GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2C3

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO356_05100 AO356_05100 long-chain fatty acid--CoA ligase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_05100
          Length = 563

 Score =  237 bits (605), Expect = 8e-67
 Identities = 161/540 (29%), Positives = 266/540 (49%), Gaps = 42/540 (7%)

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

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

Query: 172 -----TVVWIDDEAGQGADEPGLLRFTELIARG-----NAADPRLAQVAAGLQATDPINI 221
                +V+    +       P  ++F +++++G     N A+P    VA          +
Sbjct: 162 RLLINSVIKYVKKMVPAYHLPKAVKFNDVLSKGHGQPVNEANPTSDDVAV---------L 212

Query: 222 QFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR------LCIPVPLYHCFGMVLG 275
           Q+T GTTG  KGA L+HRN++ N     +C  L  ++       L  P+PLYH +     
Sbjct: 213 QYTGGTTGVAKGAMLSHRNLVANML---QCKALMGSNLNEGCEVLITPLPLYHIYAFTFH 269

Query: 276 NLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLR 335
            +A    G   +  ++  D   +++ +   + +G  G+ T+F+A  ++  F + + S L+
Sbjct: 270 CMAMMLIGNHNILISNPRDLSAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSALK 329

Query: 336 TGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSK-RVSTVGQVQ 394
             +  G        +R  + +    I   YGMTETSPV+    T  P+   ++ T+G   
Sbjct: 330 VTLSGGMALQLAAAERW-KAVTGCPICEGYGMTETSPVA----TVNPIQNIQIGTIGIPV 384

Query: 395 PHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATM 454
           P    K+++ D G   P+G+ GE C KG  VM GYW  +  T E +D  GW+ TGD+A +
Sbjct: 385 PSTLCKVIN-DAGVEQPLGEIGELCVKGPQVMKGYWQRQEATDEILDSEGWLKTGDIALI 443

Query: 455 DAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWII 514
             +GY+ IV R KDM++  G N+YP E+E+ L   P V     +GVPD+K GE +  +I+
Sbjct: 444 QPDGYMRIVDRKKDMILISGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFIV 503

Query: 515 AKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQLGLEE 574
           A+PG   T++ +    +  +  YKVP+ + F  + P T  GKI + ++RDE   +LGL++
Sbjct: 504 ARPGVTLTKEQVMEHMRANVTGYKVPKAVEFRDALPTTNVGKILRRELRDEELRKLGLKK 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: 742
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: 563
Length adjustment: 36
Effective length of query: 542
Effective length of database: 527
Effective search space:   285634
Effective search space used:   285634
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:

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