GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_663
          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 (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