Alignments for a candidate for ilvA in Thiomicrospira microaerophila ASL8-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Thiomicrospira microaerophila ASL8-2

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_044407822.1 NA59_RS03100 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000934765.1:WP_044407822.1
          Length = 507

 Score =  518 bits (1335), Expect = e-151
 Identities = 266/500 (53%), Positives = 359/500 (71%), Gaps = 3/500 (0%)

Query: 17  LRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEE 76
           L+ VL  PVY+ A+ TP +    LS+R+ N + +KRED QPV SFKLRGAYA M  LTE+
Sbjct: 6   LKKVLTVPVYDVAEETPFELAPLLSARMQNKVWLKREDLQPVFSFKLRGAYAKMVTLTED 65

Query: 77  QKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFD 136
           QK  GVI ASAGNHAQGVA +++++G+KA IVMP  T  IKV+AVR  GGEV+LHG  FD
Sbjct: 66  QKKAGVIAASAGNHAQGVALAASKMGIKATIVMPKTTPPIKVNAVRRLGGEVVLHGDAFD 125

Query: 137 EAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLAAG 195
           EA   A +L ++  +T++ P+D   VIAGQGT+ALE+L+Q    LD VFV VGGGGL AG
Sbjct: 126 EASIHAQQLMRENKYTFIHPYDDDDVIAGQGTIALEILRQHPKPLDIVFVCVGGGGLIAG 185

Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255
           ++ ++KQ+ P+ ++I VE E++ACL  AL AG  + L +VGLFA+G AV ++G+  F++ 
Sbjct: 186 ISAVMKQVWPKTRIIGVEPEEAACLTEALKAGERIKLKQVGLFADGAAVAQVGEIPFQIA 245

Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILS 315
           Q  +D++ITV +D ICAA+KD+FED RA+AEP+GALA+AG+KK++A   + G  +A I+S
Sbjct: 246 QTCVDEMITVTNDEICAAIKDVFEDTRAIAEPAGALAVAGLKKFVAERGVSGLEMAAIVS 305

Query: 316 GANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLG-GRSVTEFNYRFADA 374
           GAN+NF  L +++ER E+GE+REA+ AV I E  GSF +FC+ LG  R++TEFNYR+ADA
Sbjct: 306 GANMNFDRLHHIAERTEIGEKREAIFAVKIKEHPGSFKQFCEDLGASRAITEFNYRYADA 365

Query: 375 KNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQER 434
            NA +FVGV+   G  E+  +L  L + GY V D+SD+EMAKLH+R+MVGGR      E+
Sbjct: 366 HNAIVFVGVKTEGGRPEQIRLLDDLREKGYQVEDMSDNEMAKLHLRHMVGGRAEDIQDEK 425

Query: 435 LYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFETRLN 493
           +Y FEFPE PGALL FL+ +   WNISLFHYR+H   YGRVL   ++  +   DFE  L+
Sbjct: 426 VYRFEFPERPGALLNFLSRMSEEWNISLFHYRNHSDAYGRVLVGVQVPANQVADFEAYLD 485

Query: 494 ELGYDCHDETNNPAFRFFLA 513
            L Y    E +NPA+  FL+
Sbjct: 486 CLKYPYVSEQDNPAYHLFLS 505


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: 672
Number of extensions: 33
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: 507
Length adjustment: 35
Effective length of query: 479
Effective length of database: 472
Effective search space:   226088
Effective search space used:   226088
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 WP_044407822.1 NA59_RS03100 (threonine ammonia-lyase, biosynthetic)
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.26047.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-236  770.9   0.5   2.9e-236  770.7   0.5    1.0  1  lcl|NCBI__GCF_000934765.1:WP_044407822.1  NA59_RS03100 threonine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000934765.1:WP_044407822.1  NA59_RS03100 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  770.7   0.5  2.9e-236  2.9e-236       2     499 .]       5     504 ..       4     504 .. 0.99

  Alignments for each domain:
  == domain 1  score: 770.7 bits;  conditional E-value: 2.9e-236
                                 TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 
                                               +l+++l+  vy++a etp+e a  ls+r++n+v+lkredlqpvfsfklrGay+km  l+++qk +Gvia
  lcl|NCBI__GCF_000934765.1:WP_044407822.1   5 ILKKVLTVPVYDVAEETPFELAPLLSARMQNKVWLKREDLQPVFSFKLRGAYAKMVTLTEDQKKAGVIA 73 
                                               6899***************************************************************** PP

                                 TIGR01124  71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltf 139
                                               asaGnhaqGval+a+k+G+ka+ivmp+ttp ikv+av+  GgevvlhG+++dea  +a++l +e+  tf
  lcl|NCBI__GCF_000934765.1:WP_044407822.1  74 ASAGNHAQGVALAASKMGIKATIVMPKTTPPIKVNAVRRLGGEVVLHGDAFDEASIHAQQLMRENKYTF 142
                                               ********************************************************************* PP

                                 TIGR01124 140 iapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalk 208
                                               i+p+dd++viaGqGt+ale+lrq+ ++ld vfv vGGGGliaG++a++kq+ p+ ++igve+e++a+l+
  lcl|NCBI__GCF_000934765.1:WP_044407822.1 143 IHPYDDDDVIAGQGTIALEILRQHPKPLDIVFVCVGGGGLIAGISAVMKQVWPKTRIIGVEPEEAACLT 211
                                               ********************************************************************* PP

                                 TIGR01124 209 qaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277
                                               +al+aGer+kl+qvGlfadG av +vG+  f++++  +d++++v  de+caaikdvfedtra++epaGa
  lcl|NCBI__GCF_000934765.1:WP_044407822.1 212 EALKAGERIKLKQVGLFADGAAVAQVGEIPFQIAQTCVDEMITVTNDEICAAIKDVFEDTRAIAEPAGA 280
                                               ********************************************************************* PP

                                 TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevl 346
                                               la+aGlkk+va++g+++ +++ai+sGan+nfdrl +++er+e+Ge+rea++av i e++Gs+++f+e l
  lcl|NCBI__GCF_000934765.1:WP_044407822.1 281 LAVAGLKKFVAERGVSGLEMAAIVSGANMNFDRLHHIAERTEIGEKREAIFAVKIKEHPGSFKQFCEDL 349
                                               *******************************************************************99 PP

                                 TIGR01124 347 G.eraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGra 413
                                               G +raitefnyr+ad+++a +fvGv+++    e+ +ll +l+e+gy+v+d++d+e+aklh+r++vGGra
  lcl|NCBI__GCF_000934765.1:WP_044407822.1 350 GaSRAITEFNYRYADAHNAIVFVGVKTEGGrPEQIRLLDDLREKGYQVEDMSDNEMAKLHLRHMVGGRA 418
                                               9569**********************9976479999********************************* PP

                                 TIGR01124 414 akvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflael 482
                                               +++++e++y+fefperpGall+fl+ + +ewnislfhyrnh  +yGrvlvg++vp ++ ++fe  l+ l
  lcl|NCBI__GCF_000934765.1:WP_044407822.1 419 EDIQDEKVYRFEFPERPGALLNFLSRMSEEWNISLFHYRNHSDAYGRVLVGVQVPANQVADFEAYLDCL 487
                                               ********************************************************************* PP

                                 TIGR01124 483 gyryedetenpayrlfl 499
                                                y y+ e +npay+lfl
  lcl|NCBI__GCF_000934765.1:WP_044407822.1 488 KYPYVSEQDNPAYHLFL 504
                                               ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (507 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: 11.90
//
[ok]

This GapMind analysis is from Apr 10 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