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.18981.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  lcl|FitnessBrowser__Koxy:BWI76_RS21475  BWI76_RS21475 bifunctional chori


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS21475  BWI76_RS21475 bifunctional chorismate mutase/prephenate dehydrogenase
   #    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 lkdlrdeidevdkellqllakrlelvaqvGkvkhraGlPiyaPereaamlakrreeaeklGiapdliedvlrr 73
                                            l++lrd+idevdk+ll+llakrlelvaqvG+vk+++GlPiy+Pere amla+rreea +lG++pdliedvlrr
  lcl|FitnessBrowser__Koxy:BWI76_RS21475  5 LTALRDQIDEVDKALLELLAKRLELVAQVGEVKSHYGLPIYVPERESAMLASRREEAAALGVPPDLIEDVLRR 77
                                            789********************************************************************** PP

                               TIGR01799 74 lmresyanen 83
                                            +mresy++en
  lcl|FitnessBrowser__Koxy:BWI76_RS21475 78 VMRESYSSEN 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: 12.60
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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