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

GapMind for Amino acid biosynthesis

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

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_012540845.1 KVAR_RS05755 bifunctional chorismate mutase/prephenate dehydratase

Query= CharProtDB::CH_024084
         (386 letters)



>NCBI__GCF_000025465.1:WP_012540845.1
          Length = 386

 Score =  684 bits (1765), Expect = 0.0
 Identities = 344/385 (89%), Positives = 362/385 (94%)

Query: 1   MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60
           MT ENPLLALR+KISALDEKLLALLAERR LAVEVGKAKL SHRPVRDIDRERDLLERL+
Sbjct: 1   MTEENPLLALRDKISALDEKLLALLAERRGLAVEVGKAKLASHRPVRDIDRERDLLERLM 60

Query: 61  TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSARIAFLGPKGSYSHLAA 120
           T+GK H+LDAHYITRLFQLIIEDSVLTQQ LLQQHLNKINPHSAR+AFLGPKGSYSHLAA
Sbjct: 61  TIGKRHNLDAHYITRLFQLIIEDSVLTQQTLLQQHLNKINPHSARVAFLGPKGSYSHLAA 120

Query: 121 RQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLSI 180
           RQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSG INDVYDLLQHTSLSI
Sbjct: 121 RQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGGINDVYDLLQHTSLSI 180

Query: 181 VGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAMEK 240
           VGE+T+ IDHC+LVS +TD   I TVYSHPQPFQQCS++L+RYPHWKIEYTESTSAAMEK
Sbjct: 181 VGELTIPIDHCVLVSTSTDADKIQTVYSHPQPFQQCSQYLSRYPHWKIEYTESTSAAMEK 240

Query: 241 VAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTTL 300
           VAQA SP VAALGSEAGG LY LQVLE  +ANQ QN TRF+VLARKA+NVSDQVPAKTTL
Sbjct: 241 VAQANSPAVAALGSEAGGALYSLQVLEHCQANQTQNITRFLVLARKAVNVSDQVPAKTTL 300

Query: 301 LMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQKALK 360
           LMATGQQAGALVEALLVLRNHNLIMT+LESRPIHGNPWEEMFYLDIQANL+S  M+KALK
Sbjct: 301 LMATGQQAGALVEALLVLRNHNLIMTKLESRPIHGNPWEEMFYLDIQANLDSLPMRKALK 360

Query: 361 ELGEITRSMKVLGCYPSENVVPVDP 385
           EL EITRSMKVLGCYPSENVVPVDP
Sbjct: 361 ELAEITRSMKVLGCYPSENVVPVDP 385


Lambda     K      H
   0.318    0.132    0.374 

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: 498
Number of extensions: 7
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_012540845.1 KVAR_RS05755 (bifunctional chorismate mutase/prephenate dehydratase)
to HMM TIGR01797 (chorismate mutase (EC 5.4.99.5))

# 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/TIGR01797.hmm
# target sequence database:        /tmp/gapView.2431361.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01797  [M=83]
Accession:   TIGR01797
Description: CM_P_1: chorismate mutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.7e-44  134.7   2.0    9.8e-44  133.7   1.7    1.7  2  NCBI__GCF_000025465.1:WP_012540845.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_012540845.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   1.7   9.8e-44   9.8e-44       1      83 []       7      89 ..       7      89 .. 0.99
   2 ?   -3.9   0.0      0.85      0.85      64      77 ..     121     134 ..     113     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 9.8e-44
                             TIGR01797  1 llalrekisaidkkllkllaerkelafevakskllsqkavrdierekkllqklitlgkkyqleaeyitrlfqlii 75
                                          llalr+kisa+d+kll+llaer+ la+ev+k+kl s+++vrdi+re++ll++l+t+gk+++l+a+yitrlfqlii
  NCBI__GCF_000025465.1:WP_012540845.1  7 LLALRDKISALDEKLLALLAERRGLAVEVGKAKLASHRPVRDIDRERDLLERLMTIGKRHNLDAHYITRLFQLII 81
                                          799************************************************************************ PP

                             TIGR01797 76 edsvltqq 83
                                          edsvltqq
  NCBI__GCF_000025465.1:WP_012540845.1 82 EDSVLTQQ 89
                                          *******8 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.85
                             TIGR01797  64 aeyitrlfqliied 77 
                                            +y +r f + ie 
  NCBI__GCF_000025465.1:WP_012540845.1 121 RQYAARHFEQFIES 134
                                           47999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.98
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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