Alignments for a candidate for ilvA in Methylococcus capsulatus Bath

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Methylococcus capsulatus Bath

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_010959715.1 MCA_RS01745 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000008325.1:WP_010959715.1
          Length = 509

 Score =  540 bits (1390), Expect = e-158
 Identities = 275/502 (54%), Positives = 362/502 (72%), Gaps = 2/502 (0%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +Y+  +LRA VY+ AQ TPL     LS RLDN +L+KRED QPV SFKLRGAY  +A LT
Sbjct: 4   KYIEKILRARVYDVAQETPLDPAPGLSRRLDNTVLIKREDLQPVFSFKLRGAYNKIASLT 63

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134
            E +A GVI ASAGNHAQGVA ++ RLG++A+IVMP  T  IKVDAVR  GGEV+LHG  
Sbjct: 64  PEARAAGVIAASAGNHAQGVALAAQRLGIRAVIVMPCTTPHIKVDAVRNRGGEVVLHGDA 123

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLA 193
           +DEA   A+EL++ Q  T+V P+D P VIAGQGT+ +E+L+Q    +  +FVPVGGGGL 
Sbjct: 124 YDEAYEHALELARDQCLTFVHPYDDPEVIAGQGTIGMEILRQHQDAIHAIFVPVGGGGLI 183

Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253
           AG+A  +K + P I+VI VE  DS CL  AL A   V L +VGLFA+GVAVK++G E F 
Sbjct: 184 AGIAAYVKFVRPDIRVIGVEPVDSDCLHRALKAKRRVILKQVGLFADGVAVKQVGKEPFH 243

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313
           L  +++D+++TVD+D ICAA+KD+F+D R++AEP+GAL +AG+KKY+A   I+   L  I
Sbjct: 244 LAHQWVDEVVTVDTDEICAAIKDIFDDTRSIAEPAGALGIAGLKKYVAETGIKNACLVAI 303

Query: 314 LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFAD 373
            SGAN+NF  LR+V+ER E+GE+RE LLAVTIPE  GSFL+FC++LG R++TEFNYRF D
Sbjct: 304 ESGANINFDRLRHVAERAEIGEKRELLLAVTIPERPGSFLEFCRVLGRRNITEFNYRFFD 363

Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQE 433
            K A +FVG+ ++ G  +R+ +++     G+ V+DL+ +E+A  H+RYMVGG     L E
Sbjct: 364 EKAAQVFVGLPVASGAIDRESLVREFERQGFGVLDLTGNELAIEHIRYMVGGHAPKLLDE 423

Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-PDFETRL 492
           ++YSFEFPE PGALLRFL+ +G  WNISLFHYR+HG  +GRVL   ++   E   F   L
Sbjct: 424 QVYSFEFPERPGALLRFLSIMGGRWNISLFHYRNHGAAFGRVLMGIQVPKPERKAFREFL 483

Query: 493 NELGYDCHDETNNPAFRFFLAG 514
             +GY   +ET NPA+R F  G
Sbjct: 484 EAIGYAFKEETQNPAYRLFAGG 505


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: 693
Number of extensions: 32
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: 509
Length adjustment: 35
Effective length of query: 479
Effective length of database: 474
Effective search space:   227046
Effective search space used:   227046
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_010959715.1 MCA_RS01745 (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.7746.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-252  824.6   0.1   1.6e-252  824.4   0.1    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010959715.1  MCA_RS01745 threonine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010959715.1  MCA_RS01745 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  824.4   0.1  1.6e-252  1.6e-252       2     498 ..       5     502 ..       4     503 .. 0.99

  Alignments for each domain:
  == domain 1  score: 824.4 bits;  conditional E-value: 1.6e-252
                                 TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 
                                               y+++il+arvy++a+etpl++a  ls+rl+n+vl+kredlqpvfsfklrGaynk+a+l++e++a+Gvia
  lcl|NCBI__GCF_000008325.1:WP_010959715.1   5 YIEKILRARVYDVAQETPLDPAPGLSRRLDNTVLIKREDLQPVFSFKLRGAYNKIASLTPEARAAGVIA 73 
                                               99******************************************************************* PP

                                 TIGR01124  71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltf 139
                                               asaGnhaqGval+a++lG++avivmp+ttp+ikvdav+++GgevvlhG++ydea+++alela+++ ltf
  lcl|NCBI__GCF_000008325.1:WP_010959715.1  74 ASAGNHAQGVALAAQRLGIRAVIVMPCTTPHIKVDAVRNRGGEVVLHGDAYDEAYEHALELARDQCLTF 142
                                               ********************************************************************* PP

                                 TIGR01124 140 iapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalk 208
                                               ++p+ddp viaGqGt+++e+lrq+++ ++a+fvpvGGGGliaG+aa+vk ++p+i+vigve+ ds++l+
  lcl|NCBI__GCF_000008325.1:WP_010959715.1 143 VHPYDDPEVIAGQGTIGMEILRQHQDAIHAIFVPVGGGGLIAGIAAYVKFVRPDIRVIGVEPVDSDCLH 211
                                               ********************************************************************* PP

                                 TIGR01124 209 qaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277
                                               +al+a +rv l+qvGlfadGvavk+vG+e f+l+++++d++v+vdtde+caaikd+f+dtr+++epaGa
  lcl|NCBI__GCF_000008325.1:WP_010959715.1 212 RALKAKRRVILKQVGLFADGVAVKQVGKEPFHLAHQWVDEVVTVDTDEICAAIKDIFDDTRSIAEPAGA 280
                                               ********************************************************************* PP

                                 TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevl 346
                                               l++aGlkkyva+ gi++  lvai sGan+nfdrlr+v+erae+Ge+re llavtipe++Gs+l+f++vl
  lcl|NCBI__GCF_000008325.1:WP_010959715.1 281 LGIAGLKKYVAETGIKNACLVAIESGANINFDRLRHVAERAEIGEKRELLLAVTIPERPGSFLEFCRVL 349
                                               ********************************************************************* PP

                                 TIGR01124 347 GeraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGraa 414
                                               G r+itefnyr+ d+++a++fvG+ +a+   +r++l++++e++g+ v+dlt +ela  h+ry+vGG a 
  lcl|NCBI__GCF_000008325.1:WP_010959715.1 350 GRRNITEFNYRFFDEKAAQVFVGLPVASGaIDRESLVREFERQGFGVLDLTGNELAIEHIRYMVGGHAP 418
                                               ************************9988748************************************** PP

                                 TIGR01124 415 kvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelg 483
                                               k+ +e++ysfefperpGall+fl+ + ++wnislfhyrnhGa++Grvl+g++vp+ e ++f +fl+ +g
  lcl|NCBI__GCF_000008325.1:WP_010959715.1 419 KLLDEQVYSFEFPERPGALLRFLSIMGGRWNISLFHYRNHGAAFGRVLMGIQVPKPERKAFREFLEAIG 487
                                               ********************************************************************* PP

                                 TIGR01124 484 yryedetenpayrlf 498
                                               y +++et+npayrlf
  lcl|NCBI__GCF_000008325.1:WP_010959715.1 488 YAFKEETQNPAYRLF 502
                                               **************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (509 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: 8.73
//
[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