GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Caulobacter crescentus NA1000

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate CCNA_00074 CCNA_00074 multifunctional fatty acid oxidation complex subunit alpha FadJ

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__Caulo:CCNA_00074
          Length = 733

 Score =  426 bits (1094), Expect = e-123
 Identities = 269/724 (37%), Positives = 384/724 (53%), Gaps = 29/724 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           F + V  D +A++T DVPG  MNTL A    ++  I+++++ + E++GVV  S K   F 
Sbjct: 4   FKIEVDSDGVALVTFDVPGRSMNTLTASVIKEIGEIVERIKSDAEIKGVVITSGKTTGFC 63

Query: 67  AGADINMIGN----CKTAQEAEALARQG-------QQLMAEIHALPIQVIAAIHGACLGG 115
           AGAD+  +G        A   EA  +          +    +      V AAI+G  +GG
Sbjct: 64  AGADLGELGGGGGMAGGAAGGEAALKAAFDAGFALNKAFRGLETCGKPVAAAINGLAMGG 123

Query: 116 GLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLR 175
           GLE+ALACH RV  D PK  L LPE ++GLLPG+GGTQRLPRL+GV  A   +L GK ++
Sbjct: 124 GLEIALACHYRVVADHPKIQLALPEAKVGLLPGAGGTQRLPRLMGVMAAAPYLLEGKSMK 183

Query: 176 AKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG-----PLGRALLFK 230
             +AL   +V +VVP   ++EAA    K +     P   ++  L G     P G   +F 
Sbjct: 184 PAEALANKVVHEVVPVDQVVEAAKTWVKTKGDPVAPWDKKDFKLPGGGPYTPTG-GQVFI 242

Query: 231 MVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RSIF 289
           M       +T GNYPA   IL+ V  G      +    E R F +  M+PQ++ + R++F
Sbjct: 243 MGNAMLRKQTYGNYPAQLNILKAVYEGTQVPFDAAIRIETRYFLKTMMSPQAKGMIRTLF 302

Query: 290 FASTDVKKDPG--SDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINH 347
            +  ++ K  G  +D PP+    V +LG G+MG GIAYV A  AGI   + D + +    
Sbjct: 303 LSLQELGKGSGRPADVPPSEAKKVAVLGAGMMGAGIAYVQAM-AGIETVLIDQSQEAAEK 361

Query: 348 ALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMV 407
              Y+ + L+  V R  +   + D  LALI+ TTDY      DL+IEAVFE+ E+K  + 
Sbjct: 362 GKGYAENLLKKAVSRGKMTQDKADAVLALITPTTDYAHVKGSDLVIEAVFESREIKADVT 421

Query: 408 AEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSA 467
            + E   A   IF SNTS+LPI  +A  + RP+  IG+HFFSPV+KM LVEII    TS 
Sbjct: 422 QKAEAQLAEDAIFGSNTSTLPITGLAKASVRPKNFIGIHFFSPVDKMGLVEIIMGEETSD 481

Query: 468 QTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFG 527
           + +A ++    K  KTPIVV D  GFY +R    ++ E + ML  G     ID      G
Sbjct: 482 EALAKSIDYVLKIKKTPIVVNDSRGFYTSRCFGTFVQEGLEMLADGIAPAIIDNVGRATG 541

Query: 528 FPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFS----APANVVSSILNDDRKGRKNGRGF 583
            P GP+++ D+V +D G K+    +   G++F     AP  +   ++   R GRKNG+GF
Sbjct: 542 MPRGPLEMNDDVALDLGYKVTQQTKKDLGDKFEDRPFAPI-IEKMVVELQRFGRKNGKGF 600

Query: 584 YLYGQKGRKSKKQVDPAIYPL-IGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642
           Y Y + G K+  +    + P+ I    Q  I   ++  R +     EA RC +E VI   
Sbjct: 601 YDYPETGPKTLWKGLSELAPVTIAEADQALIQ--EIRTRLLYRQAVEAARCFEEGVITDP 658

Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702
           R+ D+GA+ G GF P+ GGP   ID +GA   V    +LA +YG RF P   L EM  +G
Sbjct: 659 READVGAILGWGFAPWTGGPISLIDGVGAKAFVETCDQLAQKYGKRFAPPALLREMAEKG 718

Query: 703 ESFW 706
           E+F+
Sbjct: 719 ETFY 722


Lambda     K      H
   0.319    0.137    0.393 

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: 1043
Number of extensions: 48
Number of successful extensions: 8
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: 714
Length of database: 733
Length adjustment: 40
Effective length of query: 674
Effective length of database: 693
Effective search space:   467082
Effective search space used:   467082
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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