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

GapMind for Amino acid biosynthesis

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

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_008807867.1 KVAR_RS25010 cystathionine gamma-synthase

Query= SwissProt::P00935
         (386 letters)



>NCBI__GCF_000025465.1:WP_008807867.1
          Length = 386

 Score =  728 bits (1878), Expect = 0.0
 Identities = 370/385 (96%), Positives = 374/385 (97%)

Query: 1   MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA 60
           MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA
Sbjct: 1   MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA 60

Query: 61  LAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL 120
           LAELEGGAGAVLTNTGMSAI LVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRV 
Sbjct: 61  LAELEGGAGAVLTNTGMSAILLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVQ 120

Query: 121 FVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPA 180
           FVDQ DEQALRAALAEKPKLVLVESPSNPLLRVVDIAKIC LARE GAVSVVDNTFLSPA
Sbjct: 121 FVDQNDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICGLAREAGAVSVVDNTFLSPA 180

Query: 181 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYL 240
           LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIA DP  VTELAWWANNIGVTGGAFDSYL
Sbjct: 181 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIANDPATVTELAWWANNIGVTGGAFDSYL 240

Query: 241 LLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML 300
           LLRGLRTL PRME+AQRNA AIV+YL+TQPLVKKLYHPSLPENQGHEIAARQQKGFGAML
Sbjct: 241 LLRGLRTLSPRMEVAQRNALAIVEYLKTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML 300

Query: 301 SFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL 360
           SFELDGDEQTLRRFL GLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL
Sbjct: 301 SFELDGDEQTLRRFLSGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL 360

Query: 361 RISTGIEDGEDLIADLENGFRAANK 385
           RISTGIEDGEDLIADLENGFRAAN+
Sbjct: 361 RISTGIEDGEDLIADLENGFRAANE 385


Lambda     K      H
   0.319    0.136    0.394 

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: 612
Number of extensions: 15
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: 386
Length of database: 386
Length adjustment: 30
Effective length of query: 356
Effective length of database: 356
Effective search space:   126736
Effective search space used:   126736
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: 50 (23.9 bits)

Align candidate WP_008807867.1 KVAR_RS25010 (cystathionine gamma-synthase)
to HMM TIGR02080 (metB: O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48))

# 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/TIGR02080.hmm
# target sequence database:        /tmp/gapView.20147.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02080  [M=382]
Accession:   TIGR02080
Description: O_succ_thio_ly: O-succinylhomoserine (thiol)-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-213  695.0   0.0   1.2e-213  694.8   0.0    1.0  1  lcl|NCBI__GCF_000025465.1:WP_008807867.1  KVAR_RS25010 cystathionine gamma


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_008807867.1  KVAR_RS25010 cystathionine gamma-synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.8   0.0  1.2e-213  1.2e-213       2     381 ..       3     382 ..       2     383 .. 1.00

  Alignments for each domain:
  == domain 1  score: 694.8 bits;  conditional E-value: 1.2e-213
                                 TIGR02080   2 rkkatiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadav 70 
                                               rk+atiavrsGl++d+qyg+vvpPi+ls+ty+f+gfnepra+dysr+gnPtrd++++alaele+Ga+av
  lcl|NCBI__GCF_000025465.1:WP_008807867.1   3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAV 71 
                                               89******************************************************************* PP

                                 TIGR02080  71 vtssGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpkl 139
                                               +t++Gmsai l+++++lkp+dllvaPhdcyGG+yrl+++lak+g+++vq+vdq+de+al++alaekpkl
  lcl|NCBI__GCF_000025465.1:WP_008807867.1  72 LTNTGMSAILLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVQFVDQNDEQALRAALAEKPKL 140
                                               ********************************************************************* PP

                                 TIGR02080 140 vlietPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaG 208
                                               vl+e+PsnPllrvvdiak+c la++agav+vvdntflsP+lq+PlalGadlvlhs+tkylnGhsdv+aG
  lcl|NCBI__GCF_000025465.1:WP_008807867.1 141 VLVESPSNPLLRVVDIAKICGLAREAGAVSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAG 209
                                               ********************************************************************* PP

                                 TIGR02080 209 aviakdkqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyyp 277
                                               +via+d+ +++elawwan++Gvtg+afdsylllrGlrtl+ r+++++rna +iveyl++qplvkk+y+p
  lcl|NCBI__GCF_000025465.1:WP_008807867.1 210 VVIANDPATVTELAWWANNIGVTGGAFDSYLLLRGLRTLSPRMEVAQRNALAIVEYLKTQPLVKKLYHP 278
                                               ********************************************************************* PP

                                 TIGR02080 278 glpdhagheiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGvesliahpatmthaamek 346
                                               +lp+++gheiaa+qqkGfGa+lsfel+G+e+++++fl+ l+lftlaeslGGvesli+h+atmtha+m++
  lcl|NCBI__GCF_000025465.1:WP_008807867.1 279 SLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLSGLSLFTLAESLGGVESLISHAATMTHAGMAP 347
                                               ********************************************************************* PP

                                 TIGR02080 347 eareeaGikdellrlsvGledaddliadleqalaa 381
                                               ear++aGi+++llr+s+G+ed++dliadle++++a
  lcl|NCBI__GCF_000025465.1:WP_008807867.1 348 EARAAAGISETLLRISTGIEDGEDLIADLENGFRA 382
                                               *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (386 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.94
//
[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