GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Azospirillum brasilense Sp245

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AZOBR_RS31155 AZOBR_RS31155 AMP-dependent synthetase

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



>lcl|FitnessBrowser__azobra:AZOBR_RS31155 AZOBR_RS31155
           AMP-dependent synthetase
          Length = 567

 Score =  232 bits (592), Expect = 3e-65
 Identities = 167/556 (30%), Positives = 278/556 (50%), Gaps = 34/556 (6%)

Query: 23  DVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGD 82
           + P+  + + A   D  AR  ER  L  +  G+R TYA++     R A     +G++ G 
Sbjct: 25  NAPIPVKPLTALLEDAAARFAERPFLDFM--GKRSTYAEVARMVDRAARGFQAIGVSKGV 82

Query: 83  RVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSD 142
           RVG++  N   +V+   A  + G  +VN NP Y   E+ + +   G +L+V++       
Sbjct: 83  RVGLFLPNTPYFVICYFAILKAGGTVVNFNPLYAERELHHQITDSGVELMVTLDLKVL-- 140

Query: 143 YLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPG---LLRFTELIARG 199
           Y  M R LA     +      A  LP  K  ++   +  + A  P     L F  L+A  
Sbjct: 141 YGKMARMLAESGLKRLVICPMADILPFPKNWLFPIVKRAEVARIPADDRHLSFRRLVAND 200

Query: 200 NAADPRLAQVAAGLQATDPINI-QFTSGTTGFPKGATLTHRNILNNG-----FFIGECMK 253
            A  P        +  T+ + + Q+T GTTG PKGA LTH N+  N      +F+G    
Sbjct: 201 GAPKP------VAIDPTEDVAVLQYTGGTTGVPKGAMLTHANLFANTEQCSLWFVG---A 251

Query: 254 LTPADRLCIPVPLYHCFGM-VLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHG 312
               +R+   +P +H F M V+ N +       ++ P   F+   V++T+   + T    
Sbjct: 252 RQGEERMLGVLPFFHVFAMTVVMNFSIRIGAEIVMLPR--FELDQVMETIHARKPTLFPA 309

Query: 313 VPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSP 372
           VPT++ A   H    +++LS++R  +  G+P P EV K   E+     +   YG++E+SP
Sbjct: 310 VPTIYTAINHHRHLEKYDLSSIRYCLSGGAPLPVEV-KEAFERNTGCVLVEGYGLSESSP 368

Query: 373 VSCQSSTDTPLS--KRVSTVGQVQPHLEVKIVD-PDTGAVVPIGQRGEFCTKGYSVMHGY 429
           V    +T  P++   +  ++G   P   ++IV   +   V+P+G++GE C +G  VM GY
Sbjct: 369 V----ATANPITGLNKAGSIGLPLPGTLIEIVSLEEPRRVLPVGEKGEVCIRGPQVMKGY 424

Query: 430 WGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRH 489
           W   ++T   + +G  +HTGD+  MD +GY +IV RIKDM++  G N+YPR +EE +Y H
Sbjct: 425 WNKPSETALTLVDGR-LHTGDVGYMDEDGYTHIVDRIKDMILCSGFNVYPRNVEEAIYLH 483

Query: 490 PQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSF 549
           P V +  V G+PD+  G+ + A+I    G   T +++  F K +++  ++P+ I F    
Sbjct: 484 PAVAECVVAGLPDEYRGQTVKAYIRVDDGKTLTREELIGFLKDKLSPIEMPKAIEFRGEL 543

Query: 550 PMTVTGKIQKFKIRDE 565
           P T+ GK+ +  + DE
Sbjct: 544 PKTMIGKLSRKALLDE 559


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: 724
Number of extensions: 40
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: 1
Length of query: 578
Length of database: 567
Length adjustment: 36
Effective length of query: 542
Effective length of database: 531
Effective search space:   287802
Effective search space used:   287802
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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