Alignments for a candidate for ilvA in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Thioalkalivibrio denitrificans ALJD

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_077278673.1 B1C78_RS08215 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_002000365.1:WP_077278673.1
          Length = 504

 Score =  551 bits (1419), Expect = e-161
 Identities = 283/500 (56%), Positives = 365/500 (73%), Gaps = 4/500 (0%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           YL  +L A VY+ A+ TPL  M  LS RL+N +L+KRED QPV SFKLRGAY  +  LTE
Sbjct: 5   YLEKILTARVYDVARETPLDPMPTLSRRLENTVLLKREDLQPVFSFKLRGAYNRIFHLTE 64

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
           E+KA GVI ASAGNHAQGVA S+  LG++A+IVMP  T  IKVDAVR  GG+ +LHG ++
Sbjct: 65  EEKARGVIAASAGNHAQGVALSARALGIRAVIVMPQTTPGIKVDAVRSLGGKAVLHGDSY 124

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLAA 194
           DEA A A  L ++ G+T++ PFD P VIAGQGT+A+ELL+Q    +D VFV VGGGGL A
Sbjct: 125 DEACAHAEALMEKHGYTFIHPFDDPYVIAGQGTVAMELLRQHPDPIDAVFVCVGGGGLLA 184

Query: 195 GVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRL 254
           G+A  IK L P I+VI VE +D+  +  AL     + L +VG+FA+G AV++ G ET+RL
Sbjct: 185 GMAAYIKSLRPDIRVIGVEPDDAPSMAEALRRKRRIVLDQVGIFADGAAVRQAGVETYRL 244

Query: 255 CQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHIL 314
            ++Y+D++I V +D ICAA+KD+F+D R +AEP+GALALAG+KKY+      G+ LA +L
Sbjct: 245 ARKYVDEMILVSADEICAAIKDVFDDTRVMAEPAGALALAGLKKYVETRGATGKTLAAVL 304

Query: 315 SGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADA 374
           SGAN+NF  LRYV+ER ELGE+REALLA TIPE  GSF  FC+ +G R +TEFNYR+AD+
Sbjct: 305 SGANINFDRLRYVAERAELGERREALLAATIPERPGSFRAFCRAIGKRGITEFNYRYADS 364

Query: 375 KNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQER 434
            +A +FVG++LS G EER  IL  L   GY++VDL+D+E+AK H+R+MVGG       ER
Sbjct: 365 SDAHVFVGIKLSGGEEERAAILDSLRGQGYALVDLTDNEVAKAHLRHMVGGHGGDVRDER 424

Query: 435 LYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL--GDHEPDFETRL 492
           ++ FEFPE PGALLRFL  +G  WNISLFHYR+HG  YGRVLA  ++  GD +  F+  L
Sbjct: 425 VFRFEFPERPGALLRFLTRMGQDWNISLFHYRNHGAAYGRVLAGIQVPAGDRK-RFQRFL 483

Query: 493 NELGYDCHDETNNPAFRFFL 512
           +ELGY   +ET NP +R FL
Sbjct: 484 DELGYPYWEETENPVYRMFL 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: 744
Number of extensions: 33
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 WP_077278673.1 B1C78_RS08215 (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.27188.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-250  817.8   0.0   1.7e-250  817.7   0.0    1.0  1  lcl|NCBI__GCF_002000365.1:WP_077278673.1  B1C78_RS08215 threonine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002000365.1:WP_077278673.1  B1C78_RS08215 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  817.7   0.0  1.7e-250  1.7e-250       2     499 .]       5     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 817.7 bits;  conditional E-value: 1.7e-250
                                 TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 
                                               yl++il+arvy++a etpl+++ +ls+rl+n+vllkredlqpvfsfklrGayn++ +l++e+ka+Gvia
  lcl|NCBI__GCF_002000365.1:WP_077278673.1   5 YLEKILTARVYDVARETPLDPMPTLSRRLENTVLLKREDLQPVFSFKLRGAYNRIFHLTEEEKARGVIA 73 
                                               89******************************************************************* PP

                                 TIGR01124  71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltf 139
                                               asaGnhaqGvalsa+ lG++avivmp+ttp ikvdav++ Gg+ vlhG++ydea a+a +l +++g tf
  lcl|NCBI__GCF_002000365.1:WP_077278673.1  74 ASAGNHAQGVALSARALGIRAVIVMPQTTPGIKVDAVRSLGGKAVLHGDSYDEACAHAEALMEKHGYTF 142
                                               ********************************************************************* PP

                                 TIGR01124 140 iapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalk 208
                                               i+pfddp viaGqGtva+ellrq+ +++davfv vGGGGl+aG+aa++k l+p+i+vigve++d+ +++
  lcl|NCBI__GCF_002000365.1:WP_077278673.1 143 IHPFDDPYVIAGQGTVAMELLRQHPDPIDAVFVCVGGGGLLAGMAAYIKSLRPDIRVIGVEPDDAPSMA 211
                                               ********************************************************************* PP

                                 TIGR01124 209 qaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277
                                               +al   +r+ ldqvG+fadG av++ G et+rl+++y+d+++lv +de+caaikdvf+dtr ++epaGa
  lcl|NCBI__GCF_002000365.1:WP_077278673.1 212 EALRRKRRIVLDQVGIFADGAAVRQAGVETYRLARKYVDEMILVSADEICAAIKDVFDDTRVMAEPAGA 280
                                               ********************************************************************* PP

                                 TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevl 346
                                               lalaGlkkyv+++g+++ktl+a+lsGan+nfdrlryv+eraelGe+realla tipe++Gs++ f++ +
  lcl|NCBI__GCF_002000365.1:WP_077278673.1 281 LALAGLKKYVETRGATGKTLAAVLSGANINFDRLRYVAERAELGERREALLAATIPERPGSFRAFCRAI 349
                                               ********************************************************************* PP

                                 TIGR01124 347 GeraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGraa 414
                                               G+r itefnyr+ad+++ah+fvG++l+   eer+ +l +l+ +gy+ vdltd+e+ak h+r++vGG   
  lcl|NCBI__GCF_002000365.1:WP_077278673.1 350 GKRGITEFNYRYADSSDAHVFVGIKLSGGeEERAAILDSLRGQGYALVDLTDNEVAKAHLRHMVGGHGG 418
                                               **************************97648999*********************************** PP

                                 TIGR01124 415 kvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelg 483
                                               +v++er+++fefperpGall+fl+ + ++wnislfhyrnhGa+yGrvl+g++vp  + ++f+ fl+elg
  lcl|NCBI__GCF_002000365.1:WP_077278673.1 419 DVRDERVFRFEFPERPGALLRFLTRMGQDWNISLFHYRNHGAAYGRVLAGIQVPAGDRKRFQRFLDELG 487
                                               ********************************************************************* PP

                                 TIGR01124 484 yryedetenpayrlfl 499
                                               y y++etenp+yr+fl
  lcl|NCBI__GCF_002000365.1:WP_077278673.1 488 YPYWEETENPVYRMFL 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: 11.80
//
[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