GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Caulobacter crescentus NA1000

Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate CCNA_03750 CCNA_03750 threonine dehydratase

Query= reanno::Caulo:CCNA_03750
         (400 letters)



>FitnessBrowser__Caulo:CCNA_03750
          Length = 400

 Score =  784 bits (2025), Expect = 0.0
 Identities = 400/400 (100%), Positives = 400/400 (100%)

Query: 1   MTLDLAAIQAAAGRLQGQIERTPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKL 60
           MTLDLAAIQAAAGRLQGQIERTPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKL
Sbjct: 1   MTLDLAAIQAAAGRLQGQIERTPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKL 60

Query: 61  MLLSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIVMPKTTPFVKVQHTRDFGATVVI 120
           MLLSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIVMPKTTPFVKVQHTRDFGATVVI
Sbjct: 61  MLLSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIVMPKTTPFVKVQHTRDFGATVVI 120

Query: 121 EGETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPVPIGGG 180
           EGETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPVPIGGG
Sbjct: 121 EGETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPVPIGGG 180

Query: 181 GLISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRGVAAHCGGQTIAEGVAVKQVGELTY 240
           GLISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRGVAAHCGGQTIAEGVAVKQVGELTY
Sbjct: 181 GLISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRGVAAHCGGQTIAEGVAVKQVGELTY 240

Query: 241 GVVRPLLDDVLLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLIL 300
           GVVRPLLDDVLLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLIL
Sbjct: 241 GVVRPLLDDVLLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLIL 300

Query: 301 CGGNIDTRLLASVLTRELVRAQRLASLRIIGDDRPGLLSTVASVIGAMGANIIEVNHNRL 360
           CGGNIDTRLLASVLTRELVRAQRLASLRIIGDDRPGLLSTVASVIGAMGANIIEVNHNRL
Sbjct: 301 CGGNIDTRLLASVLTRELVRAQRLASLRIIGDDRPGLLSTVASVIGAMGANIIEVNHNRL 360

Query: 361 ALDVPAKGAEFDITIETRDAQHTQEVMEALRESGYPPRVV 400
           ALDVPAKGAEFDITIETRDAQHTQEVMEALRESGYPPRVV
Sbjct: 361 ALDVPAKGAEFDITIETRDAQHTQEVMEALRESGYPPRVV 400


Lambda     K      H
   0.319    0.136    0.390 

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: 620
Number of extensions: 16
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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: 50 (23.9 bits)

Align candidate CCNA_03750 CCNA_03750 (threonine dehydratase)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (EC 4.3.1.19))

# 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/TIGR01127.hmm
# target sequence database:        /tmp/gapView.17542.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-129  417.4   0.0   3.2e-129  417.2   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03750  CCNA_03750 threonine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03750  CCNA_03750 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.2   0.0  3.2e-129  3.2e-129       1     377 [.      22     396 ..      22     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 417.2 bits;  conditional E-value: 3.2e-129
                             TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgik 73 
                                           tp  +s+tls+itgaev++k enlq t ++k rGalnk+  lse ek+rGv+aasaGnhaqG a+   + g++
  lcl|FitnessBrowser__Caulo:CCNA_03750  22 TPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKLMLLSETEKQRGVIAASAGNHAQGLAYHGARLGVP 94 
                                           8999********************************************************************* PP

                             TIGR01127  74 akivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledl 146
                                            +ivmP+ +p  kv+ t+ +Ga v+++G+++D+a ++a++l +e+g++fvh+fdD  ++aGqGt++le+led 
  lcl|FitnessBrowser__Caulo:CCNA_03750  95 VTIVMPKTTPFVKVQHTRDFGATVVIEGETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDA 167
                                           ************************************************************************* PP

                             TIGR01127 147 pdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdl 219
                                           pd++++ vP+GGGGLisGva+a+k l+p++++iG e    ps+++ ++   + a+   +tia+G+avk++g+l
  lcl|FitnessBrowser__Caulo:CCNA_03750 168 PDLEILPVPIGGGGLISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRG--VAAHCGGQTIAEGVAVKQVGEL 238
                                           ***********************************98888888887654..6788899*************** PP

                             TIGR01127 220 tfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkkvavvvsGGnidlnlle 292
                                           t+ +v+ l D+v+  +e  + +a+ l  + +k++aegaGa+++aa+l+      gkk +++++GGnid++ll 
  lcl|FitnessBrowser__Caulo:CCNA_03750 239 TYGVVRPLLDDVLLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLILCGGNIDTRLLA 311
                                           ************************************************9888********************* PP

                             TIGR01127 293 kiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehle 365
                                            +++++Lv+  r++ ++ +  D+PG L +++ vi   +ani++++h+rl+ +++   a+  +++e+++ +h +
  lcl|FitnessBrowser__Caulo:CCNA_03750 312 SVLTRELVRAQRLASLRIIGDDRPGLLSTVASVIGAMGANIIEVNHNRLALDVPAKGAEFDITIETRDAQHTQ 384
                                           ************************************************************************* PP

                             TIGR01127 366 ellktlrdkgye 377
                                           e+++ lr+ gy 
  lcl|FitnessBrowser__Caulo:CCNA_03750 385 EVMEALRESGYP 396
                                           **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (400 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: 00:00:00.01
# Mc/sec: 7.84
//
[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