GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas putida KT2440

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_4550 PP_4550 long-chain-fatty-acid/CoA ligase

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



>lcl|FitnessBrowser__Putida:PP_4550 PP_4550
           long-chain-fatty-acid/CoA ligase
          Length = 562

 Score =  243 bits (621), Expect = 1e-68
 Identities = 166/534 (31%), Positives = 258/534 (48%), Gaps = 43/534 (8%)

Query: 54  GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112
           G   +YA+L+  +   A+ L     L PG+R+ +   N  ++ +      + GL++VN N
Sbjct: 47  GVTLSYAELERHSAAFAAWLQQHTDLKPGERIAVQMPNVLQYPIAVFGAMRAGLIVVNTN 106

Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEW------QGQQPGHLQAAK 166
           P Y   E+ +     G + LV +  F        ++E+ P+       + +    L AAK
Sbjct: 107 PLYTEREMRHQFKDSGARALVYLNMFGKR-----VQEVLPDTGIEYLIEAKMGDLLPAAK 161

Query: 167 LPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSG 226
              + TVV    +       P  + F +++  G    P+       L   D   +Q+T G
Sbjct: 162 GWLVNTVVDKLKKMVPAYRLPQAVPFKQVLREGRGLSPK----PVSLNLDDIAVLQYTGG 217

Query: 227 TTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCFGMVLGN 276
           TTG  KGA LTH N++ N   +  C      D           +  P+PLYH +     N
Sbjct: 218 TTGLAKGAMLTHGNLVANMLQVLACFSQHGPDGQKLLKDGQEVMIAPLPLYHIYAFT-AN 276

Query: 277 LACF----THGATIVYPND--GFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFN 330
             C      H   I  P D  GF     ++ +   R + L G+ T+F+A +DHP F + +
Sbjct: 277 CMCMMVTGNHNVLITNPRDIPGF-----IKELGKWRFSALLGLNTLFVALMDHPGFRQLD 331

Query: 331 LSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTV 390
            S L+     G+       +R  +    R I   YG+TETSPV+  S+       R+ TV
Sbjct: 332 FSALKVTNSGGTALVKATAERWEDLTGCR-IVEGYGLTETSPVA--STNPYGQLARLGTV 388

Query: 391 GQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGD 450
           G        K++D D G  +P+G+RGE C KG  VM GYW     T +A+D  GW  TGD
Sbjct: 389 GIPVAGTAFKVIDDD-GNELPLGERGELCIKGPQVMKGYWQQPEATAQALDAEGWFKTGD 447

Query: 451 LATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELC 510
           +A +D +G+  IV R KDM+I  G N+YP EIE+ +  HP+V +   +GVPD++ GE + 
Sbjct: 448 IAVIDPDGFTRIVDRKKDMIIVSGFNVYPNEIEDVVMGHPKVANCAAIGVPDERSGEAVK 507

Query: 511 AWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
            +++ + G   + D+++A+CK     YKVP++I    S PMT  GKI + ++RD
Sbjct: 508 LFVVPREGGL-SVDELKAYCKANFTGYKVPKHIVLRESLPMTPVGKILRRELRD 560


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: 787
Number of extensions: 46
Number of successful extensions: 6
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: 562
Length adjustment: 36
Effective length of query: 542
Effective length of database: 526
Effective search space:   285092
Effective search space used:   285092
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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