GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Dechlorosoma suillum PS

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Dsui_3212 Dsui_3212 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>lcl|FitnessBrowser__PS:Dsui_3212 Dsui_3212 acyl-CoA synthetase
           (AMP-forming)/AMP-acid ligase II
          Length = 555

 Score =  213 bits (543), Expect = 1e-59
 Identities = 165/542 (30%), Positives = 256/542 (47%), Gaps = 17/542 (3%)

Query: 29  QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIW 87
           +++G  F    A+  +R A +++  G   TY +L   +   A+ L   + L  G RV + 
Sbjct: 23  KSLGQLFEQSCAQYRDRVAYINMGVG--ITYGELDRLSRDFAAYLQDVLKLPQGARVALM 80

Query: 88  SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTS--DYLG 145
             N  ++ +      + G V+VN NP Y   E+E+ L   G + +V +  F  +    L 
Sbjct: 81  MPNLLQYPVCMFGALRAGYVVVNCNPLYTHRELEHQLKDSGAEAIVIVENFAHTLEQALP 140

Query: 146 MLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPR 205
           ++  L           L A K   +  VV    +       P  ++F   +ARG  A  R
Sbjct: 141 LVPGLKHVIVTSLGDMLGALKGTVVNLVVRHVKKMVPAWKLPRHVKFKAAMARGKGATLR 200

Query: 206 LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK--LTPADRLCIP 263
             QV       D   +Q+T GTTG  KGA L HRNI+ N       ++  L    +L I 
Sbjct: 201 PVQVGH----EDIAYLQYTGGTTGVAKGAMLLHRNIIANLQQAHAWIEPFLHKDQQLIIT 256

Query: 264 -VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD 322
            +PLYH F +    L     GAT V   +  D    ++ +   + T + GV T+F A L+
Sbjct: 257 ALPLYHIFSLTANCLTFLKIGATNVLITNPRDIPGFVKELAQYKFTVITGVNTLFNALLN 316

Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382
           +P FA+ + S LR  +  G      V ++   Q+  + +  AYG+TETSP +  +  D  
Sbjct: 317 NPDFAKLDFSALRAALGGGMAVQKSVAQKW-RQVTGKPLIEAYGLTETSPAATINPLD-- 373

Query: 383 LSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDE 442
           L +    +G      E+ I D D G  +P+GQ GE C +G  VM GYW    +T      
Sbjct: 374 LGEFNGAIGLPISSTEIVIRD-DLGNDLPVGQAGEICIRGPQVMKGYWLRPDETATVFYA 432

Query: 443 GGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPD 502
            G++ TGD+  MD +G+V IV R KDM++  G N+YP E+E  +  HP V +V  VGVP 
Sbjct: 433 DGFLRTGDVGVMDEKGFVRIVDRKKDMILVSGFNVYPNEVEAVVAMHPAVMEVAAVGVPS 492

Query: 503 QKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKI 562
           +  GE +  +++ K     T++ + A CK  +  YKVP  + F    P T  GKI +  +
Sbjct: 493 EHSGEAVKIFVVLK-DKSVTKEQLIAHCKENLTGYKVPHLVEFRDDLPKTNVGKILRRAL 551

Query: 563 RD 564
           ++
Sbjct: 552 KE 553


Lambda     K      H
   0.320    0.136    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: 715
Number of extensions: 39
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: 578
Length of database: 555
Length adjustment: 36
Effective length of query: 542
Effective length of database: 519
Effective search space:   281298
Effective search space used:   281298
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 (21.8 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, the preprint on GapMind for carbon sources, 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