GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Dechlorosoma suillum PS

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Dsui_0317 Dsui_0317 acetyl-CoA acetyltransferase

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



>lcl|FitnessBrowser__PS:Dsui_0317 Dsui_0317 acetyl-CoA
           acetyltransferase
          Length = 399

 Score =  285 bits (728), Expect = 2e-81
 Identities = 163/394 (41%), Positives = 242/394 (61%), Gaps = 7/394 (1%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAG-IDPKEVEDVVMGAAMQQG 61
           +A IV+  R P+ K   G    T    +L HA++  + +   +DP  VEDV++G AM + 
Sbjct: 7   DAYIVAATRLPVAKR-NGMFKTTRPDDMLAHALKSVMAQVPQLDPALVEDVIVGCAMPEA 65

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
             G N+AR  LL AGLP T  G TI+R C+SG+QA+A AA  +     ++ +  G E++S
Sbjct: 66  EQGMNVARIGLLLAGLPDTVPGLTINRFCSSGVQAVADAAARIRLGEADVMLAAGTETMS 125

Query: 122 LVQNDKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSLESQRRTA 179
           L+ +  M    +++PA+     +V +A  M  TAE VA+++GISR+ QD +++ S ++  
Sbjct: 126 LM-SQMMGNKVSLNPAIFEKDENVAIAYGMGLTAEKVAQKWGISRDDQDAFAVASHQKAV 184

Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239
           AA   GKF DEI+P + +  + D  +G V   +     DEGPRP+++ +GLA LK V   
Sbjct: 185 AAIAAGKFKDEISPYTVRAHLPDLKSGTVRIVEKVCDTDEGPRPDSSLQGLAKLKPVFNA 244

Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299
             ++TAGN+SQ+SDGA A +++S+K      L+PL  F G    G  P+ MGIGP+ A+P
Sbjct: 245 RGSVTAGNSSQMSDGAGAVLLVSEKILKQFNLQPLARFAGFSVAGVPPEIMGIGPIAAIP 304

Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359
           ++L + G+  DD+   ELNEAFA Q L    +LG+DP K+N  GGAI++GHP G +GA +
Sbjct: 305 KVLAQAGIKQDDLDWIELNEAFAAQALAVTRELGLDPAKINPQGGAIALGHPLGATGA-I 363

Query: 360 AGHALIEG-RRRKAKYAVVTMCVGGGMGSAGLFE 392
               L+ G RR   K+ +VTMC+G GMG+AGLFE
Sbjct: 364 RTATLVHGMRRENKKWGMVTMCIGTGMGAAGLFE 397


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: 413
Number of extensions: 14
Number of successful extensions: 2
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: 399
Length adjustment: 31
Effective length of query: 364
Effective length of database: 368
Effective search space:   133952
Effective search space used:   133952
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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