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_053544285.1 CDES_RS03450 acyl-CoA carboxylase subunit beta

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_001277995.1:WP_053544285.1
          Length = 537

 Score =  660 bits (1703), Expect = 0.0
 Identities = 322/531 (60%), Positives = 414/531 (77%), Gaps = 1/531 (0%)

Query: 16  PDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERIDMLLDEGSFVELDEHA 75
           PD+ TTAGKL+DL  R  EA     + +V K H  G++TARERI+ LLD+G+FVE+D  A
Sbjct: 8   PDLTTTAGKLSDLRSRLAEAQAPMGQESVEKAHEAGQKTARERIEYLLDQGTFVEIDALA 67

Query: 76  RHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSLGEVFGEKIVKVMDLA 135
           RHRS NFG+DA RP  DGVVTG+GT+DGR+VC+FSQD  VF G+LGEV GEKIVKVMDLA
Sbjct: 68  RHRSKNFGLDAKRPATDGVVTGYGTIDGRKVCIFSQDGAVFDGTLGEVNGEKIVKVMDLA 127

Query: 136 MKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQISLIMGPCAGGAVYSP 195
           +KTG PL+ IN+  GARI+EG+ +LG+Y+++F RNT ASG++PQISL+MG  AGG VYSP
Sbjct: 128 IKTGVPLIAINEGAGARIKEGIVSLGMYSKMFYRNTQASGLVPQISLVMGESAGGNVYSP 187

Query: 196 AITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNERSGNAHYLATDEDDAI 255
           A++DF VMV+ TS M++T P++IKTVTG+DV+ E+LGGA TH   SG +HY A +E DA+
Sbjct: 188 ALSDFLVMVNGTSQMYVTSPEIIKTVTGDDVTTEELGGATTHMATSGTSHYSAANETDAL 247

Query: 256 SYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLELDALVPDSPNQPYDMREVI 315
            +V+ELLS+LPSNN + +P  P  E+  GS+ + V D D ELD+++PDS +QPYDMR ++
Sbjct: 248 DWVRELLSYLPSNNRAEAPRTP-VEITTGSIQENVTDLDRELDSIIPDSNHQPYDMRTIL 306

Query: 316 TRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGTLDIDASEKAARFVRF 375
           +R+VDE EF E+   +A N+LCGF RIEG SVG+VANQP QLAG LDI A EKAARF+R 
Sbjct: 307 SRVVDEAEFFEIQKDYAENILCGFARIEGRSVGIVANQPTQLAGCLDIKAMEKAARFIRT 366

Query: 376 CDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVPLVTVITRKAYGGAYD 435
           CDAFNIP++  VDVPGFLPGT QE+NG+IRRGAKL+YAYAEATV  +T+ITRK+ G AY 
Sbjct: 367 CDAFNIPIVEFVDVPGFLPGTAQEFNGLIRRGAKLVYAYAEATVGKITIITRKSIGTAYS 426

Query: 436 VMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGEDVEALRARLQQEYED 495
           +MGSK +GAD+  AWPTA+IAV+ A GA + +Y ++L +AA  G+DV  +    + +YE+
Sbjct: 427 IMGSKDMGADLVYAWPTAEIAVLAASGAVSDIYAKELKQAATEGKDVTEVMKGYEAQYEE 486

Query: 496 TLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKKHGNIPL 546
           +  NPY+AAERG VD+VIPPS TRG +   LR+L  K   +PAKKHGNIPL
Sbjct: 487 SHLNPYLAAERGLVDAVIPPSETRGQILEGLRLLDRKVVNVPAKKHGNIPL 537


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: 739
Number of extensions: 20
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: 537
Length adjustment: 35
Effective length of query: 511
Effective length of database: 502
Effective search space:   256522
Effective search space used:   256522
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