Aligments for a candidate for mcm-large in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcm-large in Dechlorosoma suillum PS

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate Dsui_1105 Dsui_1105 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>FitnessBrowser__PS:Dsui_1105
          Length = 1093

 Score =  310 bits (795), Expect = 1e-88
 Identities = 219/596 (36%), Positives = 322/596 (54%), Gaps = 50/596 (8%)

Query: 5    DKEVLKKIKEEEKRWEETT--------VKKFLEKAPERKEKFMTDDGFEIKRIYTP--AD 54
            + E+  K K+    W +T         V K  +K    K    +  G +IK++  P   D
Sbjct: 503  ESELDAKAKKLLDMWPDTVKAYSGDEYVVKIRDKEIRTKLVSESLSGTKIKKVVLPRFTD 562

Query: 55   LGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQT 114
             GE   ++ K   PG +P+T GV+A    G   T R +AG   A  +N+R+K + S+G  
Sbjct: 563  DGETLRFLMKENVPGSFPYTAGVFAFKREGEDPT-RMFAGEGDAFRTNRRFKKV-SEGMP 620

Query: 115  G--LSVAFDLPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMT 169
               LS AFD  T  G D D  P   G++G  GV+I +L DM++L+ G  L     S SMT
Sbjct: 621  AHRLSTAFDSVTLYGCDPDVRPDIYGKIGNSGVSIATLDDMKVLYSGFDLVCPTTSVSMT 680

Query: 170  INSTAANLLAMYILVAEEQGVSQ--------------EKLR--------GTVQNDILKEY 207
            IN  A  +LA +   A +Q + +              EK+R        GTVQ DILKE 
Sbjct: 681  INGPAPIILACFFNTAIDQQLDKFRADNGREPTEDEAEKIREWVLASVRGTVQADILKED 740

Query: 208  IARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAGANAVQEVAFTLADG 266
              + T IF  + ++++  DI  +   N V  +  +SISGYHI EAGAN + ++AFTLA+G
Sbjct: 741  QGQNTCIFSTEFALKMMGDIQEFFVHNQVQNFYSVSISGYHIAEAGANPISQLAFTLANG 800

Query: 267  IEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWAYIMKEWFNAKNPR 325
              YV++ + RGM +D FAP LSFFF+  N    E +   R ARR+WA  MK  + A N R
Sbjct: 801  FTYVESYLARGMHIDDFAPNLSFFFS--NGMDPEYSVIGRVARRIWAVAMKNKYGA-NER 857

Query: 326  SMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSYDEALSLPTEKSVR 385
            S  L++H QT+G +L AQ+ + N +R  +QAL A+     SLHTN+YDEA++ PTE+SVR
Sbjct: 858  SQKLKYHIQTSGRSLHAQEMDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTEESVR 917

Query: 386  IALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGGMMRAIERGY 445
             A+  Q II  E GV    +P  GA+ I+ LTD + E  LK  E I   GG++ A+E GY
Sbjct: 918  RAMAIQLIINREWGVAKNENPNQGAFIIDELTDLVEEAVLKEFEAIASRGGVLGAMETGY 977

Query: 446  VQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDE---PIEVEILKVDPSIREKQIERLKKL 502
             + +I E +  Y+ +  +G   I+GVN F+  +    +E+E+ +     ++ QI RLK  
Sbjct: 978  QRGKIQEESLYYEHKKHDGSYPIIGVNTFLNPKGSAQVEIELARSTEEEKQSQIARLKDF 1037

Query: 503  RSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLREIWGEYR 558
              +R+  K    L KL+     E+ N+   ++EA R + +L ++T  L E+ G+YR
Sbjct: 1038 H-QRNADKAPAMLAKLKQTV-IENGNVFAVLVEAVR-VCSLGQITGALYEVGGQYR 1090


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: 1212
Number of extensions: 66
Number of successful extensions: 7
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: 1093
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1052
Effective search space:   549144
Effective search space used:   549144
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: 55 (25.8 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