Alignments for a candidate for mcm-large in Pelobacter propionicus DSM 2379

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Pelobacter propionicus DSM 2379

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_011734468.1 PPRO_RS02565 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000015045.1:WP_011734468.1
          Length = 551

 Score =  710 bits (1832), Expect = 0.0
 Identities = 358/554 (64%), Positives = 439/554 (79%), Gaps = 9/554 (1%)

Query: 12  IKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYM---EKLGFP 68
           I E++K+W +T V KFL ++PER EKF+T    EI+R++TP     D++Y    EKLGFP
Sbjct: 3   IAEKKKQWTDTKVAKFLTRSPERYEKFLTTSNLEIERVFTP-----DFDYPGYDEKLGFP 57

Query: 69  GEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGY 128
           G YP+TRGV  TMYRGR WTMRQYAG+  A+ESN+RYKYLL  GQTGLS+AFDLPTQ+GY
Sbjct: 58  GSYPYTRGVQPTMYRGRFWTMRQYAGFGNAKESNERYKYLLGAGQTGLSIAFDLPTQMGY 117

Query: 129 DSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQ 188
           DSD  +++GEVGKVGVAIDSL D+ +LFDGIPLDKVSTSMT+NSTAA LL MYI VAE+Q
Sbjct: 118 DSDAAMSQGEVGKVGVAIDSLADVEVLFDGIPLDKVSTSMTVNSTAAILLCMYIAVAEKQ 177

Query: 189 GVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHI 248
           GVS +K+ GT+QNDILKEY+ARGTYI+PP+ SMRL TDI  YC +NVPKWN ISISGYHI
Sbjct: 178 GVSADKISGTIQNDILKEYMARGTYIYPPKESMRLITDIFAYCKDNVPKWNTISISGYHI 237

Query: 249 REAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAAR 308
           REAG++AVQEVAFTLADGI YV A I+ G+DVD FAPRL+FFF AHNN LEE+AKFRAAR
Sbjct: 238 REAGSSAVQEVAFTLADGIAYVDAAIKAGLDVDDFAPRLAFFFNAHNNLLEEVAKFRAAR 297

Query: 309 RLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLH 368
           R+WA IMKE F AK  +S MLRFHTQTAG TLTAQQP+NNI+RV IQ LAAVLGGTQSLH
Sbjct: 298 RIWAKIMKERFGAKLEKSQMLRFHTQTAGCTLTAQQPDNNIMRVTIQTLAAVLGGTQSLH 357

Query: 369 TNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYI 428
           TNS DEAL+LPTE SVRIALRTQQ++AYESGV D++DPL G++++E LTD I + A +YI
Sbjct: 358 TNSRDEALALPTEDSVRIALRTQQVVAYESGVADSIDPLAGSFFVESLTDQIEKAAWEYI 417

Query: 429 EKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVEILKVD 488
           EKI K+GG + AI  G+ QKEI ++AY YQK IE+ + IIVGVN F   EP    +LKV 
Sbjct: 418 EKIDKLGGAVEAISNGFQQKEIQDSAYAYQKAIEKNELIIVGVNKFTISEPPPTGLLKVT 477

Query: 489 PSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTD 548
             +   Q + L +++++RD   V+ AL KL  AA K  +NL+P I+EA +  ATL E+ D
Sbjct: 478 GEVETNQKKALAEVKAKRDGAAVKAALAKLEVAA-KGTDNLIPLILEAVKVYATLGEIAD 536

Query: 549 VLREIWGEYRAPLI 562
           V R ++G+++  ++
Sbjct: 537 VFRGVFGKHQETVV 550


Lambda     K      H
   0.318    0.134    0.388 

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: 875
Number of extensions: 32
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: 563
Length of database: 551
Length adjustment: 36
Effective length of query: 527
Effective length of database: 515
Effective search space:   271405
Effective search space used:   271405
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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