Alignments for a candidate for mcm-large in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Sulfuritalea hydrogenivorans DSM 22779

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_041096999.1 SUTH_RS03085 fused isobutyryl-CoA mutase/GTPase IcmF

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000828635.1:WP_041096999.1
          Length = 1089

 Score =  302 bits (773), Expect = 5e-86
 Identities = 204/556 (36%), Positives = 307/556 (55%), Gaps = 43/556 (7%)

Query: 38   FMTDDGFEIKRIYTPA--DLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGY 95
            + T  G  I+++  P   D GE   ++ +   PG +P+T GV+A        T R +AG 
Sbjct: 539  YETLSGTRIRKVALPRFDDEGELLKFLMRENVPGSFPYTAGVFAFKRENEDPT-RMFAGE 597

Query: 96   ATAEESNKRYKYLLSQGQTG--LSVAFDLPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDM 152
              A  +NKR+   +S+G     LS AFD  T  G D D  P   G+VG  GV+I +L D+
Sbjct: 598  GDAFRTNKRF-LKVSEGMPAKRLSTAFDSVTLYGCDPDPRPDIYGKVGNSGVSIATLDDL 656

Query: 153  RILFDGIPL--DKVSTSMTINSTAANLLAMYILVAEEQGVSQ------------------ 192
            ++L+ G  L     S SMTIN  A  +LAM++  A +Q + +                  
Sbjct: 657  KVLYSGFDLCDPATSVSMTINGPAPMILAMFLNTAIDQQIEKFREQNGRDATEEEAEKIR 716

Query: 193  ----EKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYH 247
                  +RGTVQ DILKE   + T IF  + ++++  DI  Y   N +  +  +SISGYH
Sbjct: 717  EWTLSSVRGTVQADILKEDQGQNTCIFSTEFALKMMGDIQEYFVHNQIRNFYSVSISGYH 776

Query: 248  IREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RA 306
            I EAGAN + ++AFTLA+G  YV+  + RGM +D FA  LSFFF+  N    E +   R 
Sbjct: 777  IAEAGANPISQLAFTLANGFTYVETYLARGMHIDDFAGNLSFFFS--NGMDPEYSVIGRV 834

Query: 307  ARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQS 366
            ARR+WA  MK  + A N RS  L++H QT+G +L AQ+ + N +R  +QAL A+     S
Sbjct: 835  ARRIWAVAMKNRYGA-NERSQKLKYHIQTSGRSLHAQEMDFNDIRTTLQALIAIYDNCNS 893

Query: 367  LHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALK 426
            LHTN+YDEA++ PTE+SVR A+  Q II  E GV    +P  GA+ IE LTD + E  LK
Sbjct: 894  LHTNAYDEAITTPTEESVRRAMAIQLIINREWGVAKNENPNQGAFIIEELTDLVEEAVLK 953

Query: 427  YIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDE----PIEV 482
              E I   GG++ A+E GY + +I E +  Y+ +  +G   I+GVN F+         E+
Sbjct: 954  EFEAIASRGGVLGAMETGYQRGKIQEESMHYEHKKHDGSYPIIGVNTFLNPHGSGVASEI 1013

Query: 483  EILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLAT 542
            E+ +     ++ Q+ RLK  ++ R+  + +  L +L+ A   +++N+   ++EA RH  +
Sbjct: 1014 ELARSTEGEKQSQLARLKDFQT-RNAGEAEACLARLKQAV-IDNQNVFAVMMEAVRH-CS 1070

Query: 543  LQEVTDVLREIWGEYR 558
            L ++++ L E+ G+YR
Sbjct: 1071 LGQISNALYEVGGQYR 1086


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: 1197
Number of extensions: 58
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: 1089
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1048
Effective search space:   547056
Effective search space used:   547056
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 Apr 09 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