Alignments for a candidate for ilvA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Pseudomonas putida KT2440

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PP_5149 PP_5149 threonine deaminase

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__Putida:PP_5149
          Length = 504

 Score =  530 bits (1365), Expect = e-155
 Identities = 263/500 (52%), Positives = 361/500 (72%), Gaps = 2/500 (0%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +Y++ +L + VY+ A  TPLQ   +LS RL N IL+KRED QPV SFK+RGAY  +A L+
Sbjct: 4   QYVKKILTSRVYDVAVETPLQSAGQLSKRLGNQILLKREDLQPVFSFKIRGAYNKLAQLS 63

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134
            E+ A GV+TASAGNHAQG+A ++  +G+KA IVMP  T +IKV+ VR  GG+V+LHG +
Sbjct: 64  PEELARGVVTASAGNHAQGLALAAREMGIKATIVMPKTTPEIKVEGVRSRGGKVVLHGDS 123

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLA 193
           F EA A +++L  ++GF +V P+D P  IAGQGT+A+E+L+Q    LD +FVPVGGGGL 
Sbjct: 124 FPEALAYSLKLVDEKGFVYVHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLI 183

Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253
           AG+A  +K L P+IK+I VE +DS CL+AA+ AG  V LP+VGLFA+GVAV +IG  TF 
Sbjct: 184 AGIAAYVKYLRPEIKIIGVEPDDSNCLQAAMAAGERVVLPQVGLFADGVAVAQIGQHTFD 243

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313
           +C+ ++D+++TV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+ L+ + G+ L  I
Sbjct: 244 ICRHHVDEVVTVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVELYGVSGQTLVAI 303

Query: 314 LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFAD 373
            SGANVNF  LR+V+ER ELGE+REA++AVTIPE  GSF  FC+ +G R +TEFNYR   
Sbjct: 304 DSGANVNFDRLRHVAERAELGEKREAIIAVTIPERPGSFKAFCEAIGKRQITEFNYRKHT 363

Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQE 433
           +  A IFVGV+     + R  ++Q L + G+ V DL+D+E+AKLH+R+MVGG  +    E
Sbjct: 364 SDEAHIFVGVQTHPENDPRAALVQQLTEQGFPVTDLTDNELAKLHIRHMVGGHSAGASDE 423

Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPDF-ETRL 492
            +  FEFPE PGAL  FLN LG  WNIS+FHYR+HG   GRV+A  ++ + E       L
Sbjct: 424 MVLRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPEDERHLVPAAL 483

Query: 493 NELGYDCHDETNNPAFRFFL 512
            ++GY   DET NPA++ FL
Sbjct: 484 AKIGYPYWDETENPAYKLFL 503


Lambda     K      H
   0.321    0.138    0.403 

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: 710
Number of extensions: 44
Number of successful extensions: 4
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: 514
Length of database: 504
Length adjustment: 34
Effective length of query: 480
Effective length of database: 470
Effective search space:   225600
Effective search space used:   225600
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: 52 (24.6 bits)

Align candidate PP_5149 PP_5149 (threonine deaminase)
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.12265.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.7e-247  805.8   0.0   7.6e-247  805.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5149  PP_5149 threonine deaminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5149  PP_5149 threonine deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  805.7   0.0  7.6e-247  7.6e-247       1     499 []       4     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 805.7 bits;  conditional E-value: 7.6e-247
                           TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGn 75 
                                         +y+++il++rvy++avetpl+ a +ls+rl+n++llkredlqpvfsfk+rGaynk+aqls+e+ a+Gv++asaGn
  lcl|FitnessBrowser__Putida:PP_5149   4 QYVKKILTSRVYDVAVETPLQSAGQLSKRLGNQILLKREDLQPVFSFKIRGAYNKLAQLSPEELARGVVTASAGN 78 
                                         699************************************************************************ PP

                           TIGR01124  76 haqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplvia 150
                                         haqG+al+a+++G+ka+ivmp+ttpeikv+ v+++Gg+vvlhG+++ ea a++l+l +ekg+ +++p+ddp  ia
  lcl|FitnessBrowser__Putida:PP_5149  79 HAQGLALAAREMGIKATIVMPKTTPEIKVEGVRSRGGKVVLHGDSFPEALAYSLKLVDEKGFVYVHPYDDPHTIA 153
                                         *************************************************************************** PP

                           TIGR01124 151 GqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlf 225
                                         GqGtva+e+lrq+   lda+fvpvGGGGliaG+aa+vk l+peik+igve++ds++l++a++aGerv l qvGlf
  lcl|FitnessBrowser__Putida:PP_5149 154 GQGTVAMEILRQHPGRLDAIFVPVGGGGLIAGIAAYVKYLRPEIKIIGVEPDDSNCLQAAMAAGERVVLPQVGLF 228
                                         *************************************************************************** PP

                           TIGR01124 226 adGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvai 300
                                         adGvav ++G++tf++c++++d++v+v tde+caaikd+++dtr+++epaGal++aG+kkyv+  g++++tlvai
  lcl|FitnessBrowser__Putida:PP_5149 229 ADGVAVAQIGQHTFDICRHHVDEVVTVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVELYGVSGQTLVAI 303
                                         *************************************************************************** PP

                           TIGR01124 301 lsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee 375
                                          sGan+nfdrlr+v+eraelGe+rea++avtipe++Gs++ f+e +G+r+itefnyr   +++ahifvGvq++ e
  lcl|FitnessBrowser__Putida:PP_5149 304 DSGANVNFDRLRHVAERAELGEKREAIIAVTIPERPGSFKAFCEAIGKRQITEFNYRKHTSDEAHIFVGVQTHPE 378
                                         ************************************************************************987 PP

                           TIGR01124 376 ee.rkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislf 449
                                         ++ r+ l+++l+e+g+ v dltd+elaklh+r++vGG +a +++e +++fefperpGal +fl++l ++wnis+f
  lcl|FitnessBrowser__Putida:PP_5149 379 NDpRAALVQQLTEQGFPVTDLTDNELAKLHIRHMVGGHSAGASDEMVLRFEFPERPGALFNFLNKLGGRWNISMF 453
                                         553899********************************************************************* PP

                           TIGR01124 450 hyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                         hyrnhGa+ Grv++gl+vp++e +    +la++gy y+detenpay+lfl
  lcl|FitnessBrowser__Putida:PP_5149 454 HYRNHGAADGRVVAGLQVPEDERHLVPAALAKIGYPYWDETENPAYKLFL 503
                                         *************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (504 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: 8.59
//
[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