GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Dyella japonica UNC79MFTsu3.2

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate N515DRAFT_1417 N515DRAFT_1417 long-chain acyl-CoA synthetase

Query= SwissProt::P39062
         (572 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1417
          Length = 562

 Score =  155 bits (393), Expect = 3e-42
 Identities = 139/519 (26%), Positives = 223/519 (42%), Gaps = 49/519 (9%)

Query: 72  EKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131
           ++ ++ ++ E S +    L     + KGDR+ I MP   +    + GA++ G +      
Sbjct: 49  KELSYGQIDELSRQFAGYLTGVLKLGKGDRIAIMMPNVLQYPIALFGALRAGLVVVNTNP 108

Query: 132 AFMEGAVKDRLENSEAKVVVTTPELLERIP-VDKLPHLQHVFVVGGEAESGTN--IINY- 187
            +    +K +LE++ AK +V        +  V     ++H+   G     G    +IN+ 
Sbjct: 109 MYTARELKHQLEDAGAKAIVVLDNFAATLQQVVAETEVEHIVTTGIGDLLGLKGTLINFV 168

Query: 188 --------------------DEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHV 227
                               D  A+  +  +    +   D   L YT G+TG  KG +  
Sbjct: 169 LKHIKKMVPDYRLPHAVRFRDALAQGAAHPVPKVDLGHDDLAFLQYTGGTTGVAKGAMLS 228

Query: 228 HEAMI-QQYQTGKWV-LDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGR--- 282
           H  M+    Q G W+  + K  +    TA P      +Y IF+   NG     +GG    
Sbjct: 229 HGNMVANMLQAGAWIGTNAKPGEEVIITALP------LYHIFSLTANGLVFTRLGGLNWL 282

Query: 283 -FSPESWYGTIEQLGVNVWYSAPTAFRMLMGA--GDEMAAKYDLTSLRHVLSVGEPLNPE 339
             +P    G +++L  +  ++A T    L          A+ D + L   L  G  +   
Sbjct: 283 ITNPRDMPGFVKELKKSR-FTALTGVNTLFNGLLNTPGFAEVDFSRLHLSLGGGMAVQRA 341

Query: 340 VIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIKP--GSMGKPIPGVEAAIVDNQGNE 397
           V     KV    + + + +TET S   C  P +D+K    S+G PIP  + AI       
Sbjct: 342 VAERWKKVTGVTLAEAYGLTET-SPAACINP-LDLKDYNSSIGLPIPSTDVAIWSEDSQP 399

Query: 398 LPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVD 457
           LP   +G L +K   P +M   W  P++        GW  +GD A MD  GY +   R  
Sbjct: 400 LPIGEVGELMVKG--PQVMQGYWKRPDETAKVLGADGWLHTGDIARMDANGYVYIVDRKK 457

Query: 458 DVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKE 517
           D+I+ SG  V P EVE  ++ HP +AE   +G PD   GE++K F+  ++     + LKE
Sbjct: 458 DMILVSGFNVYPNEVEDIVMTHPGVAEVAAVGVPDEHSGEVVKLFVVRKDPNLTVEALKE 517

Query: 518 EIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLK 556
               F ++ L  +  P+ IEF+D LPK+  GKI+RR L+
Sbjct: 518 ----FCRENLTGYKRPKLIEFRDALPKSNVGKILRRELR 552


Lambda     K      H
   0.318    0.136    0.425 

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: 774
Number of extensions: 35
Number of successful extensions: 5
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: 572
Length of database: 562
Length adjustment: 36
Effective length of query: 536
Effective length of database: 526
Effective search space:   281936
Effective search space used:   281936
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 (21.7 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