GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Azospirillum brasilense Sp245

Align Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) (characterized)
to candidate AZOBR_RS21100 AZOBR_RS21100 methylmalonyl-CoA carboxyltransferase

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



>FitnessBrowser__azobra:AZOBR_RS21100
          Length = 510

 Score =  821 bits (2121), Expect = 0.0
 Identities = 400/510 (78%), Positives = 452/510 (88%)

Query: 1   MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDSFEEWDMFKEHRCT 60
           M +I+ +L+  R  ARLGGG+KR+  QH KGKLTARER+EL LD  SFEE+DMF +HRC 
Sbjct: 1   MQEILAKLDAMRSGARLGGGEKRVAGQHAKGKLTARERIELFLDEGSFEEFDMFVQHRCN 60

Query: 61  DFGMAETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVGA 120
           DFGM   K PGDGVVTG+GT+NGRLVFVFSQDFTVFGGSLSE HAEKICK+MD AMKVGA
Sbjct: 61  DFGMEGQKVPGDGVVTGHGTVNGRLVFVFSQDFTVFGGSLSEAHAEKICKIMDQAMKVGA 120

Query: 121 PVIGLNDSGGARIQEGVASLGGYADVFQRNVMASGVIPQISMIMGPCAGGAVYSPAMTDF 180
           PVIGLNDSGGARIQEGVASLGGYA+VFQRNV ASGVIPQIS+IMGPCAGGAVYSPAMTDF
Sbjct: 121 PVIGLNDSGGARIQEGVASLGGYAEVFQRNVNASGVIPQISLIMGPCAGGAVYSPAMTDF 180

Query: 181 IFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEALNYLRR 240
           IFMVKDSSYMFVTGP+VVKTVTHE VTAEELGGA+TH++KSGVAD+AFENDVEAL  LRR
Sbjct: 181 IFMVKDSSYMFVTGPDVVKTVTHEVVTAEELGGAITHSSKSGVADMAFENDVEALLQLRR 240

Query: 241 LVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDCDFFEIQ 300
            ++FLPA+NRE+ P + T DP +R D SLDTLVP+N NKPYDMKELI+K VD+ DFFE+Q
Sbjct: 241 FIDFLPASNRERAPERPTADPIDRDDLSLDTLVPENPNKPYDMKELILKTVDEGDFFELQ 300

Query: 301 PDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIPVVTLVD 360
           PDYAKNII GF RM+G  VGIVANQP+VLAGCLDI SS KAARFVRFCDAF IP++TLVD
Sbjct: 301 PDYAKNIIIGFGRMNGGTVGIVANQPMVLAGCLDIDSSKKAARFVRFCDAFEIPILTLVD 360

Query: 361 VPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHLRGDVNL 420
           VPGFMPGTSQEYGGIIKHGAKLL+AYAE TVPK+T+ITRKAYGGAYDVM+SKHLRGD+N 
Sbjct: 361 VPGFMPGTSQEYGGIIKHGAKLLFAYAEATVPKITVITRKAYGGAYDVMASKHLRGDINY 420

Query: 421 AWPSAEIAVMGPKGAVEIIFREEKNDPAKLAEREAEYKAKFANPFVAGARGFIDDVIMPN 480
           AWPSAEIAVMGPKGAVEIIFR +  D AK+  R  EY+ KFANPFVA +RG+IDDVIMP+
Sbjct: 421 AWPSAEIAVMGPKGAVEIIFRGDIGDTAKIEARTEEYRQKFANPFVAASRGYIDDVIMPH 480

Query: 481 ETRKRICRSLAMLRDKKLDNPWRKHGNIPL 510
            TR+R+ ++L+ML++K+L NPWRKH NIPL
Sbjct: 481 GTRRRVIKALSMLKNKQLQNPWRKHDNIPL 510


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: 914
Number of extensions: 31
Number of successful extensions: 2
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: 510
Length adjustment: 34
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
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 17 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