GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_3212
          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 (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