Alignments for a candidate for prpE in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Caulobacter crescentus NA1000

Align 2-methylpropanoate--CoA ligase CCL4; HlCCL4; 2-methylbutanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate CCNA_01889 CCNA_01889 long-chain-fatty-acid--CoA ligase

Query= SwissProt::M4IQQ5
         (556 letters)



>FitnessBrowser__Caulo:CCNA_01889
          Length = 544

 Score =  234 bits (597), Expect = 6e-66
 Identities = 175/545 (32%), Positives = 269/545 (49%), Gaps = 29/545 (5%)

Query: 12  SPLTPLGFLERAATVYGDCTSVVYDAVSYTWSQTHR---RCLCLASSIASLGIENGHVVS 68
           +PLT    L+ AA  +G+   V  +    T +   R   R   LA+++   G+  G  V+
Sbjct: 8   TPLTLSSLLDHAARFHGEVEIVSREPGGVTRTNYARVAVRARKLAAALRRRGLREGDRVA 67

Query: 69  VLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEA 128
            LA N  +  EL++    AG ILN VN RL    I+ +L H+E++++F D     L+   
Sbjct: 68  SLALNSARHLELYYGATGAGGILNTVNPRLFPEQIAFILRHAENRIVFFDPAFGPLLETL 127

Query: 129 IALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI 188
           +   P+      L      S +G+   L      +Y+DL+     D  W +  SE    I
Sbjct: 128 VDQAPQVEAYVCL------SSAGDMPSLRLPNLIAYEDLLAPEADDAPWTVV-SENAGAI 180

Query: 189 LNYTSGTTSSPKGVVHCHRGIFI--MTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGM 246
           L YTSGTT  PKGV++ HR + +            + ++   L   P+FH N W  P+  
Sbjct: 181 LCYTSGTTGDPKGVLYSHRSLALHAFVATGADGMAISRRDSILLVTPLFHVNAWGIPFS- 239

Query: 247 AAVGGTNICL--RKFDSEIIYDMIKRHGVTHMCGAPVV-LNMLSN-APGSEPLKTT---- 298
           AA+ G  + L     D E ++++++    T   G P V L  L   A   E L       
Sbjct: 240 AAMCGAKLVLPGAAVDGENLFNLMRAERCTFSLGVPTVWLGFLDYVATHREELDLAGLAL 299

Query: 299 VQIMTAGAPPPSAVLFRTE-SLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLK 357
            +I+  G+  P +++ R +  LG  V H +G+TET+ L        E   L    R  ++
Sbjct: 300 ERILVGGSAAPRSMIERFDYMLGVYVIHAWGMTETSPLATIGTPLPEHAFLDRQARYDIQ 359

Query: 358 SRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADG 417
           + QG   +   ++ +VD   G     DG  +G++ +RG  V+  Y K     A + T DG
Sbjct: 360 ALQG-RAIYGVELRIVD-ADGVVAPHDGMAVGDLQVRGPWVVRRYFK---ADAPATTEDG 414

Query: 418 WFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEF 477
           WF TGDV  +HP+GYL++ DRSKD+I SGGE +SSV++E++  +HPDI EAAV+  P   
Sbjct: 415 WFPTGDVAKIHPNGYLQLTDRSKDIIKSGGEWISSVDLENVAIAHPDIREAAVIGVPHPK 474

Query: 478 WGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFIL 537
           W E P   +      T  P + +I+++  S++ R+ VP  VV  E LP T+TGK+ K  L
Sbjct: 475 WQERPLLIIVPAPETT--PDKDDILKFLASRVARWQVPDDVVIVESLPHTATGKLLKAKL 532

Query: 538 RDMAR 542
           R+  R
Sbjct: 533 RETYR 537


Lambda     K      H
   0.319    0.135    0.412 

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: 789
Number of extensions: 47
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: 556
Length of database: 544
Length adjustment: 36
Effective length of query: 520
Effective length of database: 508
Effective search space:   264160
Effective search space used:   264160
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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
changes to Amino acid biosynthesis since the original publication.

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 Amino acid biosynthesis