Alignments for a candidate for metA in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for metA in Klebsiella variicola At-22

Align homoserine O-succinyltransferase (EC 2.3.1.46) (characterized)
to candidate WP_012969171.1 KVAR_RS24220 homoserine O-succinyltransferase

Query= BRENDA::P07623
         (309 letters)



>NCBI__GCF_000025465.1:WP_012969171.1
          Length = 309

 Score =  595 bits (1534), Expect = e-175
 Identities = 284/309 (91%), Positives = 297/309 (96%)

Query: 1   MPIRVPDELPAVNFLREENVFVMTTSRASGQEIRPLKVLILNLMPKKIETENQFLRLLSN 60
           MPIRV DELPAV+FLR ENVFVMTT+RA+ QEIRPLKVLILNLMPKKIETENQFLRLLSN
Sbjct: 1   MPIRVQDELPAVSFLRNENVFVMTTTRATTQEIRPLKVLILNLMPKKIETENQFLRLLSN 60

Query: 61  SPLQVDIQLLRIDSRESRNTPAEHLNNFYCNFEDIQDQNFDGLIVTGAPLGLVEFNDVAY 120
           SPLQVDIQLLRID+RESRNTP EHLNNFYCNF++I DQNFDGLIVTGAPLGLVEFNDVAY
Sbjct: 61  SPLQVDIQLLRIDARESRNTPTEHLNNFYCNFDEICDQNFDGLIVTGAPLGLVEFNDVAY 120

Query: 121 WPQIKQVLEWSKDHVTSTLFVCWAVQAALNILYGIPKQTRTEKLSGVYEHHILHPHALLT 180
           WPQIKQVLEW+KDHVTSTLFVCWAVQAALNILYGIPKQTR EK+SGVYEHHILHPHALLT
Sbjct: 121 WPQIKQVLEWAKDHVTSTLFVCWAVQAALNILYGIPKQTRAEKISGVYEHHILHPHALLT 180

Query: 181 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA 240
           RGFDDSFLAPHSRYADFPA LIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA
Sbjct: 181 RGFDDSFLAPHSRYADFPAGLIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA 240

Query: 241 QTLAQEFFRDVEAGLDPDVPYNYFPHNDPQNTPRASWRSHGNLLFTNWLNYYVYQITPYD 300
            TLA E+FRDVEAGL+P+VPYNYFP NDPQN PRA+WRSHGNLLF NWLNYYVYQITPYD
Sbjct: 241 NTLASEYFRDVEAGLNPEVPYNYFPQNDPQNKPRATWRSHGNLLFANWLNYYVYQITPYD 300

Query: 301 LRHMNPTLD 309
           LRHMNPTL+
Sbjct: 301 LRHMNPTLE 309


Lambda     K      H
   0.321    0.138    0.424 

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: 484
Number of extensions: 13
Number of successful extensions: 1
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: 309
Length of database: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_012969171.1 KVAR_RS24220 (homoserine O-succinyltransferase)
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01001.hmm
# target sequence database:        /tmp/gapView.15020.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01001  [M=301]
Accession:   TIGR01001
Description: metA: homoserine O-succinyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-168  543.9   0.2   6.8e-168  543.8   0.2    1.0  1  lcl|NCBI__GCF_000025465.1:WP_012969171.1  KVAR_RS24220 homoserine O-succin


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_012969171.1  KVAR_RS24220 homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.8   0.2  6.8e-168  6.8e-168       1     301 []       1     302 [.       1     302 [. 1.00

  Alignments for each domain:
  == domain 1  score: 543.8 bits;  conditional E-value: 6.8e-168
                                 TIGR01001   1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditl 69 
                                               mpirv delpav +l++en+fvmt+ ra++q+irpl+vlilnlmpkkietenq+lrllsnsplqvdi+l
  lcl|NCBI__GCF_000025465.1:WP_012969171.1   1 MPIRVQDELPAVSFLRNENVFVMTTTRATTQEIRPLKVLILNLMPKKIETENQFLRLLSNSPLQVDIQL 69 
                                               9******************************************************************** PP

                                 TIGR01001  70 lridsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtst 138
                                               lrid+r+s+ntp+ehl++fy++++e+ d++fdGlivtGap++l+ef+dvayw+++k++lew+k++vtst
  lcl|NCBI__GCF_000025465.1:WP_012969171.1  70 LRIDARESRNTPTEHLNNFYCNFDEICDQNFDGLIVTGAPLGLVEFNDVAYWPQIKQVLEWAKDHVTST 138
                                               ********************************************************************* PP

                                 TIGR01001 139 lyicwaaqaalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltd 206
                                               l++cwa+qaal++lygipk+t+ ek+sGvy+h+i+ +++ll+rgfdd+flaphsryad+++ li+++td
  lcl|NCBI__GCF_000025465.1:WP_012969171.1 139 LFVCWAVQAALNILYGIPKQTRAEKISGVYEHHILhPHALLTRGFDDSFLAPHSRYADFPAGLIRDYTD 207
                                               **********************************98999****************************** PP

                                 TIGR01001 207 leilaesdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpias 275
                                               leilae++e+++yl+askd+r++fvtGhpeyd++tl+ ey+rdv++gl++++p+ny+p++dp+++p+a+
  lcl|NCBI__GCF_000025465.1:WP_012969171.1 208 LEILAETEEGDAYLFASKDKRIAFVTGHPEYDANTLASEYFRDVEAGLNPEVPYNYFPQNDPQNKPRAT 276
                                               ********************************************************************* PP

                                 TIGR01001 276 wrshanllfanwlnyavyqktpydle 301
                                               wrsh+nllfanwlny+vyq+tpydl+
  lcl|NCBI__GCF_000025465.1:WP_012969171.1 277 WRSHGNLLFANWLNYYVYQITPYDLR 302
                                               ************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (301 nodes)
Target sequences:                          1  (309 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.93
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis