEKGKAHAA 371

Query: 340 KNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAH 399
                   +G +  +   K ++LI       +++ ADL+IEAVFE   VK++     +A 
Sbjct: 372 DLIAKEMQKGRMSEEDKQKLLSLIIPTADYADLEGADLVIEAVFEDREVKRQATEKAEAV 431

Query: 400 AKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTA 459
            K  A+ ASNTS L I  +A  ++RP++ +G+HFFSP + M L E++ G KT   AL  A
Sbjct: 432 LKSSAIFASNTSTLPISGLAKVSERPKNFIGIHFFSPVDKMMLVEVILGKKTGDKALAVA 491

Query: 460 VSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPF 519
           +   + I K P+VV    GF  NR +     ++  +L EG  P  ++      GMP+GP 
Sbjct: 492 LDYVRAIKKTPIVVNDTRGFYVNRCVLRYMSEAYNMLIEGVPPAMIENAARMAGMPVGPL 551

Query: 520 AMGDLAGLDIGWRSRK----DRGIKS------EIADALC-EAGRFGQKTGKGYYKYEQGS 568
           A+ D   +D+  +  K    D G K+      E+ D L  E  R G+K GKG+Y Y    
Sbjct: 552 ALNDETAIDLSQKILKAALADLGPKAVDPRHVELVDKLVNEFDRKGRKNGKGFYDYPAKP 611

Query: 569 RAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDID 628
                 PE++TL              +  EE+ ER ++ +  E AR++EE I   P + D
Sbjct: 612 AKKHLWPELKTLYPQQ------DPDKVNVEELKERFLFTIALEAARVMEEGIVTDPREAD 665

Query: 629 VVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           V  +  +G+  Y GG + Y D +G K    R     K        P  LL  +A  G+TF
Sbjct: 666 VGSILAFGFAPYTGGTLSYIDGMGAKKFVRRAKELQKKYGAQFKAP-KLLTDMADNGETF 724

Query: 689 ASLTQPSKA 697
                P KA
Sbjct: 725 YQRFDPYKA 733


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: 1052
Number of extensions: 58
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: 740
Length adjustment: 40
Effective length of query: 659
Effective length of database: 700
Effective search space:   461300
Effective search space used:   461300
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 24 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)
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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 2024 update 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