GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Marinobacter adhaerens HP15

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate GFF3271 HP15_3213 threonine dehydratase biosynthetic

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__Marino:GFF3271
          Length = 511

 Score =  543 bits (1400), Expect = e-159
 Identities = 275/499 (55%), Positives = 369/499 (73%), Gaps = 2/499 (0%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           Y++ +L A VY+ A  TPL +   LS R  N IL+KRED QPV SFK+RGAY  +A L+E
Sbjct: 5   YIKKILDARVYDVAIETPLTEARSLSKRFGNNILLKREDLQPVFSFKIRGAYNRIAQLSE 64

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
           EQKA GVI ASAGNHAQGVA ++  LG+KA+IVMP  T +IKV +VR  G +V+L G  F
Sbjct: 65  EQKAKGVICASAGNHAQGVALAAKNLGIKAVIVMPQTTPEIKVRSVRDHGAKVVLKGDAF 124

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLAA 194
           DEA A A EL  + G+T++PP+D P VIAGQGT+A+E++ Q +  +  +F+ VGGGGL A
Sbjct: 125 DEAAAHAQELIAKHGYTYIPPYDDPDVIAGQGTVAMEIMWQFSKPIHAIFICVGGGGLIA 184

Query: 195 GVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRL 254
           G+A  IK L P+IKVI VE EDS CL+AA+ AG  V L  VG+FA+GVAVK+IG   + +
Sbjct: 185 GMAAYIKYLRPEIKVIGVEPEDSNCLQAAMKAGKRVVLDEVGIFADGVAVKQIGKYPWEI 244

Query: 255 CQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHIL 314
           C++++D++ITV +D ICAA+KD+FED R++AEP+GAL +AG+KKYI    + GE L   L
Sbjct: 245 CKDHVDEVITVSTDEICAAIKDVFEDTRSIAEPAGALGVAGIKKYIEREKVEGENLIATL 304

Query: 315 SGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADA 374
           SGAN+NF  LRY+SER E+GE+REA+LAVTIPE+ G+F  F   L  RS+TEFNYR+ADA
Sbjct: 305 SGANMNFDRLRYISERTEVGEKREAILAVTIPEKPGAFKTFINALHKRSITEFNYRYADA 364

Query: 375 KNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQER 434
            NA IFVG++++ G   R++++Q L + GYSVVDL+D ++AK H+R+MVGG       E+
Sbjct: 365 TNATIFVGIQIAAGGHGREDLVQDLRESGYSVVDLTDSDLAKQHIRHMVGGHAPTITNEK 424

Query: 435 LYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-PDFETRLN 493
           ++ FEFPE PGALL+FL +LGT WNIS+FHYR+HG  Y RVL   ++ DHE  DFE  L+
Sbjct: 425 VFQFEFPERPGALLKFLMSLGTRWNISMFHYRNHGAAYSRVLLGAQVDDHEVQDFEKMLD 484

Query: 494 ELGYDCHDETNNPAFRFFL 512
           ++G+   + T+N A++ FL
Sbjct: 485 KVGFRYENMTDNEAYQLFL 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: 691
Number of extensions: 31
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: 511
Length adjustment: 35
Effective length of query: 479
Effective length of database: 476
Effective search space:   228004
Effective search space used:   228004
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 GFF3271 HP15_3213 (threonine dehydratase 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.17993.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-247  808.5   1.2   1.2e-247  808.3   1.2    1.0  1  lcl|FitnessBrowser__Marino:GFF3271  HP15_3213 threonine dehydratase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3271  HP15_3213 threonine dehydratase biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.3   1.2  1.2e-247  1.2e-247       2     499 .]       5     503 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 808.3 bits;  conditional E-value: 1.2e-247
                           TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnh 76 
                                         y+++il arvy++a+etpl +a++ls+r +n++llkredlqpvfsfk+rGayn++aqls+eqkakGvi+asaGnh
  lcl|FitnessBrowser__Marino:GFF3271   5 YIKKILDARVYDVAIETPLTEARSLSKRFGNNILLKREDLQPVFSFKIRGAYNRIAQLSEEQKAKGVICASAGNH 79 
                                         89************************************************************************* PP

                           TIGR01124  77 aqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaG 151
                                         aqGval+ak+lG+kavivmp+ttpeikv +v+ +G++vvl+G+++dea+a+a+el  ++g t+i+p+ddp+viaG
  lcl|FitnessBrowser__Marino:GFF3271  80 AQGVALAAKNLGIKAVIVMPQTTPEIKVRSVRDHGAKVVLKGDAFDEAAAHAQELIAKHGYTYIPPYDDPDVIAG 154
                                         *************************************************************************** PP

                           TIGR01124 152 qGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfa 226
                                         qGtva+e++ q +++++a+f+ vGGGGliaG+aa++k l+peikvigve+eds++l++a++aG+rv ld+vG+fa
  lcl|FitnessBrowser__Marino:GFF3271 155 QGTVAMEIMWQFSKPIHAIFICVGGGGLIAGMAAYIKYLRPEIKVIGVEPEDSNCLQAAMKAGKRVVLDEVGIFA 229
                                         *************************************************************************** PP

                           TIGR01124 227 dGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvail 301
                                         dGvavk++G++ +++ck+++d++++v tde+caaikdvfedtr+++epaGal++aG+kky++++++e+++l+a l
  lcl|FitnessBrowser__Marino:GFF3271 230 DGVAVKQIGKYPWEICKDHVDEVITVSTDEICAAIKDVFEDTRSIAEPAGALGVAGIKKYIEREKVEGENLIATL 304
                                         *************************************************************************** PP

                           TIGR01124 302 sGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee. 375
                                         sGan+nfdrlry+ser+e+Ge+rea+lavtipe++G+++ f++ l +r+itefnyr+ad+ +a+ifvG+q+a   
  lcl|FitnessBrowser__Marino:GFF3271 305 SGANMNFDRLRYISERTEVGEKREAILAVTIPEKPGAFKTFINALHKRSITEFNYRYADATNATIFVGIQIAAGg 379
                                         **********************************************************************99875 PP

                           TIGR01124 376 eerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfh 450
                                         + r++l+++l+e+gy+vvdltd +lak h+r++vGG a +++ne++++fefperpGallkfl +l ++wnis+fh
  lcl|FitnessBrowser__Marino:GFF3271 380 HGREDLVQDLRESGYSVVDLTDSDLAKQHIRHMVGGHAPTITNEKVFQFEFPERPGALLKFLMSLGTRWNISMFH 454
                                         889************************************************************************ PP

                           TIGR01124 451 yrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                         yrnhGa+y rvl+g +v+d+e ++fe++l+++g+rye+ t+n+ay+lfl
  lcl|FitnessBrowser__Marino:GFF3271 455 YRNHGAAYSRVLLGAQVDDHEVQDFEKMLDKVGFRYENMTDNEAYQLFL 503
                                         ************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (511 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.09
//
[ok]

This GapMind analysis is from Apr 09 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:

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