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:

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