Alignments for a candidate for ilvA in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Pseudomonas fluorescens FW300-N2E2

Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate Pf6N2E2_802 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= SwissProt::Q9WYJ1
         (401 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802
          Length = 335

 Score =  231 bits (589), Expect = 2e-65
 Identities = 126/306 (41%), Positives = 189/306 (61%), Gaps = 4/306 (1%)

Query: 20  RTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIAHLSEEERKRGVVAASAGNH 79
           RT L  +  LSE  G  I LK E+LQ T SFKIRGAYNK+  L+ E+R RGV+ ASAGNH
Sbjct: 29  RTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVQLTPEQRARGVITASAGNH 88

Query: 80  AQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILEGNIFDEAYEAALRIQEKTG 139
           AQGVALAA+  GI A+IVMP   P  K+   RN GA+ IL G  F  A   AL + E++G
Sbjct: 89  AQGVALAARELGISASIVMPVTTPQLKVLGVRNRGAEAILHGESFPFALAHALELAEQSG 148

Query: 140 AVFVHPFNDPHVIAGQGTIGLEIMEDLP-DVEVVVVPVGGGGLISGVSVAIKSMNPEVKV 198
             FV PF+DP VIAGQGT+ +EI+   P  ++ + VPVGGGGLI+G++  +K + PEV++
Sbjct: 149 WEFVSPFDDPDVIAGQGTVAMEILRQHPGQLDAIFVPVGGGGLIAGIAAYVKYLRPEVRI 208

Query: 199 IGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLTFELVKKYVDEMVAVNEEE 258
           IGV++++   + A+L  G    +    T ADG+AV + G    ++ +  VDE++ V+ ++
Sbjct: 209 IGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVDEVMTVSNDQ 268

Query: 259 IADAILFLLEQAKVVAEGAGAVGVAAVLNKL---DVKGKKVAIVISGGNIDVNMIDRIIN 315
           +  AI  + +  + + E +GA+ VA +   +     +G+ +  + SG NI+ + +  +  
Sbjct: 269 LCAAIKDIYDDTRSITEPSGALAVAGIKQYVAGTGARGQTLVAIDSGANINFDSLRHVAE 328

Query: 316 KGLVKS 321
           +  V +
Sbjct: 329 RAAVSA 334


Lambda     K      H
   0.317    0.136    0.367 

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: 272
Number of extensions: 12
Number of successful extensions: 2
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: 401
Length of database: 335
Length adjustment: 30
Effective length of query: 371
Effective length of database: 305
Effective search space:   113155
Effective search space used:   113155
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate Pf6N2E2_802 (Threonine dehydratase biosynthetic (EC 4.3.1.19))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (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/TIGR01124.hmm
# target sequence database:        /tmp/gapView.28768.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01124  [M=499]
Accession:   TIGR01124
Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   9.7e-153  495.2   1.2   1.2e-152  495.0   1.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802  Threonine dehydratase biosynthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802  Threonine dehydratase biosynthetic (EC 4.3.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.0   1.2  1.2e-152  1.2e-152       2     320 ..      14     332 ..      13     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 495.0 bits;  conditional E-value: 1.2e-152
                                     TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkak 66 
                                                   y+++il a vye av tpl+ a  lse l+nr+llkredlqp fsfk+rGaynk+ ql++eq+a+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802  14 YVKKILAAPVYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVQLTPEQRAR 78 
                                                   899************************************************************** PP

                                     TIGR01124  67 GviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalel 131
                                                   Gvi+asaGnhaqGval+a++lG++a ivmp ttp++kv  v+++G+e +lhGe++  a a+alel
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802  79 GVITASAGNHAQGVALAARELGISASIVMPVTTPQLKVLGVRNRGAEAILHGESFPFALAHALEL 143
                                                   ***************************************************************** PP

                                     TIGR01124 132 aqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikv 196
                                                   a++ g  f++pfddp+viaGqGtva+e+lrq+  +lda+fvpvGGGGliaG+aa+vk l+pe+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 144 AEQSGWEFVSPFDDPDVIAGQGTVAMEILRQHPGQLDAIFVPVGGGGLIAGIAAYVKYLRPEVRI 208
                                                   ***************************************************************** PP

                                     TIGR01124 197 igveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaai 261
                                                   igve++ sa+l++al+aGerv+l +vG fadGvav ++G++ +++c+  +d++++v  d++caai
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 209 IGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVDEVMTVSNDQLCAAI 273
                                                   ***************************************************************** PP

                                     TIGR01124 262 kdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvserael 320
                                                   kd+++dtr+++ep+Gala+aG+k+yva  g++++tlvai sGan+nfd+lr+v+era +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 274 KDIYDDTRSITEPSGALAVAGIKQYVAGTGARGQTLVAIDSGANINFDSLRHVAERAAV 332
                                                   ********************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (335 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: 00:00:00.02
# Mc/sec: 6.87
//
[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:

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