GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS31155
          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:

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