Aligments for a candidate for fadB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Aligments 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:

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