Alignments for a candidate for pccB in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Desulfobulbus mediterraneus DSM 13871

Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate WP_028582881.1 G494_RS0100190 acyl-CoA carboxylase subunit beta

Query= reanno::PS:Dsui_0517
         (510 letters)



>NCBI__GCF_000429965.1:WP_028582881.1
          Length = 518

 Score =  645 bits (1664), Expect = 0.0
 Identities = 319/510 (62%), Positives = 397/510 (77%), Gaps = 4/510 (0%)

Query: 5   IHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCTDFGM 64
           I EL+K+R AA LGGGQ +ID  H KGK TARER+  L+DP SFEE+D FK HRC +FGM
Sbjct: 9   IEELKKRRAAALLGGGQAKIDKIHAKGKKTARERINQLVDPGSFEEYDCFKLHRCVNFGM 68

Query: 65  AETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVGAPVIG 124
            +TK  GDG++TG G INGR V++++QDF+V  GSLSET AEKI KVM+  MK G PVIG
Sbjct: 69  EKTKFAGDGIITGCGKINGRPVYLYAQDFSVLAGSLSETLAEKIVKVMELGMKNGIPVIG 128

Query: 125 LNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTDFIFMV 184
           LNDSGGARIQEG+ +L GY D+F RN++ASGV+PQIS + GPCAGGAVYSPA+TDFI  V
Sbjct: 129 LNDSGGARIQEGIEALRGYTDIFLRNILASGVVPQISGVFGPCAGGAVYSPALTDFIVQV 188

Query: 185 KDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLRRLVNF 244
           K+ SYMF+TGP+VVKTV +E+VT E+LGGA  HTTKSGV D   EN+ +A+ Y++ L+++
Sbjct: 189 KEQSYMFLTGPKVVKTVLNEDVTVEQLGGASMHTTKSGVTDYGAENEDDAIWYIQTLLSY 248

Query: 245 LPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEIQPDYA 304
           LP NN E PPV +++DP  R   SL+ ++PDN N  YDMK +I + VDD  +FEI+ ++A
Sbjct: 249 LPQNNMEDPPVVESDDPTTRRCESLNDIIPDNPNAAYDMKNVICETVDDGVYFEIKENFA 308

Query: 305 KNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLVDVPGF 364
            NI+ GFAR  G  VGI+ANQP   AG LDI +SIK ARFVRFCD FNIPV+T VDVPGF
Sbjct: 309 PNIVIGFARYGGKSVGILANQPAYYAGVLDIDASIKGARFVRFCDCFNIPVITFVDVPGF 368

Query: 365 MPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVNLAWPS 424
           +PGT QE+GG+I++GAKL+YAY E TVPK+T+ITRKAYGGAY VMSSKHLR DVN +WP+
Sbjct: 369 LPGTDQEFGGVIRNGAKLMYAYGEATVPKITIITRKAYGGAYCVMSSKHLRCDVNYSWPT 428

Query: 425 AEIAVMGPKGAVEIIF---REEKNDPAK-LAEREAEYKAKFANPFVAGARGFIDDVIMPN 480
            EIAVMG KGAVE+++    + ++DPA  LAE+EAEY   F+NP+ A  RG+IDDVI P 
Sbjct: 429 GEIAVMGGKGAVEVLYARAAKGEDDPAAFLAEKEAEYTTNFSNPYCAAERGYIDDVIEPA 488

Query: 481 ETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510
           ETR RI  +LA +  K+  NP +KHGNIPL
Sbjct: 489 ETRTRIINALASIGGKRDTNPAKKHGNIPL 518


Lambda     K      H
   0.320    0.137    0.409 

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: 862
Number of extensions: 37
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: 518
Length adjustment: 35
Effective length of query: 475
Effective length of database: 483
Effective search space:   229425
Effective search space used:   229425
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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