GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Herbaspirillum seropedicae SmR1

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate HSERO_RS15655 HSERO_RS15655 methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>FitnessBrowser__HerbieS:HSERO_RS15655
          Length = 384

 Score =  700 bits (1806), Expect = 0.0
 Identities = 340/380 (89%), Positives = 359/380 (94%)

Query: 19  EPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGK 78
           + A  + KKSVALSGVTAGNTALCTVG+TGNDLHYRGYDILD+A++CEFEEIAHLLVHGK
Sbjct: 5   QAAGFKPKKSVALSGVTAGNTALCTVGKTGNDLHYRGYDILDVADSCEFEEIAHLLVHGK 64

Query: 79  LPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHNT 138
           LPT +EL AYKAKLKSLRGLPANVKAALEW+PA++HPMDVMRTGVS LG VLPEK+DHNT
Sbjct: 65  LPTAAELRAYKAKLKSLRGLPANVKAALEWLPAASHPMDVMRTGVSALGCVLPEKDDHNT 124

Query: 139 PGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWERA 198
           PGARDIADRLMASLGSMLLYWYHYSHNG RIEVETDDDSIG HFLHLLHGEKPS  WE+A
Sbjct: 125 PGARDIADRLMASLGSMLLYWYHYSHNGNRIEVETDDDSIGAHFLHLLHGEKPSEAWEKA 184

Query: 199 MHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKRY 258
           MHTSL LYAEHEFNASTFT RVIAGTGSDMYS+I+GAIGALRGPKHGGANEVAFEIQKRY
Sbjct: 185 MHTSLILYAEHEFNASTFTGRVIAGTGSDMYSAITGAIGALRGPKHGGANEVAFEIQKRY 244

Query: 259 DNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDIAER 318
           DNPDEA+ADI RRV NKEVVIGFGHPVYT  DPRN+VIKEVA+KLSK+AGS KMFDIAER
Sbjct: 245 DNPDEAEADIRRRVENKEVVIGFGHPVYTISDPRNKVIKEVARKLSKEAGSTKMFDIAER 304

Query: 319 LETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIR 378
           LETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIR
Sbjct: 305 LETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIR 364

Query: 379 PSANYTGPENLKFVPIGKRK 398
           PSANY GPE+LKFVPI KRK
Sbjct: 365 PSANYVGPEDLKFVPISKRK 384


Lambda     K      H
   0.317    0.133    0.396 

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: 633
Number of extensions: 13
Number of successful extensions: 1
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: 398
Length of database: 384
Length adjustment: 31
Effective length of query: 367
Effective length of database: 353
Effective search space:   129551
Effective search space used:   129551
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: 50 (23.9 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