GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E3

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO353_03310 AO353_03310 long-chain fatty acid--CoA ligase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_03310 AO353_03310 long-chain
           fatty acid--CoA ligase
          Length = 566

 Score =  243 bits (620), Expect = 2e-68
 Identities = 162/534 (30%), Positives = 266/534 (49%), Gaps = 30/534 (5%)

Query: 54  GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112
           G+  TY +L   +   A+ L     L PGDR+ +   N  ++ +      + GL++VN N
Sbjct: 47  GKTLTYGELYELSGAFAAYLQQHTDLQPGDRIAVQLPNLLQYPIAVFGAIRAGLIVVNTN 106

Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKL-PQLK 171
           P Y   E+E+  N  G K LV +A         +   + P+   +     + A L P LK
Sbjct: 107 PLYTAREMEHQFNDSGAKALVCLANMAH-----LAEAVVPKTGVKHVIVTEVADLLPPLK 161

Query: 172 -----TVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSG 226
                +V+    +       P  ++F +++++G+      A  A+    +D   +Q+T G
Sbjct: 162 RLLINSVIKYVKKMVPAYHLPKAVKFNDVLSKGHGQPVTEANPAS----SDVAVLQYTGG 217

Query: 227 TTGFPKGATLTHRNILNNGFFIGECMKLTPADR------LCIPVPLYHCFGMVLGNLACF 280
           TTG  KGA LTHRN++ N   + +C  L  ++       L  P+PLYH +      +A  
Sbjct: 218 TTGVAKGAMLTHRNLVAN---MMQCRALMGSNLNEGCEILITPLPLYHIYAFTFHCMAMM 274

Query: 281 THGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMA 340
             G   +  ++  D   +++ +   + +G  G+ T+F+A  ++  F + + S L+  +  
Sbjct: 275 LIGNHNILISNPRDLPAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSGLKITLSG 334

Query: 341 GSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVK 400
           G        +R  + +    I   YGMTETSPV+  +      + ++ T+G   P    K
Sbjct: 335 GMALQLAAAERW-KAVTGCAICEGYGMTETSPVATVNPNQ---NIQIGTIGIPVPSTLCK 390

Query: 401 IVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYV 460
           ++D D G   P+G+ GE C KG  VM GYW  +  T E +D  GW+ TGD+A +  +GY+
Sbjct: 391 VID-DAGVEQPLGEIGELCVKGPQVMKGYWQRQEATDEILDSEGWLKTGDIALIQPDGYM 449

Query: 461 NIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQ 520
            IV R KDM++  G N+YP E+E+ L   P V     +GVPD+K GE +  +I+AKPG  
Sbjct: 450 RIVDRKKDMILVSGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFIVAKPGVT 509

Query: 521 PTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQLGLEE 574
            T++ +    +  +  YKVPR I F  + P T  GKI + ++RDE   +LGL++
Sbjct: 510 LTKEQVMTHMRANVTGYKVPRAIEFRDALPTTNVGKILRRELRDEELKKLGLKK 563


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: 749
Number of extensions: 36
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: 566
Length adjustment: 36
Effective length of query: 542
Effective length of database: 530
Effective search space:   287260
Effective search space used:   287260
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 preprint 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