GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_1726 3-methylmercaptopropionyl-CoA ligase (DmdB)

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1726
          Length = 540

 Score =  614 bits (1583), Expect = e-180
 Identities = 293/544 (53%), Positives = 388/544 (71%), Gaps = 17/544 (3%)

Query: 18  NYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTVAI 77
           N+TALTPL F++R A V+P   +VIHGS   TW  TY RCRRLASALA R IG   TVA+
Sbjct: 14  NHTALTPLSFIERTASVYPDYPAVIHGSIRRTWADTYRRCRRLASALAGRGIGKNDTVAV 73

Query: 78  IAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAEDSL 137
           + PNIPAM EAHFGVPM GAVLN +N+RL+A  +AF+L+H ++ V++ D+EF  + + ++
Sbjct: 74  MLPNIPAMLEAHFGVPMIGAVLNALNVRLDAEAIAFMLAHGEAKVLIADREFHDVVQAAI 133

Query: 138 RLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPADEW 197
            +++         PL+I + D    PE      +   ++YE FLA GDP++ WQ P DEW
Sbjct: 134 GMLDHP-------PLVIDLDD----PE-YGEGQAVSELDYEAFLAEGDPDFAWQWPDDEW 181

Query: 198 QSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCFPW 257
           Q+I+L YTSGTT +PKGVV HHRGAY+ +L N + W M +  VYLWTLPMFHCNGWC+PW
Sbjct: 182 QAISLNYTSGTTGNPKGVVYHHRGAYLNSLGNQMTWAMGNHPVYLWTLPMFHCNGWCYPW 241

Query: 258 SLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTVHV 317
           ++  L+G  + LR+V  +++ ++I ++++TH C AP+VLNA+VN P +     + H V  
Sbjct: 242 TVTALAGVHVFLRRVDPQKILNLIREHQITHLCGAPIVLNALVNMP-DSAKAAIDHPVSA 300

Query: 318 MTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNARQG 377
           M AGAAPP  V+ ++ + G +V H YGL+E YGP T+CAW   WD LP E +A++ ARQG
Sbjct: 301 MVAGAAPPAKVIGAVEEMGIKVTHVYGLTEVYGPVTLCAWHAAWDELPLEQRAQIKARQG 360

Query: 378 VRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFHSG 437
           VRY  +E L V D +T +P P DG+T GEI  RGN VMKGYLKNP A  E F GGWFH+G
Sbjct: 361 VRYPTLEGLMVADPRTLEPTPHDGQTIGEIFMRGNTVMKGYLKNPSATAEAFEGGWFHTG 420

Query: 438 DIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQESP 497
           D+AV H D Y+EI+DR KD+IISGGENIS++E+E V+Y HPAVLEA+VVARPDE+W E+P
Sbjct: 421 DLAVTHADGYVEIRDRLKDIIISGGENISTIELEGVLYRHPAVLEAAVVARPDEKWGETP 480

Query: 498 CAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILRTK 557
           CAF+TLKSD+     +    +I+ FCRE L  + VP++VVF  LPKT+TGKIQK +LR  
Sbjct: 481 CAFITLKSDH----TDVREAEIISFCREHLAGFKVPRTVVFTQLPKTSTGKIQKFVLRDM 536

Query: 558 AKEM 561
           AK +
Sbjct: 537 AKNL 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: 890
Number of extensions: 39
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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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