Aligments for a candidate for acs in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Pseudomonas putida KT2440

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate PP_3553 PP_3553 AMP-binding domain protein

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__Putida:PP_3553
          Length = 540

 Score =  614 bits (1584), Expect = e-180
 Identities = 301/545 (55%), Positives = 387/545 (71%), Gaps = 19/545 (3%)

Query: 18  NYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTVAI 77
           N+ ALTPL F++R A V+    +VIHG+    W++TY RCRRLASALA R IG G TVA+
Sbjct: 14  NHVALTPLSFIERTAAVYGNYPAVIHGAIRRNWQETYQRCRRLASALAGRGIGRGDTVAV 73

Query: 78  IAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAEDSL 137
           + PN P M EAHFGVPM GAVLN +N+RL+A  +AF+L H ++ V++ D+EF  + E +L
Sbjct: 74  MLPNTPTMLEAHFGVPMTGAVLNTLNVRLDAEAIAFMLQHGEAKVLITDREFHAVIEGAL 133

Query: 138 RLMEEKAGSSFKRPLLIVIGDHTCAPE-SLNRALSKGAIEYEDFLATGDPNYPWQPPADE 196
            L+E         PL++ + D    PE    RA+S+  ++YE  L  GDP + W+ P DE
Sbjct: 134 ALLEHP-------PLVVDVDD----PEYGEGRAVSQ--LDYEALLNEGDPEFAWEWPDDE 180

Query: 197 WQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCFP 256
           WQ+I+L YTSGTT +PKGVV HHRGAY+ AL N + W M    VYLWTLPMFHCNGWC+P
Sbjct: 181 WQAISLNYTSGTTGNPKGVVYHHRGAYLNALGNQMTWAMGHRPVYLWTLPMFHCNGWCYP 240

Query: 257 WSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTVH 316
           W++  L+GT + LR+V  +++ ++I ++KV+H C AP+VLNA+VN P E     + H V 
Sbjct: 241 WTITALAGTHVFLRRVDPQKILTLIREHKVSHLCGAPIVLNALVNMP-EAAKAAIEHPVQ 299

Query: 317 VMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNARQ 376
            M AGAAPP  V+ ++ Q G +V HTYGL+E YGP TVCAW  EWD+L  E +A++ +RQ
Sbjct: 300 AMVAGAAPPAKVIGAVEQMGIKVTHTYGLTEVYGPVTVCAWHDEWDALSLEERARIKSRQ 359

Query: 377 GVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFHS 436
           GVRY  ++ L V D QT +PVP DG T GEI  RGN VMKGYLKNPEA  E F GGWFH+
Sbjct: 360 GVRYPTLDGLMVADPQTLQPVPRDGDTLGEIFMRGNTVMKGYLKNPEATAEAFRGGWFHT 419

Query: 437 GDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQES 496
           GD+AV H D YIEIKDR KD+IISGGENIS++EVE+ +Y H AVLEA+VVARPDE+W E+
Sbjct: 420 GDLAVWHADGYIEIKDRLKDIIISGGENISTIEVEDALYKHSAVLEAAVVARPDEKWGET 479

Query: 497 PCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILRT 556
           PCAFV LK   E    +    DI  +CRE L  + VPK+VVFG LPKT+TGKIQK++LR 
Sbjct: 480 PCAFVALKPGRE----DTREADITSWCREHLAGFKVPKTVVFGELPKTSTGKIQKYVLRD 535

Query: 557 KAKEM 561
           +AK +
Sbjct: 536 RAKAL 540


Lambda     K      H
   0.319    0.134    0.422 

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: 913
Number of extensions: 37
Number of successful extensions: 4
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: 569
Length of database: 540
Length adjustment: 36
Effective length of query: 533
Effective length of database: 504
Effective search space:   268632
Effective search space used:   268632
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources