GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Algiphilus aromaticivorans DG1253

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_043765768.1 U743_RS04305 long-chain-fatty-acid--CoA ligase

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



>NCBI__GCF_000733765.1:WP_043765768.1
          Length = 513

 Score =  231 bits (589), Expect = 5e-65
 Identities = 167/529 (31%), Positives = 253/529 (47%), Gaps = 35/529 (6%)

Query: 40  ARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQL 99
           A Q   +A  +V   RR ++ ++     RLA A+  +G+  GDRV I S N+  ++    
Sbjct: 10  AVQTRGDATATVCGDRRRSWREVADRVARLAGAVQALGVQRGDRVAILSLNSDRYIEYLY 69

Query: 100 ATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQP 159
           A A  G     +N      E+ Y L   G ++L     F  +  L  LRE          
Sbjct: 70  AVAWAGAAANPVNIRMAPGEIAYTLEDSGSRVLFVDDTF--APMLPALRE---------- 117

Query: 160 GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPI 219
                 ++  L+ V++     G G    G   F  LIA    A   +    AG +  D  
Sbjct: 118 ------QVSALEQVIF----CGDGELPEGTQGFEALIA----AHGPVPDADAGEE--DLA 161

Query: 220 NIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLAC 279
            + +T GTTG  KG  L+H N+++N       +    +       P++H   M       
Sbjct: 162 GLFYTGGTTGKAKGVMLSHDNVMHNMLNAIPILGYDASTVYLHAGPMFHLADMASTFAVT 221

Query: 280 FTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIM 339
              G   V P    +PL  L+ +Q E+ T    VPTM    L   R  EF+LS+LR  + 
Sbjct: 222 AAGGVHCVIPRFDIEPL--LEIMQREKVTHTMLVPTMINMLLASGRIQEFDLSSLRRMLY 279

Query: 340 AGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPL--SKRVSTVGQVQPHL 397
             SP P  V+ R +E +     T  YG TE +P+      +     S ++++ G     +
Sbjct: 280 GASPMPEAVLLRAMEALPTTGFTQGYGQTEAAPLITFMPPEAHYAGSDKLASAGVPGYSV 339

Query: 398 EVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAE 457
           +V I+D D G  +P GQ GE C +G ++M GYW    +T   + +G W+ TGDL  MD +
Sbjct: 340 DVAIMDED-GTALPNGQVGEVCARGGNIMQGYWKRAEQTAATLRDG-WLRTGDLGYMDDD 397

Query: 458 GYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP 517
           G+V IV R KDM+I GGEN++  E+E  +Y+HP VQ+  V+GVP +++GE + A ++ K 
Sbjct: 398 GFVFIVDRAKDMIISGGENVFSVEVEGAIYQHPDVQETAVIGVPSERWGEAVHAVVVPKA 457

Query: 518 GTQPTEDDIRAFCKGQIAHYKVPRYIRFVTS-FPMTVTGKIQKFKIRDE 565
           G  PTE  I   C+G IA YK+PR +   +   P++  GKI K  +RD+
Sbjct: 458 GATPTEQAIIEHCRGVIADYKLPRSVEIRSEPLPVSGAGKILKTTLRDD 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: 697
Number of extensions: 41
Number of successful extensions: 6
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: 513
Length adjustment: 35
Effective length of query: 543
Effective length of database: 478
Effective search space:   259554
Effective search space used:   259554
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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