Alignments for a candidate for prpE in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Sinorhizobium meliloti 1021

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 SMc00741 SMc00741 fatty-acid-CoA ligase

Query= SwissProt::Q3UNX5
         (580 letters)



>FitnessBrowser__Smeli:SMc00741
          Length = 548

 Score =  249 bits (637), Expect = 2e-70
 Identities = 168/548 (30%), Positives = 269/548 (49%), Gaps = 25/548 (4%)

Query: 36  NYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFEELG 95
           +Y+ + ++F+  IPE FN    V D W   +     L +        +G  L  ++ +  
Sbjct: 7   DYDELYREFRWRIPERFNIGVAVSDAWAARDPERICLQH-----FSPDGAHLALTYGDFA 61

Query: 96  LLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILY 155
             S  FA  L  A  +  G+RV ++LP+  E  +A+ A  + G + +P       + + Y
Sbjct: 62  ARSSAFAGGLA-AHDVSPGERVAILLPQGFEAAIAHAAIYKLGAIALPLALLFGVEALAY 120

Query: 156 RLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLKEMMKYASDSHTC 215
           RL+ + A  ++T+      + A+  +   L   ++  +  + G    +++          
Sbjct: 121 RLKDAGAAAVVTNRFGYERLAAIRGELPELRMVVLAEEDEKPGTVRFRDIAA-GQGRFDP 179

Query: 216 VDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIAS--DVMWNTSDTG 273
            +TK D+   + +TSGTTGPPK   H H    LG     +F    +    D MW  +D  
Sbjct: 180 AETKPDDPALMIYTSGTTGPPKGALHGHRVL-LGHLPGFQFHHHFLPQPGDRMWTPADWA 238

Query: 274 WAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQ---- 329
           WA    +++      G  V +    +F++ +  + + +  +      PTA R+L      
Sbjct: 239 WAGGLLNALLPSLFFGVPVVSSPAQKFDAHTAFRIIEEMEVRNAFIPPTALRLLKSVERP 298

Query: 330 NDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMKI-K 388
            D  + K  ++    SAGE +  E  E  R   G+++ E YGQTE  ++  +  G+ + K
Sbjct: 299 RDRCALKLRTVG---SAGEALGRETFEWARAALGVEVSEFYGQTECNIVISSATGLGVAK 355

Query: 389 PGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFG-LFTHYVDNPSKTASTLR 447
            GSMGK +P   V I+D  G  LPPG  G +A++    RP   +F  Y  N   T +   
Sbjct: 356 AGSMGKAAPGHQVAIIDGEGRVLPPGTVGQVAIR----RPDPVMFLGYWRNEEATEAKFI 411

Query: 448 GSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPD 507
           G +  TGD+G MDE+GYF F  R DD+I SSGYRIGP E+E  L  HP +  +A V  PD
Sbjct: 412 GDWMTTGDQGVMDEEGYFTFFGRDDDVITSSGYRIGPSEIEDCLAGHPDVQLAAAVGKPD 471

Query: 508 PIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKV 567
           P+R E+VKA++VL P   + D  +    I++ VK   + ++YPR++ F++ LP T SGKV
Sbjct: 472 PLRTEIVKAYVVLKPGVAAGD--ETAAGIRDWVKNRLSMHEYPREIAFVDSLPLTTSGKV 529

Query: 568 KRNELRKK 575
            R  LR+K
Sbjct: 530 IRRLLREK 537


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: 797
Number of extensions: 42
Number of successful extensions: 8
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: 548
Length adjustment: 36
Effective length of query: 544
Effective length of database: 512
Effective search space:   278528
Effective search space used:   278528
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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Steps (tab-delimited)
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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