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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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:

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. 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:

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:

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