GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Paraburkholderia bryophila 376MFSha3.1

Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate H281DRAFT_06634 H281DRAFT_06634 2-methylcitrate synthase (EC 2.3.3.5)

Query= SwissProt::Q937N9
         (385 letters)



>FitnessBrowser__Burk376:H281DRAFT_06634
          Length = 287

 Score =  489 bits (1260), Expect = e-143
 Identities = 236/273 (86%), Positives = 254/273 (93%)

Query: 11  KPKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPTKS 70
           KPKKSVALSGVTAGNTALCTVG+TGNDLHYRGYDILDIA  CEFEEIA+LLVH KLPT++
Sbjct: 15  KPKKSVALSGVTAGNTALCTVGKTGNDLHYRGYDILDIAGNCEFEEIAYLLVHEKLPTQA 74

Query: 71  ELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHNTPGARD 130
           EL AYK KLK+LRGLPANVKAALEW+PA+AHPMDVMRTGVSVLGTVLPEK+DHN PGARD
Sbjct: 75  ELTAYKTKLKALRGLPANVKAALEWIPAAAHPMDVMRTGVSVLGTVLPEKDDHNLPGARD 134

Query: 131 IADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWERAMNTSL 190
           IAD+LMASLGSMLLYWYHYSHNG+RIEVETDDDSIGGHFLHLLHG +PS  W  AM+ SL
Sbjct: 135 IADKLMASLGSMLLYWYHYSHNGKRIEVETDDDSIGGHFLHLLHGVEPSKSWVDAMHVSL 194

Query: 191 NLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKRYDNPDE 250
           NLYAEHEFNASTFT RVIAGTGSD+YS+I+GAIGALRGPKHGGANEVAFEIQ RY  PDE
Sbjct: 195 NLYAEHEFNASTFTGRVIAGTGSDIYSAITGAIGALRGPKHGGANEVAFEIQSRYQTPDE 254

Query: 251 AQADITRRVENKEVVIGFGHPVYTTGDPRNQVI 283
           A++DI RRVENKEVVIGFGHPVYT  DPRN+VI
Sbjct: 255 AESDIRRRVENKEVVIGFGHPVYTISDPRNKVI 287


Lambda     K      H
   0.317    0.133    0.394 

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: 457
Number of extensions: 8
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: 385
Length of database: 287
Length adjustment: 28
Effective length of query: 357
Effective length of database: 259
Effective search space:    92463
Effective search space used:    92463
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: 49 (23.5 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