GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Corynebacterium deserti GIMN1.010

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_053544286.1 CDES_RS03455 acyl-CoA carboxylase subunit beta

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_001277995.1:WP_053544286.1
          Length = 543

 Score =  665 bits (1716), Expect = 0.0
 Identities = 328/534 (61%), Positives = 410/534 (76%), Gaps = 1/534 (0%)

Query: 13  AEAPDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERIDMLLDEGSFVELD 72
           A  PDI+TTAGK+ADL  R  EA     E+AV K HA G+ TARER+D LLDEGSF+E D
Sbjct: 11  ANLPDINTTAGKIADLKARRAEAHFPMGEKAVEKVHAAGRLTARERLDYLLDEGSFIETD 70

Query: 73  EHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSLGEVFGEKIVKVM 132
           + ARHR+T FG+ + RP  DG+VTGWGT+DGR VC+FSQD TVFGG+LGEV+GEK++K+M
Sbjct: 71  QLARHRTTAFGLGSKRPATDGIVTGWGTIDGREVCIFSQDGTVFGGALGEVYGEKMIKIM 130

Query: 133 DLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQISLIMGPCAGGAV 192
           +LA+ TG PL+G+ +  GARIQ+G  +L   ++ F +N  ASGVIPQIS+IMG CAGG  
Sbjct: 131 ELAIDTGRPLIGLYEGAGARIQDGAVSLDYISQTFYQNIQASGVIPQISVIMGACAGGNA 190

Query: 193 YSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNERSGNAHYLATDED 252
           Y PA+TDF VMVD++S MF+TGPDVIKTVTGE+++ E+LGGA TH   +GN+HY A  ++
Sbjct: 191 YGPALTDFVVMVDKSSKMFVTGPDVIKTVTGEEITQEELGGATTHMVTAGNSHYTAQTDE 250

Query: 253 DAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLELDALVPDSPNQPYDMR 312
           +A+ +V++L+SFLPSNN S +P     E EEG + D +   DL+LD ++PDS   PYD+R
Sbjct: 251 EALDWVQDLISFLPSNNRSFAPAEDFDE-EEGGIEDNITADDLKLDEIIPDSATVPYDVR 309

Query: 313 EVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGTLDIDASEKAARF 372
           +VI  L D+GE+LE+ A  A N++  FGRIEG SVG VANQP Q AG LDID+SEKAARF
Sbjct: 310 DVIQCLTDDGEYLEIQADRAENVVIAFGRIEGQSVGFVANQPTQFAGCLDIDSSEKAARF 369

Query: 373 VRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVPLVTVITRKAYGG 432
           VR CDAFNIP++ LVDVPGFLPG GQE+ GI+RRGAKLLYAY EATVP +TV  RKAYGG
Sbjct: 370 VRTCDAFNIPIVMLVDVPGFLPGAGQEYGGILRRGAKLLYAYGEATVPKITVTMRKAYGG 429

Query: 433 AYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGEDVEALRARLQQE 492
           AY VMGSK LG+D+NLAWPTAQIAVMGA GA   +YR++L  A  +G D  AL    ++E
Sbjct: 430 AYCVMGSKGLGSDVNLAWPTAQIAVMGAAGAVGFIYRKELMAADAKGLDTVALAKSFERE 489

Query: 493 YEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKKHGNIPL 546
           YED + NPY+AAERG +D+VI PS TRG +AR LR+L  K    PA+KHGN+PL
Sbjct: 490 YEDHMLNPYLAAERGLIDAVILPSETRGQIARNLRLLKHKNVTRPARKHGNMPL 543


Lambda     K      H
   0.318    0.136    0.398 

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: 802
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: 546
Length of database: 543
Length adjustment: 35
Effective length of query: 511
Effective length of database: 508
Effective search space:   259588
Effective search space used:   259588
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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