Alignments for a candidate for mmsA in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Geotalea uraniireducens Rf4

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011938764.1 GURA_RS09480 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q97YT9
         (492 letters)



>NCBI__GCF_000016745.1:WP_011938764.1
          Length = 1002

 Score =  217 bits (552), Expect = 2e-60
 Identities = 151/494 (30%), Positives = 238/494 (48%), Gaps = 19/494 (3%)

Query: 5   LGEVKKDYGKL-KLYINGEFIDSKTDTIGKAYNPA-KDEIIAEVPFSAKDEVEEAIQSAQ 62
           + EV++  GK   L+ING   D +T  +  + NPA   E+I  +  +   EVEEAI +A 
Sbjct: 498 IAEVRRQLGKTCPLHINGR--DVQTSDLLPSINPAGPSEVIGLICQAGATEVEEAIAAAG 555

Query: 63  EAFEKWREVPITTRIQYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEA 122
            AF  WR+    +R  YL      +      ++   V   GK   +A  D+   I+ +E 
Sbjct: 556 AAFPAWRDTAPGSRAGYLIKAAQAVRRRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEY 615

Query: 123 AISAAYTLYKGEHLDQVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTV 182
                  L + + +     E +     E  GV  +I P+NFP  +    +  A+V GN V
Sbjct: 616 YAREMIRLGEPQRVGHAPGETNHYFY-EAKGVAAVIAPWNFPLAISMGMVSAALVTGNCV 674

Query: 183 VVKPSEITPVPMDFIIRIFDEIKLPRGVVNVVHGAKDVVDEFLTNKL-VQGVTFVGSTRV 241
           V KPS +T V    ++ IF E  LP GV N + G   V+ +FL +   +  + F GS  V
Sbjct: 675 VYKPSGLTSVIGRHLVEIFSEAGLPAGVFNYIPGRSSVMGDFLVDHPHISLIAFTGSREV 734

Query: 242 GKYIYENAGK------NGKKAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLA 295
           G  I E A K        KK + + G KN +++  DADL++A+P ++ + F   GQ+C A
Sbjct: 735 GLRIIERAAKVHPGQAKVKKIVCEMGGKNGIIIDDDADLDEAVPHVLFSAFAFQGQKCSA 794

Query: 296 AANLVAVGNIYDEVKRKFIEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEG 355
            +  + +  +YD+   + +  ++   +G   + +  MG V    A KRI+ YIE G +EG
Sbjct: 795 CSRAIVLDGVYDKFVERLLSMARATSVGPAENPAFYMGAVADDKAMKRILEYIEIGGKEG 854

Query: 356 AKLLLDGRDVKVPEYPNGYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINII 415
             L       + P    GYF+  T+   + PE  IA+EEIFGPV +++  K+ ++A+   
Sbjct: 855 VIL------YRSPVPSEGYFVPMTIIGGIRPEHRIAREEIFGPVLAVMRAKDFEQAVEWA 908

Query: 416 NRSNYGNASSIFTTSGYYARKFRREVNTGNIGINIG-VAAPMAFFPFGGRKESFFGILHG 474
           N ++Y     +F+ S  +    RRE   GN+  N     A +   PFGG + S  G   G
Sbjct: 909 NSTSYALTGGVFSRSPEHLALARREFRVGNLYFNRNCTGALVERQPFGGSRMSGVGAKAG 968

Query: 475 QIDSVDFFTDKKVV 488
             D +  F + +VV
Sbjct: 969 GPDYLLHFMEPRVV 982


Lambda     K      H
   0.319    0.139    0.398 

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: 1032
Number of extensions: 59
Number of successful extensions: 4
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: 492
Length of database: 1002
Length adjustment: 39
Effective length of query: 453
Effective length of database: 963
Effective search space:   436239
Effective search space used:   436239
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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:

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