GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Azohydromonas australica DSM 1124

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate WP_029000548.1 H537_RS0128280 threonine ammonia-lyase, biosynthetic

Query= SwissProt::A0FKE6
         (606 letters)



>NCBI__GCF_000430725.1:WP_029000548.1
          Length = 522

 Score =  518 bits (1335), Expect = e-151
 Identities = 267/504 (52%), Positives = 351/504 (69%), Gaps = 6/504 (1%)

Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166
           +YL  IL++KVYDVA E+PL  A  LS RLG  V LKRED QPVFSFK+RGAYN MA L 
Sbjct: 19  DYLKKILTAKVYDVAVESPLDLARNLSRRLGNQVLLKREDQQPVFSFKLRGAYNKMAHLS 78

Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGATVVLVGDS 226
            EQL +GVIC+SAGNHAQGVAL A+RLGC AVIVMPVTTP +K  +V++LG  VVL GDS
Sbjct: 79  AEQLARGVICASAGNHAQGVALGAKRLGCKAVIVMPVTTPRVKIDAVQQLGGEVVLHGDS 138

Query: 227 YDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGGGLI 286
           Y +A  +A    +  G TF+ PFD PDVI GQGT+ ME+ RQ +  + A+FV +GGGGLI
Sbjct: 139 YSDAALHASALEKERGLTFVHPFDDPDVIAGQGTIAMELLRQHQGPLDAVFVAIGGGGLI 198

Query: 287 AGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEETYR 346
           +G+AAY+K V P+I++IGV+ +D++A+  S+   +RV L  VG FADG AVK+VGEET+R
Sbjct: 199 SGVAAYIKAVRPEIQVIGVQSVDSDAMVRSVRAKKRVQLSDVGLFADGTAVKLVGEETFR 258

Query: 347 LCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGLKGENVVAI 406
           +  EL+D  V+V  D +CA+IKD+F++ RSI+EP+GA+ +A  + Y   + LKG    AI
Sbjct: 259 IARELVDDFVVVDNDEVCAAIKDVFQDTRSIVEPSGAMGVAAIKKYVDQHKLKGRTFAAI 318

Query: 407 TSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVG----PMNITEFKY 462
           T GANMNFDRLR V E A+VG  REA+ A  +PE+ GSF++F E +G    P  +TEF Y
Sbjct: 319 TCGANMNFDRLRFVAERAEVGEHREALFAVTIPEERGSFRRFCEAIGTPAHPRQVTEFNY 378

Query: 463 RYNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRTNV 522
           R  SD++ A V   +G+    E + +    E     T+NLTD++L K HLRH++GGR+ +
Sbjct: 379 RI-SDQQVAHVFVGIGISKREEADKLARNFERHGFTTLNLTDDELAKQHLRHMVGGRSEL 437

Query: 523 -HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVEF 581
             +E L RFTFPE+PGAL++FL+A  P WNISLFHYR QG     +LVGIQVP  +    
Sbjct: 438 ARDERLFRFTFPERPGALLRFLEAMQPDWNISLFHYRNQGADYGRILVGIQVPRGDRAAL 497

Query: 582 EGRADSLGYEYAMESLNEAYQLIM 605
           +   D+L Y    E+ N  Y+L +
Sbjct: 498 KRFLDTLDYPCVDETDNPVYRLFL 521


Lambda     K      H
   0.318    0.136    0.393 

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: 713
Number of extensions: 23
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: 606
Length of database: 522
Length adjustment: 36
Effective length of query: 570
Effective length of database: 486
Effective search space:   277020
Effective search space used:   277020
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_029000548.1 H537_RS0128280 (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.1212569.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.2e-252  822.5   0.4     7e-252  822.3   0.4    1.0  1  NCBI__GCF_000430725.1:WP_029000548.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_029000548.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  822.3   0.4    7e-252    7e-252       1     499 []      19     521 ..      19     521 .. 0.99

  Alignments for each domain:
  == domain 1  score: 822.3 bits;  conditional E-value: 7e-252
                             TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasa 73 
                                           dyl++il+a+vy++ave+pl+ a++ls+rl+n+vllkred+qpvfsfklrGaynkma+lsaeq a+Gvi+asa
  NCBI__GCF_000430725.1:WP_029000548.1  19 DYLKKILTAKVYDVAVESPLDLARNLSRRLGNQVLLKREDQQPVFSFKLRGAYNKMAHLSAEQLARGVICASA 91 
                                           89*********************************************************************** PP

                             TIGR01124  74 GnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddp 146
                                           GnhaqGval+ak+lG+kavivmp ttp +k+dav++ GgevvlhG++y++a+ +a +l++e+gltf++pfddp
  NCBI__GCF_000430725.1:WP_029000548.1  92 GNHAQGVALGAKRLGCKAVIVMPVTTPRVKIDAVQQLGGEVVLHGDSYSDAALHASALEKERGLTFVHPFDDP 164
                                           ************************************************************************* PP

                             TIGR01124 147 lviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkl 219
                                           +viaGqGt+a+ellrq++ +ldavfv++GGGGli+Gvaa++k+++pei+vigv++ ds+a+ +++ a +rv+l
  NCBI__GCF_000430725.1:WP_029000548.1 165 DVIAGQGTIAMELLRQHQGPLDAVFVAIGGGGLISGVAAYIKAVRPEIQVIGVQSVDSDAMVRSVRAKKRVQL 237
                                           ************************************************************************* PP

                             TIGR01124 220 dqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgi 292
                                           ++vGlfadG+avk vG+etfr+++e++dd+v vd devcaaikdvf+dtr+++ep+Ga+++a +kkyv+++++
  NCBI__GCF_000430725.1:WP_029000548.1 238 SDVGLFADGTAVKLVGEETFRIARELVDDFVVVDNDEVCAAIKDVFQDTRSIVEPSGAMGVAAIKKYVDQHKL 310
                                           ************************************************************************* PP

                             TIGR01124 293 edktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGe....raitefnyrladd 361
                                           +++t++ai++Gan+nfdrlr+v+erae+Ge+real+avtipee+Gs+++f+e +G     r++tefnyr++d+
  NCBI__GCF_000430725.1:WP_029000548.1 311 KGRTFAAITCGANMNFDRLRFVAERAEVGEHREALFAVTIPEERGSFRRFCEAIGTpahpRQVTEFNYRISDQ 383
                                           *******************************************************7555589*********** PP

                             TIGR01124 362 ekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGall 434
                                           + ah+fvG+ ++++ee+++l++++e++g+++++ltddelak h+r++vGGr++ +++erl++f+fperpGall
  NCBI__GCF_000430725.1:WP_029000548.1 384 QVAHVFVGIGISKREEADKLARNFERHGFTTLNLTDDELAKQHLRHMVGGRSELARDERLFRFTFPERPGALL 456
                                           ************************************************************************* PP

                             TIGR01124 435 kfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                           +fle +q++wnislfhyrn GadyGr+lvg++vp+ + ++++ fl++l+y ++det+np+yrlfl
  NCBI__GCF_000430725.1:WP_029000548.1 457 RFLEAMQPDWNISLFHYRNQGADYGRILVGIQVPRGDRAALKRFLDTLDYPCVDETDNPVYRLFL 521
                                           ****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (522 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.27
//
[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