GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Sphingomonas koreensis DSMZ 15582

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate Ga0059261_3982 Ga0059261_3982 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)

Query= SwissProt::Q3J4E3
         (510 letters)



>FitnessBrowser__Korea:Ga0059261_3982
          Length = 508

 Score =  794 bits (2050), Expect = 0.0
 Identities = 392/510 (76%), Positives = 435/510 (85%), Gaps = 2/510 (0%)

Query: 1   MKDILQELENRRAIARAGGGQRRVEAQHKRGKLTARERIELLLDEGSFEEFDMFVRHRCT 60
           M   ++ELE RRA AR GGGQ+R++AQH +GKLTARER+E+LLDEGSFEE DM+V H C 
Sbjct: 1   MSSTIEELERRRAAARLGGGQKRIDAQHAKGKLTARERVEVLLDEGSFEELDMYVEHNCV 60

Query: 61  DFGMQDDRPAGDGVVTGWGTINGRMVYVFSQDFTVFGGSLSETHAQKICKIMDMAMQNGA 120
           DFGM D    GDGVVTG GTINGR+V+VFSQDFTVFGGSLSE HAQKICKIMDMAM+ GA
Sbjct: 61  DFGMPDQVVPGDGVVTGSGTINGRLVFVFSQDFTVFGGSLSERHAQKICKIMDMAMKVGA 120

Query: 121 PVIGLNDSGGARIQEGVASLAGYADVFQRNIMASGVIPQISVIMGPCAGGAVYSPAMTDF 180
           PVIGLNDSGGARIQEGVASLAGYA+VFQRN++ASGV+PQ+S+IMGPCAGGAVYSPAMTDF
Sbjct: 121 PVIGLNDSGGARIQEGVASLAGYAEVFQRNVLASGVVPQLSLIMGPCAGGAVYSPAMTDF 180

Query: 181 IFMVRDTSYMFVTGPDVVKTVTNEVVTAEELGGASTHTKKSSVADGAFENDVEALYEIRR 240
           IFMV+D+SYMFVTGPDVVKTVTNE+VT E+LGGA THT KS VAD AFEND+EAL   R 
Sbjct: 181 IFMVKDSSYMFVTGPDVVKTVTNEIVTQEDLGGAVTHTTKSGVADVAFENDIEALLAARD 240

Query: 241 LVDFLPLSNRTPAPVRPFFDDVARIEDSLDTLIPDNPNQPYDMKELILKIADEADFYEIQ 300
            VDFLP SNR P P RP  D   RIEDSLDTLIP + NQPYDM ELI K  DE DF+E+Q
Sbjct: 241 FVDFLPASNREPVPERPCEDPWDRIEDSLDTLIPPSANQPYDMHELIRKTVDEGDFFEVQ 300

Query: 301 KDFAANIITGFIRLEGQTVGVVANQPMVLAGCLDIDSSRKAARFVRFCDAFNIPILTLVD 360
              AANII GF R+EG+TVG+VANQPMVLAG LDI+SS+KAARFVRFCDAF IPI+T VD
Sbjct: 301 PTHAANIIIGFGRIEGRTVGIVANQPMVLAGVLDINSSKKAARFVRFCDAFEIPIVTFVD 360

Query: 361 VPGFLPGTGQEYGGVIKHGAKLLFAYGEATVPKVTVITRKAYGGAYDVMASKHLRGDFNY 420
           VPGFLPG GQE+ G+IKHGAKLLFAY EATVPK+TVITRKAYGGAYDVMASKHLRGD NY
Sbjct: 361 VPGFLPGVGQEHSGIIKHGAKLLFAYAEATVPKITVITRKAYGGAYDVMASKHLRGDLNY 420

Query: 421 AWPTAEIAVMGAKGATEILYRSELGDKEKIAARAKEYEDRFANPFVAAERGFIDEVIMPH 480
           AWPTAEIAVMGAKGA EI++R +    E+IA R  EYE RFANPFVAA +GF+DEVIMPH
Sbjct: 421 AWPTAEIAVMGAKGAVEIIFRGK--TPEEIAERTAEYEARFANPFVAASKGFVDEVIMPH 478

Query: 481 STRRRVSKAFASLRNKKLANPWKKHDNIPL 510
           STRRR++     LRNK L NPWKKHDNIPL
Sbjct: 479 STRRRIALGLRKLRNKSLENPWKKHDNIPL 508


Lambda     K      H
   0.321    0.138    0.404 

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: 863
Number of extensions: 28
Number of successful extensions: 3
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: 510
Length of database: 508
Length adjustment: 34
Effective length of query: 476
Effective length of database: 474
Effective search space:   225624
Effective search space used:   225624
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 (21.8 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