GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Caulobacter crescentus NA1000

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate CCNA_00544 CCNA_00544 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Caulo:CCNA_00544
          Length = 391

 Score =  279 bits (714), Expect = 9e-80
 Identities = 172/403 (42%), Positives = 240/403 (59%), Gaps = 21/403 (5%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M+E VIVS ARTP+G ++ GAL +   + L    IE AV RAGI P +V++V++G  +Q 
Sbjct: 1   MSEIVIVSAARTPVG-SFNGALASLPASELGKAVIEAAVSRAGIAPSDVDEVILGQVLQ- 58

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
            A G   AR+A ++AG+PV     ++++ C SGL+A+ALAA+ +     ++ V GG ES+
Sbjct: 59  AAAGQGPARQASVKAGIPVEAPAWSLNQLCGSGLRAVALAAQQIADGSAKVVVAGGQESM 118

Query: 121 S-------LVQNDKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYS 171
           S       L    KM     VD  ++    D +    M  TAE +A R+ I+RE QD+++
Sbjct: 119 SQAPHAQNLRGGQKMGDLQFVDTMIKDGLWDAFHGYHMGQTAENIASRWQITREDQDKFA 178

Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231
           + SQ R  AAQ+ GKF+DEI PI+ K        G     D  + +DE  R   T E + 
Sbjct: 179 VTSQNRAEAAQKAGKFDDEIVPITIK--------GRKG--DTIVDKDEFIRHGATIESVQ 228

Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291
           GLK V  +  ++TA NAS L+DGA+A V+MS + AA +GLKPL       + G EP+ MG
Sbjct: 229 GLKPVFNKEGSVTAANASGLNDGAAALVLMSAEEAAKRGLKPLARIASWANAGVEPEIMG 288

Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351
            GP+ A  + L++ G SV D+ L E NEAFA Q L    +LG+DP K+NVNGGAI++GHP
Sbjct: 289 TGPIPASKKALEKAGWSVSDLDLVESNEAFAAQALCVVRELGLDPAKVNVNGGAIAIGHP 348

Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
            G SGAR+    + E +R  AK  + T+CVGGGMG A   E V
Sbjct: 349 IGASGARILTTLVHEMKRSGAKKGLATLCVGGGMGVAMCVEAV 391


Lambda     K      H
   0.316    0.134    0.378 

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: 438
Number of extensions: 24
Number of successful extensions: 6
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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