Alignments for a candidate for ilvA in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Pseudomonas fluorescens FW300-N1B4

Align L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 (characterized)
to candidate Pf1N1B4_2280 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= SwissProt::P04968
         (514 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280
          Length = 504

 Score =  529 bits (1362), Expect = e-154
 Identities = 263/500 (52%), Positives = 359/500 (71%), Gaps = 2/500 (0%)

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

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

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLA 193
           F EA A +++L  ++G+ ++ P+D P  IAGQGT+A+E+L+Q    LD +FVPVGGGGL 
Sbjct: 124 FPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLI 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 AGIAAYVKYLRPDIKIIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHTFD 243

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313
           +C++Y+D++ITV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+    + G     I
Sbjct: 244 ICKDYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVEQRGVTGHTFVAI 303

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

Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQE 433
              A IFVGV+     + R  +L  L++ G+ V+DL+D+E+AKLH+R+MVGGR  H + E
Sbjct: 364 GSEAHIFVGVQTHPENDPRSALLASLSEQGFPVLDLTDNELAKLHIRHMVGGRAVHVVDE 423

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

Query: 493 NELGYDCHDETNNPAFRFFL 512
            E+GY   DE++NPA++ FL
Sbjct: 484 EEIGYPYWDESDNPAYQLFL 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: 38
Number of successful extensions: 5
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 Pf1N1B4_2280 (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.2880.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.3e-248  811.5   0.0   1.5e-248  811.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280  Threonine dehydratase biosynthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280  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 !  811.3   0.0  1.5e-248  1.5e-248       1     499 []       4     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 811.3 bits;  conditional E-value: 1.5e-248
                                      TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqk 64 
                                                    +y+++il++rvy++avetpl++a++lserl+n ++lkredlqpvfsfk+rGaynk++qls+e++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280   4 QYVKKILTSRVYDVAVETPLQTARQLSERLGNDIWLKREDLQPVFSFKIRGAYNKLTQLSDEER 67 
                                                    699************************************************************* PP

                                      TIGR01124  65 akGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakaka 128
                                                    a+Gv++asaGnhaqG+al+ak lGvka+ivmp+ttpeikv+ v+++Gg+vvlhG+++ ea a++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280  68 ARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHGDSFPEALAYS 131
                                                    **************************************************************** PP

                                      TIGR01124 129 lelaqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllp 192
                                                    l+l +ekg  +i+p+ddp  iaGqGtva+e+lrq+   lda+fvpvGGGGliaG+aa+vk l+p
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280 132 LKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLIAGIAAYVKYLRP 195
                                                    **************************************************************** PP

                                      TIGR01124 193 eikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtde 256
                                                    +ik+igve++ds++l++a++aGerv l +vGlfadGvav ++G++tf++ck+y+d++++v tde
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280 196 DIKIIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHTFDICKDYVDEVITVSTDE 259
                                                    **************************************************************** PP

                                      TIGR01124 257 vcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvserael 320
                                                    +caaikd+++dtr+++epaGal++aG+kkyv+++g++++t+vai sGan+nfdrlr+v+erael
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280 260 ICAAIKDIYDDTRSITEPAGALGVAGIKKYVEQRGVTGHTFVAIDSGANVNFDRLRHVAERAEL 323
                                                    **************************************************************** PP

                                      TIGR01124 321 GeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeeee.rkella 383
                                                    Ge rea++avtipe++Gs++ f+e +G+r+itefnyr+   ++ahifvGvq++ e++ r+ lla
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280 324 GEGREAIIAVTIPEKPGSFKAFCEAIGKRQITEFNYRYNTGSEAHIFVGVQTHPENDpRSALLA 387
                                                    ****************************************************988553899*** PP

                                      TIGR01124 384 rleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnis 447
                                                    +l+e+g+ v+dltd+elaklh+r++vGGra +v +e +++fefperpGal +fl++l ++wnis
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280 388 SLSEQGFPVLDLTDNELAKLHIRHMVGGRAVHVVDEVVLRFEFPERPGALFNFLNKLGGRWNIS 451
                                                    **************************************************************** PP

                                      TIGR01124 448 lfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                                    +fhyrnhGa+ Grv++gl+vp++e +    +l+e+gy y+de++npay+lfl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280 452 MFHYRNHGAADGRVVAGLQVPHDERHLVPAALEEIGYPYWDESDNPAYQLFL 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: 10.81
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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