Alignments for a candidate for mcm-large in Leeuwenhoekiella blandensis MED217

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Leeuwenhoekiella blandensis MED217

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_009781429.1 MED217_RS15175 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000152985.1:WP_009781429.1
          Length = 1139

 Score =  247 bits (631), Expect = 2e-69
 Identities = 149/372 (40%), Positives = 228/372 (61%), Gaps = 12/372 (3%)

Query: 193  EKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREA 251
            +++RGTVQ DILKE  A+ T IF  + ++RL  D+  Y  EN V  +  +SISGYHI EA
Sbjct: 771  KQVRGTVQADILKEDQAQNTCIFSTEFALRLMGDVQEYFIENQVRNFYSVSISGYHIAEA 830

Query: 252  GANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRL 310
            GAN + ++AFTLA+G  YV+  + RGMD++KF P LSFFF+  N    E A   R ARR+
Sbjct: 831  GANPITQLAFTLANGFTYVEYYLSRGMDINKFGPNLSFFFS--NGIDPEYAVIGRVARRI 888

Query: 311  WAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTN 370
            W+  +K  + A NPR+ ML++H QT+G +L AQ+ + N +R  +QAL A+     SLHTN
Sbjct: 889  WSKALKHKYGA-NPRAQMLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTN 947

Query: 371  SYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEK 430
            +YDEA++ PTE+SVR A+  Q II  E G+    +P+ GA+ IE LTD + E  L   ++
Sbjct: 948  AYDEAITTPTEESVRRAMAIQLIINKELGLAKNENPIQGAFIIEELTDLVEEAVLTEFDR 1007

Query: 431  IQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPI----EVEILK 486
            I + GG++ A+E  Y + +I E +  Y+     G   I+GVN F++ +        E+++
Sbjct: 1008 ITERGGVLGAMETMYQRSKIQEESLYYETLKHNGDFPIIGVNTFLSSKGSPTVKPAEVIR 1067

Query: 487  VDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEV 546
               + ++ QI  L KL    ++ + + AL K++ AA   D N+   ++EA + + +L ++
Sbjct: 1068 ATEAEKQAQINTLTKLHKAYED-QAENALRKVQEAAINND-NIFEQLMEATK-ICSLGQI 1124

Query: 547  TDVLREIWGEYR 558
            T  L E+ G+YR
Sbjct: 1125 TAALFEVGGQYR 1136



 Score = 71.6 bits (174), Expect = 2e-16
 Identities = 53/152 (34%), Positives = 74/152 (48%), Gaps = 9/152 (5%)

Query: 68  PGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYL-LSQGQTGLSVAFDLPTQL 126
           PGE+P+T G+Y     G   T R +AG    E +N+R+ Y+ +      LS AFD  T  
Sbjct: 577 PGEFPYTAGLYPFKRTGEDPT-RMFAGEGGPERTNRRFHYVSMGLPAKRLSTAFDSVTLY 635

Query: 127 GYDSDH-PLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMTINSTAANLLAMYIL 183
           G D DH P   G++G  GV+I  L D + L+ G  L     S SMTIN  A  LL  ++ 
Sbjct: 636 GNDPDHRPDIYGKIGNAGVSICCLDDAKKLYSGFDLANPMTSVSMTINGPAPMLLGFFMN 695

Query: 184 VAEEQG----VSQEKLRGTVQNDILKEYIARG 211
            A +Q     +++  L   V+  I   Y   G
Sbjct: 696 AAVDQACEKYITENNLEDEVEQTIHSIYKENG 727


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: 1284
Number of extensions: 71
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 563
Length of database: 1139
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1098
Effective search space:   573156
Effective search space used:   573156
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 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)
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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 2024 update 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