Aligments for a candidate for prpC in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Aligments for a candidate for prpC in Dyella japonica UNC79MFTsu3.2

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate N515DRAFT_0021 N515DRAFT_0021 2-methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0021
          Length = 381

 Score =  580 bits (1494), Expect = e-170
 Identities = 282/380 (74%), Positives = 322/380 (84%)

Query: 18  SEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHG 77
           SE   P+ KKSVALSGV AGNTALCTVGR+GNDLHYRGYDI D+A    FEE+A+LLVHG
Sbjct: 2   SEQVLPKAKKSVALSGVAAGNTALCTVGRSGNDLHYRGYDIHDLAAKGCFEEVAYLLVHG 61

Query: 78  KLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHN 137
            LP  +EL AY+AKLK LRGLPA VK+ALE +PA+ HPMDVMRTG SVLGTVLPEK+DHN
Sbjct: 62  VLPNWAELNAYRAKLKRLRGLPAPVKSALELLPAATHPMDVMRTGCSVLGTVLPEKDDHN 121

Query: 138 TPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWER 197
             GARDIADRLMAS GSMLLYWYH+SHNG+RIE ETDD+SI  HFLHLLHG+K S L   
Sbjct: 122 LTGARDIADRLMASFGSMLLYWYHFSHNGKRIETETDDESIAAHFLHLLHGKKASELHAH 181

Query: 198 AMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKR 257
           A+  SL LYAEHEFNASTF ARVIAGTGSDMYS+I+GAIGALRGPKHGGANEVA EI  R
Sbjct: 182 ALDKSLILYAEHEFNASTFAARVIAGTGSDMYSAITGAIGALRGPKHGGANEVAMEIIAR 241

Query: 258 YDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDIAE 317
           Y N  EA+ADI  RV  KE++IGFGHPVYT  DPRN++IKEV++KL  + G+  +F+++E
Sbjct: 242 YRNAAEAEADIRARVERKEIIIGFGHPVYTVSDPRNEIIKEVSRKLCTEGGNPTLFEVSE 301

Query: 318 RLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKII 377
           R+E +MW++KKMFPNLDWFSA +YHMMGVPTAMFTPLFVIARTSGW+AH+IEQR D KII
Sbjct: 302 RIEKLMWELKKMFPNLDWFSASAYHMMGVPTAMFTPLFVIARTSGWSAHVIEQRQDGKII 361

Query: 378 RPSANYTGPENLKFVPIGKR 397
           RPSANYTGPE+  +VPI KR
Sbjct: 362 RPSANYTGPEDQAYVPIEKR 381


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: 547
Number of extensions: 10
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: 381
Length adjustment: 30
Effective length of query: 368
Effective length of database: 351
Effective search space:   129168
Effective search space used:   129168
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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Protein sequences (fasta format)
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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, or view the source code.

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