GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Acidovorax sp. GW101-3H11

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate Ac3H11_663 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_663
           Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
          Length = 559

 Score =  171 bits (432), Expect = 9e-47
 Identities = 160/573 (27%), Positives = 242/573 (42%), Gaps = 69/573 (12%)

Query: 6   PRPASSSPLTPL-GFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENG 64
           P    +S  T L   ++ A   Y D  +  +     T+ QT       A+ + SLG+  G
Sbjct: 15  PADIDTSQYTSLVALMDEAFKKYADRVAYSFMGKEVTYGQTDSLSSAFAAYLQSLGLVKG 74

Query: 65  HVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDL 124
             V+++ PNVPQ      AV  AG ++  VN     R +   L  S +K I +       
Sbjct: 75  DRVAIMMPNVPQYPVAVAAVLRAGFVVVNVNPLYTPRELEHQLKDSGAKAIVIIENFAAT 134

Query: 125 ILEAIALFPKQAPVPRLVFMADESESG------------NSSELGKEF----FCSYKDLI 168
           + + IA      PV  +V  A   + G            N  ++   +       +   +
Sbjct: 135 LEQCIA----HTPVKHVVLCAMGDQLGLLKGALVNYVVRNVKKMVPAYNLPGAVRFNQAV 190

Query: 169 DRGD------PDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGV 222
            +G       PD K        D  +L YT GTT   KG V  HR I    + S   W  
Sbjct: 191 AQGTRSTLKKPDIK------PDDIALLQYTGGTTGVSKGAVLLHRNILANVLQSEA-WNS 243

Query: 223 P--------KQPVYLWTLPMFHANGWSYPW--GMAAVGGTNICLRKFDSEIIYDMIKRHG 272
           P        +QP  +  LP++H   ++      M   G T +     D   +   + +H 
Sbjct: 244 PVMSKVPAGEQPTAVCALPLYHIFAFTVNMMLSMRTGGKTILIPNPRDLPAVLKELSKHT 303

Query: 273 VTHMCGAPVVLNMLSNAPGSEPLK-TTVQIMTAGAPPPSAVLFRT--ESLGFAVSHGYGL 329
                    + N L+N P    +    +++   G       + +   E  G  +  GYGL
Sbjct: 304 FHSFPAVNTLFNGLANHPDFNTVNWKNLKVSVGGGMAVQGAVAKLWLEKTGCPICEGYGL 363

Query: 330 TETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLG 389
           +ET+    SC      N + ATE          GT M+   D    +T           G
Sbjct: 364 SETSPST-SC------NPVTATEYTGTIGVPIPGTYMKLIDDEGREITTLGEP------G 410

Query: 390 EVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGEN 449
           E+ ++G  VM GY + P+ TAK MT DG+F +GD+G+M   G+ +I DR KD+++  G N
Sbjct: 411 EIAIKGPQVMAGYWQRPDETAKVMTDDGYFKSGDIGIMDARGFFKIVDRKKDMVLVSGFN 470

Query: 450 LSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKP---TEKEIVEYCR 506
           +   EVE ++ S P +LE AVV  PDE  GE      ++K  + KK    TE ++ E+CR
Sbjct: 471 VYPNEVEEVVASCPGVLECAVVGVPDEKTGE------AVKLVIVKKDPALTEAQVKEFCR 524

Query: 507 SKLPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539
            +L  Y  PK + F+ ELPKT  GK+ +  LRD
Sbjct: 525 RELTGYKQPKVIEFRTELPKTPVGKILRRELRD 557


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: 766
Number of extensions: 41
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 556
Length of database: 559
Length adjustment: 36
Effective length of query: 520
Effective length of database: 523
Effective search space:   271960
Effective search space used:   271960
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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