Alignments for a candidate for pccB in Kocuria flava HO-9041

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Kocuria flava HO-9041

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_058858416.1 AS188_RS08020 acyl-CoA carboxylase subunit beta

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_001482365.1:WP_058858416.1
          Length = 527

 Score =  724 bits (1869), Expect = 0.0
 Identities = 365/530 (68%), Positives = 422/530 (79%), Gaps = 6/530 (1%)

Query: 17  DIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERIDMLLDEGSFVELDEHAR 76
           D+ TTAGK+AD + R   +       A+ KQHA+G+ TARER++MLLDE SFVE D  A 
Sbjct: 4   DLTTTAGKIADFHDRRARSEAPAGRAAIDKQHARGRNTARERVEMLLDEDSFVEFDALAT 63

Query: 77  HRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSLGEVFGEKIVKVMDLAM 136
           HRST FGM++ +  GDGVV+G+GTVDGR V V+SQDF VFGGSL +V GEKIVKV   A+
Sbjct: 64  HRSTAFGMESKKLLGDGVVSGYGTVDGRLVAVYSQDFAVFGGSLSQVNGEKIVKVQKFAL 123

Query: 137 KTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQISLIMGPCAGGAVYSPA 196
           + GCP++GIND GGARIQEGVA+L ++A+IF  N  +SGV+PQISLIMGPCAGGA YSPA
Sbjct: 124 RNGCPVIGINDGGGARIQEGVASLAMFADIFNMNVRSSGVVPQISLIMGPCAGGAAYSPA 183

Query: 197 ITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNERSGNAHYLATDEDDAIS 256
           +TD+ VMVD+TSHMFITGPDVIKTVTGE V  E LGGAR HN  +G A YLA DE DA  
Sbjct: 184 LTDYIVMVDKTSHMFITGPDVIKTVTGETVDMETLGGARQHNTTTGTATYLAEDEQDAFE 243

Query: 257 YVKELLSFLPSNNLSSSPVFPGAEVEEGSVADGVGDADLELDALVPDSPNQPYDMREVIT 316
           +V ELL FLP+NNL  +P+    + EE +      +ADL LD LVPDS NQPYDMR VI 
Sbjct: 244 FVHELLEFLPANNLHEAPLLEHDQEEETT------EADLALDGLVPDSANQPYDMRAVIE 297

Query: 317 RLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAGTLDIDASEKAARFVRFC 376
            +VD+G FLE+ +L+APN+L G+ R+EG +VG+VANQP+Q AGTLDI ASEKAARFVR C
Sbjct: 298 AVVDDGHFLEMQSLYAPNVLIGYARVEGHTVGIVANQPLQFAGTLDIAASEKAARFVRHC 357

Query: 377 DAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATVPLVTVITRKAYGGAYDV 436
           DAFN+PVLTLVDVPGFLPGT QE+NGIIRRGAKLLYAYAEATVPLVT+ITRKAYGGAY V
Sbjct: 358 DAFNVPVLTLVDVPGFLPGTDQEFNGIIRRGAKLLYAYAEATVPLVTLITRKAYGGAYIV 417

Query: 437 MGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERGEDVEALRARLQQEYEDT 496
           MGSK LGAD+NLAWPTAQI VMGAQGA  ILYRR LA AAERGEDV+ALRA L Q+YE+ 
Sbjct: 418 MGSKKLGADVNLAWPTAQIGVMGAQGAVEILYRRDLAAAAERGEDVDALRAELVQKYEEE 477

Query: 497 LCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAKKHGNIPL 546
           L NPY AAE GYVD+VI PS TR  V RALR L +KR   PAKKHGNIPL
Sbjct: 478 LLNPYQAAELGYVDAVIAPSETRLQVVRALRALREKRATQPAKKHGNIPL 527


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: 814
Number of extensions: 27
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: 527
Length adjustment: 35
Effective length of query: 511
Effective length of database: 492
Effective search space:   251412
Effective search space used:   251412
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources