Alignments for a candidate for mcm-large in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Cereibacter sphaeroides ATCC 17029

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_011842539.1 RSPH17029_RS18485 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000015985.1:WP_011842539.1
          Length = 563

 Score =  570 bits (1470), Expect = e-167
 Identities = 285/562 (50%), Positives = 395/562 (70%), Gaps = 3/562 (0%)

Query: 3   TFDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYM 62
           TF      +I +  + WE T V  F+ +APERKE+F T   F +KR YT AD+ +    +
Sbjct: 4   TFSHARTDEIAQAVEDWERTEVADFIARAPERKEQFYTLGDFPVKRTYTAADIAD--TPL 61

Query: 63  EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDL 122
           E +G PG+YPFTRG Y TMYRGR WTMRQ AG+ T E++NKR+K+L+ QGQTG+S  FD+
Sbjct: 62  EDIGLPGKYPFTRGPYPTMYRGRNWTMRQIAGFGTGEDTNKRFKFLIEQGQTGISTDFDM 121

Query: 123 PTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYI 182
           PT +GYDSDHP+++GEVG+ GVAID+L DMR L DGI L+K+S S+TIN TA  LLAMYI
Sbjct: 122 PTLMGYDSDHPMSDGEVGREGVAIDTLADMRALLDGIDLEKISVSLTINPTAWILLAMYI 181

Query: 183 LVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPIS 242
            + EE+G    K+ GTVQ DILKEY+A+  YIFP  PS+R+  DII +    + ++NPI+
Sbjct: 182 ALCEERGYDLNKVSGTVQADILKEYMAQKEYIFPIAPSVRIVRDIISHSTRTMKRYNPIN 241

Query: 243 ISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIA 302
           ISGYHI EAG++ + E AFTLA+ I YV+ V++ G++VD FAPRL+FFF    +F EEIA
Sbjct: 242 ISGYHISEAGSSPLHEAAFTLANLIVYVEEVLKTGVEVDDFAPRLAFFFVCQADFFEEIA 301

Query: 303 KFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLG 362
           KFRA RR +A IMKE F AK P SM LRFH QTA ++LT  Q   N++R   QALAAVLG
Sbjct: 302 KFRALRRCYAKIMKERFGAKKPESMRLRFHCQTAAASLTKPQYMVNVMRTTTQALAAVLG 361

Query: 363 GTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYE 422
           G QSLHTN YDEA ++PTE ++++ALRTQQ+IA E+GV   VDPLGG+Y++E LT+   +
Sbjct: 362 GAQSLHTNGYDEAFAIPTEHAMQLALRTQQVIADETGVTQVVDPLGGSYFVESLTNDYEK 421

Query: 423 EALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP-IE 481
           +  + ++++++ GG ++ IE G+ QK IA+ AY+     + G++ ++GVN +V DE  ++
Sbjct: 422 KIFEILDEVEERGGAIKLIEEGWFQKHIADFAYETALRKQSGEKPVIGVNRYVMDESHVK 481

Query: 482 VEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLA 541
           +E+   D +  ++QI+R + +R+ RD  KVQ  LD+L   A  E  N+MP  I+  +  A
Sbjct: 482 IEVHPYDETTAKRQIDRTRSVRAGRDEAKVQALLDELVAVARDESANVMPVTIQLVKEGA 541

Query: 542 TLQEVTDVLREIWGEYRAPLIF 563
           T+ ++ + L+ IWG YR   +F
Sbjct: 542 TMGDIVEKLKTIWGVYRETPVF 563


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: 800
Number of extensions: 30
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: 563
Length adjustment: 36
Effective length of query: 527
Effective length of database: 527
Effective search space:   277729
Effective search space used:   277729
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 Apr 10 2024. 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