Alignments for a candidate for mcm-large in Desulfallas geothermicus DSM 3669

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Desulfallas geothermicus DSM 3669

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_092483258.1 BM299_RS09140 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_900115975.1:WP_092483258.1
          Length = 556

 Score =  738 bits (1905), Expect = 0.0
 Identities = 369/560 (65%), Positives = 457/560 (81%), Gaps = 5/560 (0%)

Query: 4   FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYME 63
           FDK+ L+KIKE+++++++  ++    K PER+EKF+TD   +I  +YTP D+ +  +Y +
Sbjct: 2   FDKDSLEKIKEQKQKYQQK-LETLTAKRPERQEKFVTDSEIDINTLYTPEDI-DHLDYEK 59

Query: 64  KLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLP 123
            LGFPG+YP+TRGV   MYRGR+WTMRQYAG+ TAEE+NKR++YLL QGQTGLSVAFDLP
Sbjct: 60  DLGFPGDYPYTRGVQPNMYRGRLWTMRQYAGFGTAEETNKRFRYLLEQGQTGLSVAFDLP 119

Query: 124 TQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYIL 183
           TQ+GYDSDH LA GEVGKVGVAIDSL DM  LFD IPLDKVSTSMTINS AA LLAMYI 
Sbjct: 120 TQIGYDSDHQLAMGEVGKVGVAIDSLLDMETLFDQIPLDKVSTSMTINSPAAILLAMYIA 179

Query: 184 VAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISI 243
           VAE+QGV QE+L+GT+QNDILKEY+ARGTYIFPP+ SMRL TDI  YCA+NVP WN ISI
Sbjct: 180 VAEKQGVKQEQLKGTIQNDILKEYVARGTYIFPPEHSMRLITDIFAYCAKNVPSWNTISI 239

Query: 244 SGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAK 303
           SGYHIREAG+ A QEVAFTLADGI YV+A I+ G+DVD+FAPRLSFFF AH NF EE+AK
Sbjct: 240 SGYHIREAGSTAAQEVAFTLADGIAYVEAAIDAGLDVDEFAPRLSFFFNAHLNFFEEVAK 299

Query: 304 FRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGG 363
           FRAARRLWA IMKE F AK P+SMMLRFHTQTAG TLTAQQP+ NI+RVA QAL+AVLGG
Sbjct: 300 FRAARRLWARIMKERFGAKKPKSMMLRFHTQTAGCTLTAQQPDVNIMRVAFQALSAVLGG 359

Query: 364 TQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEE 423
           TQSLHTNS DEAL+LP++ SV IALRTQQ+I YE G  DTVDPLGG+Y++E LTD + ++
Sbjct: 360 TQSLHTNSRDEALALPSDSSVLIALRTQQVIGYEIGAADTVDPLGGSYFVESLTDAVEQK 419

Query: 424 ALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVE 483
           AL+YI+KI  +GG  +AIE  ++QKEI  +AYKYQ+EIE GK+I++GVN F   E    +
Sbjct: 420 ALEYIKKIDDLGGAPKAIE--FMQKEIHTSAYKYQQEIESGKKIVIGVNKFQMQEERPKD 477

Query: 484 ILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATL 543
           +LKVDP + ++Q  +L +LR+ERDN+KVQ+ L ++  AA   +ENL+PY +EA ++ ATL
Sbjct: 478 LLKVDPEVGKRQEAKLARLRAERDNEKVQKMLQEIERAA-GTNENLLPYFVEAVKNYATL 536

Query: 544 QEVTDVLREIWGEYRAPLIF 563
            E+  VLR ++GEY+  ++F
Sbjct: 537 GEICGVLRNVFGEYQQQIVF 556


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: 877
Number of extensions: 36
Number of successful extensions: 5
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: 556
Length adjustment: 36
Effective length of query: 527
Effective length of database: 520
Effective search space:   274040
Effective search space used:   274040
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