Alignments for a candidate for tdcB in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB 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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.12345.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.29
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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 catabolism of small carbon sources