GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N1B4

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf1N1B4_572 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_572
          Length = 341

 Score =  191 bits (486), Expect = 3e-53
 Identities = 112/345 (32%), Positives = 181/345 (52%), Gaps = 14/345 (4%)

Query: 236 LTHRNILNNGFFIGECMKLTPADR------LCIPVPLYHCFGMVLGNLACFTHGATIVYP 289
           LTHRN++ N     +C  L  ++       L  P+PLYH +      +A    G   +  
Sbjct: 2   LTHRNLVANML---QCKALMGSNLNEGCEILITPLPLYHIYAFTFHCMAMMLIGNHNILI 58

Query: 290 NDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVM 349
           ++  D   +++ +   + +G  G+ T+F+A  ++  F + + S+L+  +  G        
Sbjct: 59  SNPRDLTAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSSLKITLSGGMALQLAAA 118

Query: 350 KRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAV 409
           +R  E      I   YGMTETSPV+  + +    + ++ T+G   P    K++D D G  
Sbjct: 119 ERWKEVAGC-PICEGYGMTETSPVATVNPSQ---NIQIGTIGIPVPSTLCKVID-DAGVE 173

Query: 410 VPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDM 469
            P+G  GE C KG  VM GYW  +  T E +D  GW+ TGD+A +  +GY+ IV R KDM
Sbjct: 174 QPLGAIGELCVKGPQVMKGYWQRQDATDEILDSEGWLKTGDIALIQPDGYMRIVDRKKDM 233

Query: 470 VIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAF 529
           ++  G N+YP E+E+ L   P V     +GVPD+K GE +  +I+AKPG   T+D +   
Sbjct: 234 ILVSGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKIFIVAKPGVTLTKDQVMEH 293

Query: 530 CKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQLGLEE 574
            +  +  YKVP+ + F  + P T  GKI + ++RDE   +LG+++
Sbjct: 294 MRANVTGYKVPKAVEFRDALPTTNVGKILRRELRDEELKKLGVKK 338


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: 455
Number of extensions: 26
Number of successful extensions: 3
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: 341
Length adjustment: 32
Effective length of query: 546
Effective length of database: 309
Effective search space:   168714
Effective search space used:   168714
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: 51 (24.3 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