GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Nitratiruptor tergarcus DSM 16512

Align L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized)
to candidate WP_084275803.1 B8779_RS06910 threonine ammonia-lyase

Query= SwissProt::Q9WYJ1
         (401 letters)



>NCBI__GCF_900176045.1:WP_084275803.1
          Length = 403

 Score =  369 bits (948), Expect = e-107
 Identities = 190/397 (47%), Positives = 282/397 (71%), Gaps = 2/397 (0%)

Query: 1   MITLEDIKEAQRTLKNVVHRTALAYSSVLSEVTGGEIYLKMENLQKTGSFKIRGAYNKIA 60
           MI L+DI++A + +++V  +T  AY+ +LS+  G +I+LK ENLQ TG+FK+RGA+NKIA
Sbjct: 1   MIALQDIQQAAKRIESVASKTPYAYAPILSKKCGYKIFLKKENLQVTGAFKLRGAFNKIA 60

Query: 61  HLSEEERKRGVVAASAGNHAQGVALAAQIFGIPATIVMPRYAPLSKITKTRNLGAQVILE 120
            +S+EE+ RGVVAASAGNHAQGVA ++  F IPATIVMP   PL+K+   ++ GA VIL 
Sbjct: 61  KISQEEKNRGVVAASAGNHAQGVAFSSNYFQIPATIVMPENTPLTKVNGVKSYGASVILH 120

Query: 121 GNIFDEAYEAALRIQEKTGAVFVHPFNDPHVIAGQGTIGLEIMEDLPDVEVVVVPVGGGG 180
           G+ +DEAY  A++  +     FVHPF D  V+AGQGTI LEI++   D++ ++VP+GGGG
Sbjct: 121 GSNYDEAYAYAVQYAKDHNKTFVHPFADYDVMAGQGTIALEILDQAKDLDAILVPIGGGG 180

Query: 181 LISGVSVAIKSMNPEVKVIGVQTENMPSMIASLRRGRAERVEGKPTLADGIAVKKPGDLT 240
           LI+G++ AIK +NP++++IGV     P+M  S + GR        T+ADGIAV+    +T
Sbjct: 181 LIAGIASAIKQINPKIQIIGVTAAGAPAMRESFQLGRPVDSTQVRTIADGIAVRDTSPVT 240

Query: 241 FELVKKYVDEMVAVNEEEIADAILFLLEQAKVVAEGAGAVGVAAVL-NKLDV-KGKKVAI 298
            +++ + VD++V V++EEIADAILFLLE  K+V EGAGAVGVAA+L  KL + +   +A+
Sbjct: 241 LKIILETVDDIVEVDDEEIADAILFLLENQKLVVEGAGAVGVAALLYEKLTLPENANIAV 300

Query: 299 VISGGNIDVNMIDRIINKGLVKSGRKVFIETFVMDRPGALKELLGIVAELGANVLSVFHN 358
           V+SGGNIDV M+  II KGL+KS RK+ +   ++D+PG+L +L  I+A + AN++ + ++
Sbjct: 301 VLSGGNIDVTMLSVIIEKGLIKSYRKMKLIVTLVDKPGSLMKLTEILASVSANIVQIGYD 360

Query: 359 RSAKEVPIGFAKIELELETVDEKHVEEIERVLIAKGY 395
           R++  +  G A + + LET  ++H E+I  +L   G+
Sbjct: 361 RTSANLAYGDANVSIGLETKGKEHQEQIRELLTRHGF 397


Lambda     K      H
   0.317    0.136    0.367 

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: 382
Number of extensions: 9
Number of successful extensions: 2
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: 401
Length of database: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_084275803.1 B8779_RS06910 (threonine ammonia-lyase)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (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/TIGR01127.hmm
# target sequence database:        /tmp/gapView.3434426.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-163  528.9   6.9   4.2e-163  528.7   6.9    1.0  1  NCBI__GCF_900176045.1:WP_084275803.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176045.1:WP_084275803.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.7   6.9  4.2e-163  4.2e-163       1     379 [.      21     400 ..      21     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 528.7 bits;  conditional E-value: 4.2e-163
                             TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgik 73 
                                           tp++++ +ls+ +g +++lk enlq tG+fk+rGa+nkiak+s+eek+rGvvaasaGnhaqGva++++ f i+
  NCBI__GCF_900176045.1:WP_084275803.1  21 TPYAYAPILSKKCGYKIFLKKENLQVTGAFKLRGAFNKIAKISQEEKNRGVVAASAGNHAQGVAFSSNYFQIP 93 
                                           899********************************************************************** PP

                             TIGR01127  74 akivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledl 146
                                           a+ivmPe +pl+kv+ +ksyGa viLhG+++Deay++a ++a++++++fvh+f D  v+aGqGt++leil++ 
  NCBI__GCF_900176045.1:WP_084275803.1  94 ATIVMPENTPLTKVNGVKSYGASVILHGSNYDEAYAYAVQYAKDHNKTFVHPFADYDVMAGQGTIALEILDQA 166
                                           ************************************************************************* PP

                             TIGR01127 147 pdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdl 219
                                            d+d ++vP+GGGGLi+G+asa+k++np++++iGv a +ap++ es++ g++++ ++v+tiaDGiav++++++
  NCBI__GCF_900176045.1:WP_084275803.1 167 KDLDAILVPIGGGGLIAGIASAIKQINPKIQIIGVTAAGAPAMRESFQLGRPVDSTQVRTIADGIAVRDTSPV 239
                                           ************************************************************************* PP

                             TIGR01127 220 tfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvd.vkgkkvavvvsGGnidlnll 291
                                           t +i+ e+vD++v+vd+eeia+ail+Lle++k+v+egaGavgvaa+l ek+  +++ ++avv+sGGnid+++l
  NCBI__GCF_900176045.1:WP_084275803.1 240 TLKIILETVDDIVEVDDEEIADAILFLLENQKLVVEGAGAVGVAALLYEKLTlPENANIAVVLSGGNIDVTML 312
                                           ****************************************************99999**************** PP

                             TIGR01127 292 ekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskeialgaakvelelevkgkehl 364
                                           + iiekgL+ks+rk+k+ ++l+DkPG+L+kl+e++a   aniv+i +dr+s ++a+g+a+v++ le+kgkeh+
  NCBI__GCF_900176045.1:WP_084275803.1 313 SVIIEKGLIKSYRKMKLIVTLVDKPGSLMKLTEILASVSANIVQIGYDRTSANLAYGDANVSIGLETKGKEHQ 385
                                           ************************************************************************* PP

                             TIGR01127 365 eellktlrdkgyevk 379
                                           e++++ l+ +g++++
  NCBI__GCF_900176045.1:WP_084275803.1 386 EQIRELLTRHGFRFY 400
                                           ************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (403 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: 00:00:00.00
# Mc/sec: 18.28
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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