Alignments for a candidate for ilvA in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Pseudomonas fluorescens GW456-L13

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PfGW456L13_949 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949
          Length = 504

 Score =  529 bits (1362), Expect = e-154
 Identities = 261/500 (52%), Positives = 361/500 (72%), Gaps = 2/500 (0%)

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

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

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLA 193
           F EA A +++L  ++G+ ++ P+D P  IAGQGT+A+E+L+Q    LD +FVPVGGGGL 
Sbjct: 124 FPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPQPLDAIFVPVGGGGLI 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++++D++ITV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+    + G+    I
Sbjct: 244 ICKDHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVEQRGVSGQTFVAI 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++ G+ V+DL+D+E+AKLH+R+MVGGR +H + E
Sbjct: 364 GSEAHIFVGVQTHPENDPRSALIASLSEQGFPVLDLTDNELAKLHIRHMVGGRAAHVVDE 423

Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPDF-ETRL 492
            +  FEFPE PGAL  FLN LG  WNIS+FHYR+HG   GRV+A  ++   E       L
Sbjct: 424 VILRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPHDERHLVPAAL 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: 721
Number of extensions: 37
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 PfGW456L13_949 (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.29497.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   4.3e-249  813.1   0.0   4.8e-249  812.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949  Threonine dehydratase biosynthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949  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 !  812.9   0.0  4.8e-249  4.8e-249       1     499 []       4     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 812.9 bits;  conditional E-value: 4.8e-249
                                              TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkm 56 
                                                            +y+++il++rvy++avetpl+ a++lserl+n ++lkredlqpvfsfk+rGaynk+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949   4 QYVKKILTSRVYDVAVETPLQSARQLSERLGNSIWLKREDLQPVFSFKIRGAYNKL 59 
                                                            699***************************************************** PP

                                              TIGR01124  57 aqlsaeqkakGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg 112
                                                            +qls+e++a+Gv++asaGnhaqG+al+ak lGvka+ivmp+ttpeikv+ v+++Gg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949  60 TQLSDEERARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGG 115
                                                            ******************************************************** PP

                                              TIGR01124 113 evvlhGenydeakakalelaqekgltfiapfddplviaGqGtvalellrqveedld 168
                                                            +vvlhG+++ ea a++l+l +ekg  +i+p+ddp  iaGqGtva+e+lrq+ ++ld
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 116 KVVLHGDSFPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPQPLD 171
                                                            ******************************************************** PP

                                              TIGR01124 169 avfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGl 224
                                                            a+fvpvGGGGliaG+aa+vk l+p+ik+igve++ds++l++a++aGerv l +vGl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 172 AIFVPVGGGGLIAGIAAYVKYLRPDIKIIGVEPDDSNCLQAAMAAGERVVLPTVGL 227
                                                            ******************************************************** PP

                                              TIGR01124 225 fadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalal 280
                                                            fadGvav ++G++tf++ck+++d++++v tde+caaikd+++dtr+++epaGal++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 228 FADGVAVAQIGQHTFDICKDHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGV 283
                                                            ******************************************************** PP

                                              TIGR01124 281 aGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeek 336
                                                            aG+kkyv+++g++++t+vai sGan+nfdrlr+v+eraelGe rea++avtipe++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 284 AGIKKYVEQRGVSGQTFVAIDSGANVNFDRLRHVAERAELGEGREAIIAVTIPEKP 339
                                                            ******************************************************** PP

                                              TIGR01124 337 GsllkfvevlGeraitefnyrladdekahifvGvqlaeeee.rkellarleeagyk 391
                                                            Gs++ f+e +G+r+itefnyr+   ++ahifvGvq++ e++ r+ l+a+l+e+g+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 340 GSFKAFCEAIGKRQITEFNYRYNTGSEAHIFVGVQTHPENDpRSALIASLSEQGFP 395
                                                            ************************************988553899*********** PP

                                              TIGR01124 392 vvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnis 447
                                                            v+dltd+elaklh+r++vGGraa+v +e +++fefperpGal +fl++l ++wnis
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 396 VLDLTDNELAKLHIRHMVGGRAAHVVDEVILRFEFPERPGALFNFLNKLGGRWNIS 451
                                                            ******************************************************** PP

                                              TIGR01124 448 lfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                                            +fhyrnhGa+ Grv++gl+vp++e +    +l+e+gy y+de++npay+lfl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_949 452 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.54
//
[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