GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Sphingomonas koreensis DSMZ 15582

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ga0059261_0982 Ga0059261_0982 acetyl-CoA acetyltransferases

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



>FitnessBrowser__Korea:Ga0059261_0982
          Length = 390

 Score =  255 bits (652), Expect = 1e-72
 Identities = 160/397 (40%), Positives = 230/397 (57%), Gaps = 21/397 (5%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           MTE VI +  RTP+G ++ GA  +T    L   AIE A+++A +  +EV +V++G  +  
Sbjct: 1   MTEVVITAAKRTPVG-SFLGAFASTPAHELGRIAIEAALEQAEVKGEEVSEVILGQVLT- 58

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
            A G N AR+A + AG+P       +++ C SGL+A+ALAA++V      I V GG ES+
Sbjct: 59  AAQGQNPARQASMAAGVPKEVPAWGLNQVCGSGLRAVALAAQAVQTGDATIVVAGGQESM 118

Query: 121 SLVQND-------KMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYS 171
           SL  +        KM     +D  ++    DV+    M  TAE +A++Y ++R  QDE++
Sbjct: 119 SLAAHAQSLRAGAKMGDVGLIDTMIKDGLTDVFNGYHMGITAENLAEQYQVTRGEQDEFA 178

Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231
           + SQ    AA+  G+F DEIAP++ K        G     D  + QDE  R   T + +A
Sbjct: 179 VRSQNLAEAARSEGRFKDEIAPVTIK--------GRKG--DTVVDQDEYIRAGATLDSVA 228

Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291
           GL+    +  T+TAGNAS L+DGA+A V+MS + A  +G   L   +   + G +P  MG
Sbjct: 229 GLRPAFKKDGTVTAGNASGLNDGAAALVVMSREEADKRGATVLATIKSWATAGVDPSIMG 288

Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351
           IGPV A  + L++ G +V D+ L E NEAFA Q L    +LG DP K+NVNGGAI++GHP
Sbjct: 289 IGPVPASKKALEKAGWTVADLDLIEANEAFAAQALSVGKELGFDPNKVNVNGGAIAIGHP 348

Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
            G SGAR+    L E +RR AK  + T+C+GGGMG A
Sbjct: 349 IGASGARVLTTLLYEMQRRDAKKGLATLCIGGGMGIA 385


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: 433
Number of extensions: 23
Number of successful extensions: 4
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: 390
Length adjustment: 31
Effective length of query: 364
Effective length of database: 359
Effective search space:   130676
Effective search space used:   130676
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