Alignments for a candidate for cmutase in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Klebsiella michiganensis M5al

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate BWI76_RS21475 BWI76_RS21475 bifunctional chorismate mutase/prephenate dehydrogenase

Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER
         (373 letters)



>FitnessBrowser__Koxy:BWI76_RS21475
          Length = 373

 Score =  670 bits (1729), Expect = 0.0
 Identities = 340/373 (91%), Positives = 353/373 (94%)

Query: 1   MVAELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAE 60
           MVAELTALRDQIDEVDKALL LLAKRLELVA+VGEVKS +GLPIYVPERE++MLASRR E
Sbjct: 1   MVAELTALRDQIDEVDKALLELLAKRLELVAQVGEVKSHYGLPIYVPERESAMLASRREE 60

Query: 61  AEALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTL 120
           A ALGVPPDLIEDVLRRVMRESYSSENDKGFKTL P+LRPVVIVGGGGQMGRLFEKMLTL
Sbjct: 61  AAALGVPPDLIEDVLRRVMRESYSSENDKGFKTLYPNLRPVVIVGGGGQMGRLFEKMLTL 120

Query: 121 SGYQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIGKLPPLPKDCILVDLASVKNG 180
           SGYQVRILE+ DW RA +IVADAGMVIVSVPIH+T   I +LPPLP DCILVDLASVK  
Sbjct: 121 SGYQVRILEKDDWSRADEIVADAGMVIVSVPIHITAATIAQLPPLPADCILVDLASVKAE 180

Query: 181 PLQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRI 240
           PLQAML AH GPVLGLHPMFGPDSGSLAKQVVV+CDGR+PEAYQWFLEQIQVWGARLHRI
Sbjct: 181 PLQAMLAAHKGPVLGLHPMFGPDSGSLAKQVVVYCDGRQPEAYQWFLEQIQVWGARLHRI 240

Query: 241 SAVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDP 300
           SAVEHDQNMAFIQALRHFATFAYGLHLAEENV+LEQLLALSSPIYRLELAMVGRLFAQDP
Sbjct: 241 SAVEHDQNMAFIQALRHFATFAYGLHLAEENVRLEQLLALSSPIYRLELAMVGRLFAQDP 300

Query: 301 QLYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSE 360
           QLYADIIMSSE NLALIKRYY+RFGEAI LLEQGDKQAFIDSFRKVEHWFGDYAQRFQSE
Sbjct: 301 QLYADIIMSSENNLALIKRYYQRFGEAIGLLEQGDKQAFIDSFRKVEHWFGDYAQRFQSE 360

Query: 361 SRVLLRQANDNRQ 373
           SR LLRQANDNRQ
Sbjct: 361 SRTLLRQANDNRQ 373


Lambda     K      H
   0.322    0.138    0.404 

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: 545
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: 373
Length of database: 373
Length adjustment: 30
Effective length of query: 343
Effective length of database: 343
Effective search space:   117649
Effective search space used:   117649
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS21475 BWI76_RS21475 (bifunctional chorismate mutase/prephenate dehydrogenase)
to HMM TIGR01799 (tyrA: 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/TIGR01799.hmm
# target sequence database:        /tmp/gapView.3742533.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01799  [M=83]
Accession:   TIGR01799
Description: CM_T: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    7.3e-49  150.1   0.9    1.6e-48  149.1   0.9    1.6  1  FitnessBrowser__Koxy:BWI76_RS21475  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Koxy:BWI76_RS21475  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.1   0.9   1.6e-48   1.6e-48       1      83 []       5      87 ..       5      87 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 1.6e-48
                           TIGR01799  1 lkdlrdeidevdkellqllakrlelvaqvGkvkhraGlPiyaPereaamlakrreeaeklGiapdliedvlrrlmre 77
                                        l++lrd+idevdk+ll+llakrlelvaqvG+vk+++GlPiy+Pere amla+rreea +lG++pdliedvlrr+mre
  FitnessBrowser__Koxy:BWI76_RS21475  5 LTALRDQIDEVDKALLELLAKRLELVAQVGEVKSHYGLPIYVPERESAMLASRREEAAALGVPPDLIEDVLRRVMRE 81
                                        789************************************************************************** PP

                           TIGR01799 78 syanen 83
                                        sy++en
  FitnessBrowser__Koxy:BWI76_RS21475 82 SYSSEN 87
                                        ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 nodes)
Target sequences:                          1  (373 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: 14.86
//
[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