GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_572
           Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
          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 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