Alignments for a candidate for prpE in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Caulobacter crescentus NA1000

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate CCNA_01889 CCNA_01889 long-chain-fatty-acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__Caulo:CCNA_01889
          Length = 544

 Score =  233 bits (594), Expect = 1e-65
 Identities = 169/533 (31%), Positives = 266/533 (49%), Gaps = 26/533 (4%)

Query: 22  LTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQA----SALMRRGFSREDKLSF 77
           LT    L+ A + F  +  +V R+      T Y  V V+A    +AL RRG    D+++ 
Sbjct: 10  LTLSSLLDHAAR-FHGEVEIVSREPGGVTRTNYARVAVRARKLAAALRRRGLREGDRVAS 68

Query: 78  ISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE---PYLNSLL 134
           ++ N    LE ++G   AGG+L  +N RL P+++A+I+ H++++ V  D    P L +L+
Sbjct: 69  LALNSARHLELYYGATGAGGILNTVNPRLFPEQIAFILRHAENRIVFFDPAFGPLLETLV 128

Query: 135 EVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYY 194
           +   Q++A + L    D PS     R    + Y +L+     D  P     E +   L Y
Sbjct: 129 DQAPQVEAYVCLSSAGDMPSL----RLPNLIAYEDLL-APEADDAPWTVVSENAGAILCY 183

Query: 195 TSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLN---SVYLWTLPMFHAASWGFSWATVA 251
           TSGTTG PKGV++ HR   L+A        M ++   S+ L T P+FH  +WG  ++   
Sbjct: 184 TSGTTGDPKGVLYSHRSLALHAFVATGADGMAISRRDSILLVT-PLFHVNAWGIPFSAAM 242

Query: 252 VGATNVCLDK-VDYPLIYRLVEKERVTHMCAAPTVYVNLADYMK--RNNLKFSNRV--HM 306
            GA  V     VD   ++ L+  ER T     PTV++   DY+   R  L  +      +
Sbjct: 243 CGAKLVLPGAAVDGENLFNLMRAERCTFSLGVPTVWLGFLDYVATHREELDLAGLALERI 302

Query: 307 LVAG-AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQ 365
           LV G AAP     +    +G Y+ H +G+TET    +I     E   L  + +  ++A Q
Sbjct: 303 LVGGSAAPRSMIERFDYMLGVYVIHAWGMTETSPLATIGTPLPEHAFLDRQARYDIQALQ 362

Query: 366 GIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGD 425
           G      E+ + DA+G   P DG  +G++ +RG  V   Y+K       +  DGWF +GD
Sbjct: 363 GRAIYGVELRIVDADGVVAPHDGMAVGDLQVRGPWVVRRYFK--ADAPATTEDGWFPTGD 420

Query: 426 AAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVT 485
            A +HP+GY+++ DR KD+I +GGE +SS+ +E   +  P ++  AV G P  KW E   
Sbjct: 421 VAKIHPNGYLQLTDRSKDIIKSGGEWISSVDLENVAIAHPDIREAAVIGVPHPKWQERPL 480

Query: 486 ARIELQEGVKLTEEEVIKFCKERLAHFECP-KIVEFGPIPMTATGKMQKYVLR 537
             I         +++++KF   R+A ++ P  +V    +P TATGK+ K  LR
Sbjct: 481 LIIVPAPETTPDKDDILKFLASRVARWQVPDDVVIVESLPHTATGKLLKAKLR 533


Lambda     K      H
   0.319    0.136    0.411 

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: 679
Number of extensions: 32
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: 549
Length of database: 544
Length adjustment: 36
Effective length of query: 513
Effective length of database: 508
Effective search space:   260604
Effective search space used:   260604
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: 52 (24.6 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)
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 paper from 2022 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

GapMind for catabolism of small carbon sources