Alignments for a candidate for ilvA in Caulobacter crescentus NA1000

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.3068633.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  FitnessBrowser__Caulo:CCNA_03750  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_03750  
   #    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 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgikakiv 77 
                                       tp  +s+tls+itgaev++k enlq t ++k rGalnk+  lse ek+rGv+aasaGnhaqG a+   + g++ +iv
  FitnessBrowser__Caulo:CCNA_03750  22 TPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKLMLLSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIV 98 
                                       8999************************************************************************* PP

                         TIGR01127  78 mPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledlpdvdtviv 154
                                       mP+ +p  kv+ t+ +Ga v+++G+++D+a ++a++l +e+g++fvh+fdD  ++aGqGt++le+led pd++++ v
  FitnessBrowser__Caulo:CCNA_03750  99 MPKTTPFVKVQHTRDFGATVVIEGETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPV 175
                                       ***************************************************************************** PP

                         TIGR01127 155 PvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdltfeivkelvDev 231
                                       P+GGGGLisGva+a+k l+p++++iG e    ps+++ ++   + a+   +tia+G+avk++g+lt+ +v+ l D+v
  FitnessBrowser__Caulo:CCNA_03750 176 PIGGGGLISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRG--VAAHCGGQTIAEGVAVKQVGELTYGVVRPLLDDV 250
                                       ***************************98888888887654..6788899*************************** PP

                         TIGR01127 232 vavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkkvavvvsGGnidlnllekiiekgLvksgrkvki 308
                                       +  +e  + +a+ l  + +k++aegaGa+++aa+l+      gkk +++++GGnid++ll  +++++Lv+  r++ +
  FitnessBrowser__Caulo:CCNA_03750 251 LLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLILCGGNIDTRLLASVLTRELVRAQRLASL 327
                                       ************************************9888************************************* PP

                         TIGR01127 309 etvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehleellktlrdkgye 377
                                       + +  D+PG L +++ vi   +ani++++h+rl+ +++   a+  +++e+++ +h +e+++ lr+ gy 
  FitnessBrowser__Caulo:CCNA_03750 328 RIIGDDRPGLLSTVASVIGAMGANIIEVNHNRLALDVPAKGAEFDITIETRDAQHTQEVMEALRESGYP 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 21.20
//
[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 2024 update 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 original 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