GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Amycolatopsis halophila YIM 93223

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_034275130.1 AMYHA_RS25160 acyl-CoA carboxylase subunit beta

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_000504245.1:WP_034275130.1
          Length = 549

 Score =  875 bits (2261), Expect = 0.0
 Identities = 437/549 (79%), Positives = 475/549 (86%), Gaps = 3/549 (0%)

Query: 1   MSSATEPVGVPPAEAP---DIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARE 57
           MSSATEP+G     A    DIHTTAGKLADLYRRN EAVHAGS RAV KQHAKGK+TARE
Sbjct: 1   MSSATEPLGGQHGSAEESIDIHTTAGKLADLYRRNDEAVHAGSARAVEKQHAKGKKTARE 60

Query: 58  RIDMLLDEGSFVELDEHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFG 117
           RIDMLLD GSFVELDE ARHRSTNFG DA+RPYGDGVVTG+GT+DGR VCVFSQD T+FG
Sbjct: 61  RIDMLLDPGSFVELDELARHRSTNFGQDANRPYGDGVVTGYGTIDGRPVCVFSQDVTIFG 120

Query: 118 GSLGEVFGEKIVKVMDLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVI 177
           GSLGEV+GEKIVKVMDLA+KTG P++GIN+ GGARIQEGV +LGLY EIF RN  ASGV+
Sbjct: 121 GSLGEVYGEKIVKVMDLAIKTGRPIIGINEGGGARIQEGVVSLGLYGEIFTRNVKASGVV 180

Query: 178 PQISLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTH 237
           PQISLIMG  AGG VYSPA+TDF VMVDQTSHMFITGPDVIKTVTGE+V+FE+LGG R+H
Sbjct: 181 PQISLIMGANAGGHVYSPALTDFVVMVDQTSHMFITGPDVIKTVTGEEVTFEELGGGRSH 240

Query: 238 NERSGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLEL 297
           N +SGNAHYL  DE+DAISYVKELLSFLP NNL+  PVF        SVAD + D D EL
Sbjct: 241 NTKSGNAHYLGADEEDAISYVKELLSFLPPNNLAEPPVFEAPPHTGNSVADDITDDDREL 300

Query: 298 DALVPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQL 357
           D L+PDSPN PYDM EVIT +VD+GEFLEV  LFAPN+L GFGR++G SVG+VANQP Q 
Sbjct: 301 DTLIPDSPNVPYDMHEVITHVVDDGEFLEVHELFAPNVLVGFGRVDGQSVGIVANQPTQF 360

Query: 358 AGTLDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEA 417
           AG LDIDASEKAARFVR CDAFN+PVLT VDVPGFLPGT QEWNGIIRRGAKL+YAYAEA
Sbjct: 361 AGCLDIDASEKAARFVRTCDAFNVPVLTFVDVPGFLPGTDQEWNGIIRRGAKLIYAYAEA 420

Query: 418 TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAE 477
           TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANI+YR+ LA A  
Sbjct: 421 TVPLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANIVYRKTLANAEA 480

Query: 478 RGEDVEALRARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALP 537
            G+D+E LR  L QEYEDTLCNPYVAAERGYVDSVIPPSHTRG+VAR+LR+L DKRE  P
Sbjct: 481 EGQDIEKLRGELIQEYEDTLCNPYVAAERGYVDSVIPPSHTRGYVARSLRILGDKRENQP 540

Query: 538 AKKHGNIPL 546
            KKHGNIPL
Sbjct: 541 PKKHGNIPL 549


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: 1014
Number of extensions: 39
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: 546
Length of database: 549
Length adjustment: 36
Effective length of query: 510
Effective length of database: 513
Effective search space:   261630
Effective search space used:   261630
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: 53 (25.0 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