GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Nocardioides daejeonensis MJ31

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_110205694.1 DNK54_RS04545 AMP-binding protein

Query= metacyc::MONOMER-20125
         (556 letters)



>NCBI__GCF_003194585.1:WP_110205694.1
          Length = 539

 Score =  194 bits (492), Expect = 1e-53
 Identities = 169/546 (30%), Positives = 250/546 (45%), Gaps = 46/546 (8%)

Query: 20  LERAATVYGDCTSVVYDAVS--YTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQM 77
           LER    + D  ++V  A    +TW +  R    LA  +   G+  G  + + APN    
Sbjct: 22  LERTVAAHADREALVEVASGRRWTWREFDRDVNALARGLIGAGVAVGDRIGIWAPNCAAW 81

Query: 78  YELHFAVPMAGAILNAVNLRLDARTISILLHHSE-SKLIFVDHLSRDLILEAIALFPKQA 136
               +A    GAIL  VN        +   + S  S ++             IA   ++ 
Sbjct: 82  TLTQYAAAKVGAILVNVNPAYRTHEFAYAANQSGLSMVVAATRFKESDYAGMIAATAQEC 141

Query: 137 P-VPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPK-----SEWDPMILN 190
           P + R+V++ DE+              S++ L+D G+   +  +       +  DP+ + 
Sbjct: 142 PTIERVVYLDDEA--------------SWQGLLDDGEGVTEDQLRARMDGLAPGDPINIQ 187

Query: 191 YTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYP-WGMAAV 249
           YTSGTT  PKG    HR I      +    G  +       +P +H  G      G  + 
Sbjct: 188 YTSGTTGYPKGATLSHRNILNNGYFTTELIGFTEADRLCIPVPFYHCFGMVMANLGCTSH 247

Query: 250 GGTNICLRK-FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKTTVQIMTAGA 306
           G T +     FD E+    I     + + G P +   + N P      L T    + AG+
Sbjct: 248 GATMVIPAPGFDPELTLRAIADERCSAVYGVPTMFIAMQNHPTFADHDLSTLRTGIMAGS 307

Query: 307 PPPSAVLFRT-ESLGFA-VSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGT 364
             P  V+ R    +  A V   YG+TET+   VSC  +++ +    T          +G 
Sbjct: 308 ICPVEVMKRCINDMHMAEVGIAYGMTETSP--VSCQTRRDDDLERRTA--------SIGR 357

Query: 365 VM-QTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGD 423
           V    +I VVDPVTG  V R G T GE   RG SVMLGY +D E TA+++ ADGW +TGD
Sbjct: 358 VHPHVEIKVVDPVTGETVPR-GET-GEFCTRGYSVMLGYWEDSEKTAEAIDADGWMHTGD 415

Query: 424 VGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPC 483
           + VM  DGY  I  R KD++I GGEN+   E+E  LY+HPDI +  V+  PDE +GE  C
Sbjct: 416 LAVMREDGYANIVGRIKDMVIRGGENIYPREIEEFLYTHPDIEDVQVIGVPDEKYGEELC 475

Query: 484 AFVSLKKGLTKKPTEKEIVE-YCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILR-DMA 541
           A+V L+ G    P +   V  +   KL  + +P+ V+  EE P T TGK++K  +R + A
Sbjct: 476 AWVKLRAG--ADPLDAAAVRAFATGKLAHFKIPRYVMVVEEFPMTVTGKIRKVQMREESA 533

Query: 542 RGMGSA 547
           + +G A
Sbjct: 534 QALGLA 539


Lambda     K      H
   0.319    0.135    0.412 

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: 717
Number of extensions: 47
Number of successful extensions: 5
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: 556
Length of database: 539
Length adjustment: 36
Effective length of query: 520
Effective length of database: 503
Effective search space:   261560
Effective search space used:   261560
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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