GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_4550
          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 (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