Alignments for a candidate for acs in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Dinoroseobacter shibae DFL-12

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 3607419 Dshi_0833 AMP-dependent synthetase and ligase (RefSeq)

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__Dino:3607419
          Length = 541

 Score =  561 bits (1447), Expect = e-164
 Identities = 284/550 (51%), Positives = 364/550 (66%), Gaps = 18/550 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L K  ANY  LTPL  L RAA+V+P R++V++G+R +T+ + + R  RLASALA   I P
Sbjct: 10  LDKCAANYVPLTPLSHLARAALVYPDREAVVYGARRFTYAEYHARVSRLASALAGAGIAP 69

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G  VA + PNIPAM EAHFGVP CGAVLN +NIRL+  TVA++LSH  +  ++VD +F  
Sbjct: 70  GDVVATLLPNIPAMVEAHFGVPACGAVLNTINIRLDVDTVAYILSHGGAKAVLVDSQFLP 129

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191
           LA ++   ++  A      PLLI + D      +L      G  EYEDFLA GDP++PW 
Sbjct: 130 LAAEACERLDGPA------PLLIEVADDAAGVHALG-----GYTEYEDFLAGGDPDFPWI 178

Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251
            P DEW+S+AL YTSGTT  PKGVV HHRGAY+M +   + W M     +L  +P+FHCN
Sbjct: 179 MPRDEWESLALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVLYPRWLAIVPLFHCN 238

Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311
           GW   W + +L GT +C R V+A+ +Y+ IA+  VTHF  AP+VLN IVNAP +    P 
Sbjct: 239 GWNHSWMMPMLGGTVVCCRDVSAQAIYTAIAENGVTHFGGAPIVLNMIVNAP-DAARRPF 297

Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371
            HTV V TAGA P  + L ++ + GF V   YGL+ETYG  T C W P+WD+LP   +A 
Sbjct: 298 SHTVEVFTAGAPPAAATLAAIEELGFNVTQVYGLTETYGHVTECVWNPDWDTLPQAERAA 357

Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431
           + ARQGV    ME + V+D +  + VP DG T GE++ RGN VMKGY +NP+A  E FAG
Sbjct: 358 IKARQGVALPQMEHITVMDPEM-RQVPMDGATTGEVMMRGNSVMKGYYRNPDATAEAFAG 416

Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491
           G+FHSGDIA++HPD YI+I DR+KD+IISGGENISSVEVE  + HHPAVL  +VVA+PD 
Sbjct: 417 GYFHSGDIALQHPDGYIQIADRAKDIIISGGENISSVEVEGALMHHPAVLLCAVVAKPDP 476

Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551
            W E PCAFV LK      +      +I+ F RE+L  +  PK VVF  LPKT+TGKIQK
Sbjct: 477 TWGEVPCAFVELKDGKTAEE-----AEIIAFARERLAGFKTPKKVVFTELPKTSTGKIQK 531

Query: 552 HILRTKAKEM 561
             LR +AK +
Sbjct: 532 FELRNRAKAL 541


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: 919
Number of extensions: 36
Number of successful extensions: 5
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: 541
Length adjustment: 36
Effective length of query: 533
Effective length of database: 505
Effective search space:   269165
Effective search space used:   269165
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)
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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
the source code
instructions for running GapMind on your computer

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