GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudarthrobacter sulfonivorans Ar51

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058930593.1 AU252_RS10060 o-succinylbenzoate--CoA ligase

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



>NCBI__GCF_001484605.1:WP_058930593.1
          Length = 520

 Score =  222 bits (565), Expect = 3e-62
 Identities = 166/540 (30%), Positives = 247/540 (45%), Gaps = 32/540 (5%)

Query: 31  IGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHN 90
           IG++      +   + AL+S +  R  +Y      + RLA+AL   G+  GDRV     N
Sbjct: 6   IGSWLQRRRPKSGNKTALISGN--RELSYEAFADRSVRLANALRDRGVAKGDRVAYLGEN 63

Query: 91  NAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARF-----KTSDYLG 145
           +  ++    A   +G + V +N      E+++ L   G  +LV          + SD   
Sbjct: 64  HPAFLETLFAAGLLGAIFVPLNTRLAPPEIQFQLQDCGAHILVHSQSLDVLGTRGSDATP 123

Query: 146 MLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPR 205
           + R +             A   P+ + VV ++D             F  ++A G      
Sbjct: 124 VARRIVVNDAADTAAATTAT--PRDQAVVSVED-------------FEAVLASGTE---E 165

Query: 206 LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVP 265
                 GL   D   I +TSGTTG PKGA LTH N++ N   +         D   +  P
Sbjct: 166 FRDETVGLD--DGAMILYTSGTTGRPKGALLTHGNVVWNCMNVIVDFDFASTDVALMISP 223

Query: 266 LYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPR 325
           ++H   + +G L     G T+V     F+P   L+ VQ  R T L GVPT F    +HP 
Sbjct: 224 MFHVASLDMGVLPTLLKGGTVVLEAK-FEPQRTLELVQKHRATTLSGVPTTFQMLCEHPD 282

Query: 326 FAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK 385
           +   +LS+L      GS  P  V+    EQ  L   +  YGMTET+P +     D    K
Sbjct: 283 WEGTDLSSLTKLTCGGSAVPLRVLD-AYEQRGLH-FSNGYGMTETAPGATTLPADRSREK 340

Query: 386 RVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGW 445
             S+ G      +V+I D D G   P    GE   KG +V+  YW       ++    GW
Sbjct: 341 AGSS-GLPHFFTDVRITDFD-GNQAPPETVGEIHIKGPNVIGQYWNRPEAIDQSTTADGW 398

Query: 446 MHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKY 505
             +GD+   D +G+V I  R+KDM+I GGENIYP E+E+ +     V  V V+GVPD+K+
Sbjct: 399 FKSGDMGYKDTDGFVFISDRLKDMIISGGENIYPAEVEQAITELVAVASVAVIGVPDEKW 458

Query: 506 GEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDE 565
           GE   A I+ + G   TED ++    G++A YK+P+ + FV   P T +GKI+K  +R +
Sbjct: 459 GEVPRAVILLREGAHLTEDQLKEHLNGRLARYKIPKSVVFVAEMPRTASGKIKKTGLRQQ 518


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: 652
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 578
Length of database: 520
Length adjustment: 36
Effective length of query: 542
Effective length of database: 484
Effective search space:   262328
Effective search space used:   262328
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 Apr 09 2024. 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