Alignments for a candidate for ilvA in Thioalkalivibrio halophilus HL17

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Thioalkalivibrio halophilus HL17

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_077244183.1 B1A74_RS06945 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_001995255.1:WP_077244183.1
          Length = 505

 Score =  544 bits (1402), Expect = e-159
 Identities = 276/499 (55%), Positives = 360/499 (72%), Gaps = 2/499 (0%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           YL  +L + VY+ A+ TPL  M  LS+RL   I +KRED QPV SFKLRGAY  +A L+E
Sbjct: 6   YLEKILTSSVYDVARETPLDVMPTLSNRLGCDIRLKREDLQPVFSFKLRGAYNKIAQLSE 65

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
           EQ++ GVI ASAGNHAQGVA  +   G++A+IVMP  T  IKVDAVR FGGE +L G +F
Sbjct: 66  EQRSKGVIAASAGNHAQGVALGATYRGIRAVIVMPVTTPQIKVDAVRRFGGEAVLFGDSF 125

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLAA 194
           DEA A A EL  + G+T++ PFD P VIAGQGT+A+ELL+Q    LD VFV +GGGGL +
Sbjct: 126 DEAAAHARELEAEHGYTFIHPFDDPDVIAGQGTVAMELLRQHPGPLDAVFVCIGGGGLVS 185

Query: 195 GVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRL 254
           G+A  IK+L P+I+VI VE +D+  +  AL     V L +VG+FA+G AV+++G ETFRL
Sbjct: 186 GMAAYIKRLRPEIRVIGVEPDDAPSMYKALQQNRRVSLKQVGIFADGAAVRQVGKETFRL 245

Query: 255 CQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHIL 314
            +E +D+++ VD+D+ICAA+KD+F+D R VAEP+GALA+AGMK+Y     +RG  LA +L
Sbjct: 246 TRELVDEVLLVDTDSICAAIKDIFDDTRVVAEPAGALAVAGMKQYAQREGLRGAHLAAVL 305

Query: 315 SGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADA 374
           SGAN+NF  LR+V+ER E+GE REAL AVTIPE  GSF +FC+ +G R +TEFNYR+AD 
Sbjct: 306 SGANINFDRLRHVAERAEIGEHREALFAVTIPERPGSFREFCEAIGKRGITEFNYRYADD 365

Query: 375 KNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQER 434
             A +F G++L  G  ER EIL  L + GY V+D++++E+AKLH+R+MVGG       ER
Sbjct: 366 STAHVFAGIKLEGGDAERAEILANLRERGYEVLDMTENEVAKLHLRHMVGGHGGEVRNER 425

Query: 435 LYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFETRLN 493
           LY FEFPE PGALL FLN +G  WNISLFHYR+HG+ +GRVL   ++  +    F   L 
Sbjct: 426 LYRFEFPERPGALLNFLNHMGETWNISLFHYRNHGSAHGRVLVGMQIPKEDRKRFREFLE 485

Query: 494 ELGYDCHDETNNPAFRFFL 512
           E+GY  H+ET NPA+  FL
Sbjct: 486 EVGYPWHEETGNPAYSLFL 504


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: 716
Number of extensions: 36
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: 505
Length adjustment: 34
Effective length of query: 480
Effective length of database: 471
Effective search space:   226080
Effective search space used:   226080
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_077244183.1 B1A74_RS06945 (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.11644.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-251  819.4   0.0   6.1e-251  819.2   0.0    1.0  1  lcl|NCBI__GCF_001995255.1:WP_077244183.1  B1A74_RS06945 threonine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001995255.1:WP_077244183.1  B1A74_RS06945 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  819.2   0.0  6.1e-251  6.1e-251       2     499 .]       6     504 ..       5     504 .. 1.00

  Alignments for each domain:
  == domain 1  score: 819.2 bits;  conditional E-value: 6.1e-251
                                 TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 
                                               yl++il+++vy++a etpl+ + +ls+rl+  + lkredlqpvfsfklrGaynk+aqls+eq++kGvia
  lcl|NCBI__GCF_001995255.1:WP_077244183.1   6 YLEKILTSSVYDVARETPLDVMPTLSNRLGCDIRLKREDLQPVFSFKLRGAYNKIAQLSEEQRSKGVIA 74 
                                               89******************************************************************* PP

                                 TIGR01124  71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltf 139
                                               asaGnhaqGval+a+  G++avivmp ttp+ikvdav+ fGge vl G+++dea+a+a+el+ e+g tf
  lcl|NCBI__GCF_001995255.1:WP_077244183.1  75 ASAGNHAQGVALGATYRGIRAVIVMPVTTPQIKVDAVRRFGGEAVLFGDSFDEAAAHARELEAEHGYTF 143
                                               ********************************************************************* PP

                                 TIGR01124 140 iapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalk 208
                                               i+pfddp+viaGqGtva+ellrq+  +ldavfv +GGGGl++G+aa++k+l+pei+vigve++d+ +++
  lcl|NCBI__GCF_001995255.1:WP_077244183.1 144 IHPFDDPDVIAGQGTVAMELLRQHPGPLDAVFVCIGGGGLVSGMAAYIKRLRPEIRVIGVEPDDAPSMY 212
                                               ********************************************************************* PP

                                 TIGR01124 209 qaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277
                                               +al++ +rv+l+qvG+fadG av++vG+etfrl++e++d+++lvdtd +caaikd+f+dtr v+epaGa
  lcl|NCBI__GCF_001995255.1:WP_077244183.1 213 KALQQNRRVSLKQVGIFADGAAVRQVGKETFRLTRELVDEVLLVDTDSICAAIKDIFDDTRVVAEPAGA 281
                                               ********************************************************************* PP

                                 TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevl 346
                                               la+aG+k+y++++g+++ +l+a+lsGan+nfdrlr+v+erae+Ge+real+avtipe++Gs+++f+e +
  lcl|NCBI__GCF_001995255.1:WP_077244183.1 282 LAVAGMKQYAQREGLRGAHLAAVLSGANINFDRLRHVAERAEIGEHREALFAVTIPERPGSFREFCEAI 350
                                               ********************************************************************* PP

                                 TIGR01124 347 GeraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGraa 414
                                               G+r itefnyr+add++ah+f G++l+   +er+e+la+l+e+gy+v+d+t++e+aklh+r++vGG   
  lcl|NCBI__GCF_001995255.1:WP_077244183.1 351 GKRGITEFNYRYADDSTAHVFAGIKLEGGdAERAEILANLRERGYEVLDMTENEVAKLHLRHMVGGHGG 419
                                               **************************98659************************************** PP

                                 TIGR01124 415 kvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelg 483
                                               +v+nerly+fefperpGall+fl+++ ++wnislfhyrnhG+++Grvlvg+++p+e+ ++f +fl+e+g
  lcl|NCBI__GCF_001995255.1:WP_077244183.1 420 EVRNERLYRFEFPERPGALLNFLNHMGETWNISLFHYRNHGSAHGRVLVGMQIPKEDRKRFREFLEEVG 488
                                               ********************************************************************* PP

                                 TIGR01124 484 yryedetenpayrlfl 499
                                               y  ++et npay lfl
  lcl|NCBI__GCF_001995255.1:WP_077244183.1 489 YPWHEETGNPAYSLFL 504
                                               ***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (505 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: 10.80
//
[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