GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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