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_058929096.1 AU252_RS00800 long-chain fatty acid--CoA ligase

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



>NCBI__GCF_001484605.1:WP_058929096.1
          Length = 518

 Score =  268 bits (686), Expect = 3e-76
 Identities = 176/534 (32%), Positives = 276/534 (51%), Gaps = 33/534 (6%)

Query: 31  IGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHN 90
           IG++ A    R P+R ALV    GRR +Y +L    + LA AL  +G+  GDR+ + + N
Sbjct: 5   IGSWIAGRAFRDPDRIALVDGDTGRRRSYGELHERTNALADALTRLGVRRGDRIALLAMN 64

Query: 91  NAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLREL 150
           + E++ + LA A++G + V IN      EV Y L   G  + V  A+         L E+
Sbjct: 65  SPEFLEVMLAGAKMGAITVPINFRLSADEVRYVLEDSGATVFVHSAQ---------LAEV 115

Query: 151 APEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVA 210
           A            A++   L+ V+ I     + A       + E ++ G+        + 
Sbjct: 116 ASA----------ASRGLMLRFVLEIPSSVERAAQASSA--YEEFLSTGSTET-----LE 158

Query: 211 AGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK-LTPADRLCIPVPLYHC 269
             +   D   I +TSGTTG PKGA +THRN+L     +    K L   D      PL+H 
Sbjct: 159 RDVAEEDVTLIMYTSGTTGVPKGAMITHRNLLWQTLHMITLAKGLNSYDVTVTAAPLFHI 218

Query: 270 FGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEF 329
            G+    L     G T V   + FDP   ++ ++ E+ T +  V +M+ A    P     
Sbjct: 219 GGLATHTLPLLYLGGTTVIV-ESFDPAQTVELMEREKVTVMFLVASMWTAVSLLPDLDTK 277

Query: 330 NLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVST 389
           +LS ++  I  G+P P   ++   E+  +   T  YG+TE++  SC  + +  +SK   +
Sbjct: 278 DLSAVKYAISGGAPLPLPTLEFFDERGWV--FTEGYGLTESTCASCFLAPEYVVSK-AGS 334

Query: 390 VGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTG 449
           VG    H  +++VD DT   V +G+ GE   +G ++  GYWG   +T +A   GGW HTG
Sbjct: 335 VGHPVTHQRMRLVD-DTDRDVAVGEVGEILLQGPNIFAGYWGRPRETADAF-RGGWFHTG 392

Query: 450 DLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEEL 509
           DLA  D++G++ +V R KDMVI GGEN+YP E+E+ L+RHP+V +  V+G+PD K+GE +
Sbjct: 393 DLARADSQGFLTLVDRKKDMVITGGENVYPIEVEQVLFRHPEVLEAAVIGLPDNKWGESV 452

Query: 510 CAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIR 563
            A ++  P +  TE+++ A+ + ++AH+K PR I FV   P   TGK+ K  +R
Sbjct: 453 TAIVVRTPESTLTEEELIAWTRERLAHFKCPRRIEFVEELPRNATGKLLKRDLR 506


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: 649
Number of extensions: 39
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: 2
Length of query: 578
Length of database: 518
Length adjustment: 36
Effective length of query: 542
Effective length of database: 482
Effective search space:   261244
Effective search space used:   261244
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