GapMind for catabolism of small carbon sources

 

Alignments 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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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