Alignments for a candidate for prpE in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Rhodococcus qingshengii djl-6-2

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 WP_076948477.1 C1M55_RS12980 AMP-binding protein

Query= SwissProt::Q3UNX5
         (580 letters)



>NCBI__GCF_002893965.1:WP_076948477.1
          Length = 540

 Score =  257 bits (656), Expect = 1e-72
 Identities = 184/559 (32%), Positives = 275/559 (49%), Gaps = 69/559 (12%)

Query: 56  KDVLDQWTNMEKAGKRL-------SNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEA 108
           +++LDQ+     +   L          AF  ++ +   +  ++  L   S +FA  L + 
Sbjct: 10  RELLDQYDTPHASAAELLCDRHPADGVAFTVVEADLSSVDLTYGHLREQSARFAAALADL 69

Query: 109 CSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITD 168
             ++ GD V  ++ K  +  +A +   R G V +P  T      I +RL +S AK +I+D
Sbjct: 70  -GVEPGDNVATLMGKSADLVVALLGIWRRGAVHVPLFTAFASPAIAFRLTASGAKVVISD 128

Query: 169 ----DTLAPAVDAVA------------AKCENLHSKLIVSQHSREGWGNLKEMMKYASDS 212
               + LAP  D  A            A  E     L+ +Q + +  G  + +   A   
Sbjct: 129 ANQLEKLAPGEDIPADAAWQVIVAGGAAGDELDFDALVAAQDAEDPKGAAQAVGGNAP-- 186

Query: 213 HTCVDTKHDEMMAIYFTSGTTGPPKMIG---------HTHSSFGLGLSVNGRFWLDLIAS 263
                      M   FTSGTTG PK +          H +  FGL          D+   
Sbjct: 187 -----------MVQLFTSGTTGTPKGVPVPVRALASFHAYQEFGL----------DVRED 225

Query: 264 DVMWNTSDTGWAKSAWSSVFSPWTQGA-CVFAHYLPRFESTSILQTLSKFPITVFCSAPT 322
           DV WN +D GWA   + ++  P   G   +  H    F +    Q + KF +T F +APT
Sbjct: 226 DVFWNAADPGWAYGLYYALLGPLAAGTRSLLLH--AGFSAPLTWQIIEKFGVTNFAAAPT 283

Query: 323 AYRMLVQNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNF 382
            YR L  +     +  SL+   SAGEP+ P+V+   +   G+++ + YGQTE  +   N 
Sbjct: 284 VYRSLRADKAPVPEGISLRRASSAGEPLTPDVVAWSKNSLGVEVRDHYGQTEHGMFIVNA 343

Query: 383 --KGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQ-EGDIALQVLPERPFGLFTHYVD 437
              G++  ++PGSMG+P P +   +L++N   + P + +G +A+      P   FT YVD
Sbjct: 344 WADGLRDDVRPGSMGRPLPGWSAAVLEDNSDDIAPARTQGRVAIDT-HNSPLMWFTGYVD 402

Query: 438 NPSKTASTLR--GSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHP 495
            P KT       G +YITGD G  DEDG+F+F +R DD+I+ +GYRIGPF+VES L+ H 
Sbjct: 403 APEKTKQRFSEDGRWYITGDAGMTDEDGFFFFSSRDDDVIIMAGYRIGPFDVESVLVMHE 462

Query: 496 SIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEF 555
            + E+AVV  PD + GEV++AF+VL       D  +L+KE+Q  VKK  A + YPR V F
Sbjct: 463 HVIEAAVVGMPDELCGEVLEAFVVLREGVDGDD--ELEKELQTLVKKKFAAHAYPRTVHF 520

Query: 556 IEELPKTVSGKVKRNELRK 574
           +  LPKT SGKV+R  LRK
Sbjct: 521 VPNLPKTPSGKVQRYILRK 539


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: 733
Number of extensions: 36
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 580
Length of database: 540
Length adjustment: 36
Effective length of query: 544
Effective length of database: 504
Effective search space:   274176
Effective search space used:   274176
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 24 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 2024 update 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