GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Caulobacter crescentus NA1000

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate CCNA_01889 CCNA_01889 long-chain-fatty-acid--CoA ligase

Query= metacyc::MONOMER-20125
         (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 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