Aligments for a candidate for pimF in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Aligments for a candidate for pimF in Caulobacter crescentus NA1000

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate CCNA_00074 CCNA_00074 multifunctional fatty acid oxidation complex subunit alpha FadJ

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



>FitnessBrowser__Caulo:CCNA_00074
          Length = 733

 Score =  341 bits (874), Expect = 8e-98
 Identities = 249/733 (33%), Positives = 357/733 (48%), Gaps = 54/733 (7%)

Query: 11  DQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRT-FIAGADITE 67
           D VA+VT D P   +N L+A+V + I E V    +D  ++ +V+     T F AGAD+ E
Sbjct: 11  DGVALVTFDVPGRSMNTLTASVIKEIGEIVERIKSDAEIKGVVITSGKTTGFCAGADLGE 70

Query: 68  FGKPPQPP------------------ALNDVIAALENSPKPTIAAIHGTALGGGLEVALG 109
            G                        ALN     LE   KP  AAI+G A+GGGLE+AL 
Sbjct: 71  LGGGGGMAGGAAGGEAALKAAFDAGFALNKAFRGLETCGKPVAAAINGLAMGGGLEIALA 130

Query: 110 CHFRVAVKEAK--LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKH 167
           CH+RV     K  L LPE K+GLLPGAGGTQRLPR +G   A   ++ G  +  AEAL +
Sbjct: 131 CHYRVVADHPKIQLALPEAKVGLLPGAGGTQRLPRLMGVMAAAPYLLEGKSMKPAEALAN 190

Query: 168 GLVEEVV--ENLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAA----KADRSIFTNAVAA 221
            +V EVV  + +V  A  + K    +  P+      D KL            +F    A 
Sbjct: 191 KVVHEVVPVDQVVEAAKTWVK---TKGDPVAPWDKKDFKLPGGGPYTPTGGQVFIMGNAM 247

Query: 222 MTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQ-RYAFFAERE 279
           + K+  G   A      A+     +PF+  ++ E   F+K ++S Q+K   R  F + +E
Sbjct: 248 LRKQTYGNYPAQLNILKAVYEGTQVPFDAAIRIETRYFLKTMMSPQAKGMIRTLFLSLQE 307

Query: 280 AAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQ 339
             K  G P    P    +VA++GAG MG GIA   A AGI   LI+  +E  ++G G  +
Sbjct: 308 LGKGSGRPADVPPSEAKKVAVLGAGMMGAGIAYVQAMAGIETVLIDQSQEAAEKGKGYAE 367

Query: 340 KNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAH 399
              +   +RG +  D     +ALIT      +VK +DL+IEAVFE+  +K +V    +A 
Sbjct: 368 NLLKKAVSRGKMTQDKADAVLALITPTTDYAHVKGSDLVIEAVFESREIKADVTQKAEAQ 427

Query: 400 AKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTA 459
               A+  SNTS L I  +A  + RP++ +G+HFFSP + M L EI+ G +T+ +AL  +
Sbjct: 428 LAEDAIFGSNTSTLPITGLAKASVRPKNFIGIHFFSPVDKMGLVEIIMGEETSDEALAKS 487

Query: 460 VSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPF 519
           +    KI K P+VV    GF  +R      ++  ++L +G  P  +D V    GMP GP 
Sbjct: 488 IDYVLKIKKTPIVVNDSRGFYTSRCFGTFVQEGLEMLADGIAPAIIDNVGRATGMPRGPL 547

Query: 520 AMGDLAGLDIGWR----SRKDRGIKSE-------IADALCEAGRFGQKTGKGYYKYEQGS 568
            M D   LD+G++    ++KD G K E       I   + E  RFG+K GKG+Y Y    
Sbjct: 548 EMNDDVALDLGYKVTQQTKKDLGDKFEDRPFAPIIEKMVVELQRFGRKNGKGFYDY---- 603

Query: 569 RAPMPDPEVETLINDTLAKLGLKRRD-ITDEEILERMVYPMINEGARILEEKIAARPSDI 627
             P   P+        LA + +   D    +EI  R++Y    E AR  EE +   P + 
Sbjct: 604 --PETGPKTLWKGLSELAPVTIAEADQALIQEIRTRLLYRQAVEAARCFEEGVITDPREA 661

Query: 628 DVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKT 687
           DV  + G+G+  + GGP+   D VG K   E     A+        PA LL  +A +G+T
Sbjct: 662 DVGAILGWGFAPWTGGPISLIDGVGAKAFVETCDQLAQKYGKRFAPPA-LLREMAEKGET 720

Query: 688 F-ASLTQPSKAAA 699
           F       +KAAA
Sbjct: 721 FYGRFGAKAKAAA 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: 1122
Number of extensions: 56
Number of successful extensions: 7
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: 733
Length adjustment: 40
Effective length of query: 659
Effective length of database: 693
Effective search space:   456687
Effective search space used:   456687
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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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, 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

GapMind for catabolism of small carbon sources