GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Marinobacter adhaerens HP15

Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate GFF944 HP15_923 acetyl-coA synthetase/AMP-(fatty) acid ligase

Query= SwissProt::Q3UNX5
         (580 letters)



>lcl|FitnessBrowser__Marino:GFF944 HP15_923 acetyl-coA
           synthetase/AMP-(fatty) acid ligase
          Length = 549

 Score =  262 bits (669), Expect = 3e-74
 Identities = 174/531 (32%), Positives = 267/531 (50%), Gaps = 28/531 (5%)

Query: 53  NFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQ 112
           N   ++ D+W +        S  A ++   +G +   +F EL   S +FAN L ++  + 
Sbjct: 32  NVCHEICDKWADDP------SRVALYYETEDGGDGTLTFAELKEASARFANYL-KSQGIG 84

Query: 113 RGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLA 172
           +GDRV  +LP+ PE  +     LR G V  P  T      I YR + +  K ++T+    
Sbjct: 85  KGDRVAALLPRTPELLIVIAGTLRAGAVYQPLFTAFGSGAIEYRFERASTKLVVTNPENY 144

Query: 173 PAVDAVAAKCENLHSKLIVSQHSREGWGNL---KEMMKYASDSHTCVDTKHDEMMAIYFT 229
           P ++ V           +V  ++ E   ++   +E +   S     V  K D+     FT
Sbjct: 145 PKLNDVKV------CPPVVGVNASEIGADIPDFEETLAAQSSDFEPVMIKGDDPFLQMFT 198

Query: 230 SGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQG 289
           SGT G  K +     +  L   V  ++ +DL   D  WN +D GWA   + +V  P   G
Sbjct: 199 SGTVGKSKGVAVPAKAL-LAFYVYMKYAIDLQDGDRFWNVADPGWAYGLYYAVVGPLLMG 257

Query: 290 ACVFAHYLPR-FESTSILQTLSKFPITVFCSAPTAYRMLVQND--MSSYKFNSLKHCVSA 346
                H+ P  F   S    + K+ IT   +APTAYR+L  ND  +   +   L+   SA
Sbjct: 258 HAT--HFNPGGFTPESTYDMIRKYKITNLAAAPTAYRLLKANDHVLPEGENLGLRVASSA 315

Query: 347 GEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMK--IKPGSMGKPSPAFDVKIL 404
           GEP+NPEV+   R +    + + YGQTET + C NF G+   ++ GSMG  SP   V  L
Sbjct: 316 GEPLNPEVVNWIRNRHYCPVKDHYGQTETGMTCCNFHGLAHPVREGSMGYASPGHKVVAL 375

Query: 405 DENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGY 464
           +E    +  G+ G +A+ V     F    H+              +Y+TGD      +G 
Sbjct: 376 NEKNEVVGEGEVGQLAVDVKASPLF----HFDGYTWGEKDPFVNGYYLTGDMVINHGNGN 431

Query: 465 FWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDY 524
           F F  R DDII ++GYR+GP +VES L+EH ++AES VV  PD  RG ++KA++V+  DY
Sbjct: 432 FSFSGRDDDIITTAGYRVGPADVESTLLEHAAVAESGVVGKPDEKRGSIIKAYVVIKGDY 491

Query: 525 KSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRKK 575
              D++ LK E+QE V++  + + +PR++EF++ELPKT SGK++R  LR +
Sbjct: 492 ALGDEQALKDELQELVRRRLSTHAFPREIEFVDELPKTPSGKIQRFVLRNQ 542


Lambda     K      H
   0.319    0.134    0.416 

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: 810
Number of extensions: 42
Number of successful extensions: 7
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: 580
Length of database: 549
Length adjustment: 36
Effective length of query: 544
Effective length of database: 513
Effective search space:   279072
Effective search space used:   279072
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 (21.7 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