Alignments for a candidate for ech in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Caulobacter crescentus NA1000

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate CCNA_00074 CCNA_00074 multifunctional fatty acid oxidation complex subunit alpha FadJ

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Caulo:CCNA_00074
          Length = 733

 Score =  170 bits (430), Expect = 2e-46
 Identities = 128/399 (32%), Positives = 198/399 (49%), Gaps = 27/399 (6%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSL-KEGV 60
           KV V+G+G+MG GIA + A+AG E  + D S E  ++     +  L K    G + ++  
Sbjct: 325 KVAVLGAGMMGAGIAYVQAMAGIETVLIDQSQEAAEKGKGYAENLLKKAVSRGKMTQDKA 384

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           + VLA I P TD A  +KGSD VIEAV E  E+K  + + AEA  +  A+  +NTS+LPI
Sbjct: 385 DAVLALITPTTDYAH-VKGSDLVIEAVFESREIKADVTQKAEAQLAEDAIFGSNTSTLPI 443

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           + +A     P+  +G+HFF+P   M LVEI+ G++TSDE +  + +    + K  IVV D
Sbjct: 444 TGLAKASVRPKNFIGIHFFSPVDKMGLVEIIMGEETSDEALAKSIDYVLKIKKTPIVVND 503

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
             GF+ +R     ++ G  ++  GIA    +  +     G P G   + D   LD+GY V
Sbjct: 504 SRGFYTSRCFGTFVQEGLEMLADGIA--PAIIDNVGRATGMPRGPLEMNDDVALDLGYKV 561

Query: 241 ---WKAVTARGFKAFPCSS-TEKLVSQ-GKLGVKSGSGYYQYPSPG-----KFVRPTLPS 290
               K      F+  P +   EK+V +  + G K+G G+Y YP  G     K +    P 
Sbjct: 562 TQQTKKDLGDKFEDRPFAPIIEKMVVELQRFGRKNGKGFYDYPETGPKTLWKGLSELAPV 621

Query: 291 TSKKLGRYLISPAVNEVSY--------LLREGIV-GKDDAEKGCVLGLGLPK---GILSY 338
           T  +  + LI      + Y           EG++    +A+ G +LG G      G +S 
Sbjct: 622 TIAEADQALIQEIRTRLLYRQAVEAARCFEEGVITDPREADVGAILGWGFAPWTGGPISL 681

Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
            D +G    V T +++ Q  G   ++P  LL  M ++G+
Sbjct: 682 IDGVGAKAFVETCDQLAQKYG-KRFAPPALLREMAEKGE 719



 Score = 85.5 bits (210), Expect = 8e-21
 Identities = 57/175 (32%), Positives = 91/175 (52%), Gaps = 17/175 (9%)

Query: 407 LAWIVLNRPTR-YNAINGDMIREINQALDSLEEREDVRVIAIT-GQGRVFSAGADVTEFG 464
           +A +  + P R  N +   +I+EI + ++ ++   +++ + IT G+   F AGAD+ E G
Sbjct: 13  VALVTFDVPGRSMNTLTASVIKEIGEIVERIKSDAEIKGVVITSGKTTGFCAGADLGELG 72

Query: 465 S------------LTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSAD 512
                             A  A    ++ F  ++   KPV A INGLA+GGG+E+AL+  
Sbjct: 73  GGGGMAGGAAGGEAALKAAFDAGFALNKAFRGLETCGKPVAAAINGLAMGGGLEIALACH 132

Query: 513 FRVAS--KTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEA 564
           +RV +     ++  PE  +GL+PG GGTQRL RL G       +L G+ +K  EA
Sbjct: 133 YRVVADHPKIQLALPEAKVGLLPGAGGTQRLPRLMGVMAAAPYLLEGKSMKPAEA 187



 Score = 33.9 bits (76), Expect = 3e-05
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDP---LLLSMVKE-GKLGRKSGQG 385
           G+P+G L   D++ +D+     ++ ++  G D +   P   ++  MV E  + GRK+G+G
Sbjct: 541 GMPRGPLEMNDDVALDLGYKVTQQTKKDLG-DKFEDRPFAPIIEKMVVELQRFGRKNGKG 599

Query: 386 FHTY 389
           F+ Y
Sbjct: 600 FYDY 603


Lambda     K      H
   0.316    0.134    0.377 

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: 1032
Number of extensions: 59
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 733
Length adjustment: 39
Effective length of query: 612
Effective length of database: 694
Effective search space:   424728
Effective search space used:   424728
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 (21.6 bits)
S2: 54 (25.4 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