GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_03310
          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.

Links

Downloads

Related tools

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