Alignments for a candidate for ilvA in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Geobacter lovleyi SZ

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_012468564.1 GLOV_RS02320 threonine ammonia-lyase

Query= BRENDA::Q74FW6
         (402 letters)



>NCBI__GCF_000020385.1:WP_012468564.1
          Length = 406

 Score =  537 bits (1384), Expect = e-157
 Identities = 275/397 (69%), Positives = 328/397 (82%)

Query: 2   LPYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTS 61
           L Y L+ EA DRLRKRVR TELI S+HFS +LG P+  KCENLQ TGAFK+RGA+NFMT+
Sbjct: 6   LNYELVLEAQDRLRKRVRHTELISSNHFSRQLGYPLLLKCENLQTTGAFKLRGAMNFMTA 65

Query: 62  QPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTG 121
           + R  LA+GV  ASAGNHAQGVA++ADLLGVP+ +FMPESTPPQKV ATRD GAEVVLTG
Sbjct: 66  RDRSGLAQGVTAASAGNHAQGVAYAADLLGVPAKIFMPESTPPQKVQATRDLGAEVVLTG 125

Query: 122 RNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGL 181
            NFDE++AAA     + G +F+HPFDDPLVMAGQGTIGLE+L++LPDVAN+LVPIGGGGL
Sbjct: 126 ANFDESFAAAQADSNQHGTVFIHPFDDPLVMAGQGTIGLEILKDLPDVANLLVPIGGGGL 185

Query: 182 IAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTF 241
           +AGIATAI+E +P VRIIGVE+AAAP    ++    I +VP+  T+ADGIAVKK G  T 
Sbjct: 186 LAGIATAIKEHNPQVRIIGVESAAAPCMFRAVHDNAIAEVPLGTTIADGIAVKKAGQITT 245

Query: 242 PIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVL 301
           PII++LVD++VLVEEEEIALAIVALLE++KLLVEGAGAVPLAALLN R   + GKTVC+L
Sbjct: 246 PIIQNLVDDLVLVEEEEIALAIVALLEKSKLLVEGAGAVPLAALLNGRAKGIRGKTVCLL 305

Query: 302 SGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHDRR 361
           SGGNIDV+T+++VVERGL+AAGRYLKL++E+ D PGALA LAT++AEAKANI  ITHDRR
Sbjct: 306 SGGNIDVRTLALVVERGLLAAGRYLKLRIEMQDTPGALAHLATDLAEAKANIHDITHDRR 365

Query: 362 SKSLPIGKTEVLIELETRGFEHIQEVISHLQGVGYLV 398
           +K L +G T V + LETRG EH  EV+  L   GY V
Sbjct: 366 TKGLVMGTTAVQLLLETRGQEHAHEVLGLLAKRGYSV 402


Lambda     K      H
   0.319    0.137    0.383 

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: 451
Number of extensions: 10
Number of successful extensions: 1
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: 402
Length of database: 406
Length adjustment: 31
Effective length of query: 371
Effective length of database: 375
Effective search space:   139125
Effective search space used:   139125
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: 50 (23.9 bits)

Align candidate WP_012468564.1 GLOV_RS02320 (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.22214.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-143  462.6   0.8   5.8e-143  462.4   0.8    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012468564.1  GLOV_RS02320 threonine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012468564.1  GLOV_RS02320 threonine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.4   0.8  5.8e-143  5.8e-143       1     379 [.      25     403 ..      25     404 .. 0.99

  Alignments for each domain:
  == domain 1  score: 462.4 bits;  conditional E-value: 5.8e-143
                                 TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakv 69 
                                               t l+ s+ +s+  g  + lk enlq tG+fk+rGa+n ++     +  +Gv aasaGnhaqGva+aa+ 
  lcl|NCBI__GCF_000020385.1:WP_012468564.1  25 TELISSNHFSRQLGYPLLLKCENLQTTGAFKLRGAMNFMTARDRSGLAQGVTAASAGNHAQGVAYAADL 93 
                                               78999**************************************************************** PP

                                 TIGR01127  70 fgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtl 138
                                                g++aki mPes+p++kv+at+ +Gaev+L Ga+fDe++++a+   +++g+vf+h+fdD+ v+aGqGt+
  lcl|NCBI__GCF_000020385.1:WP_012468564.1  94 LGVPAKIFMPESTPPQKVQATRDLGAEVVLTGANFDESFAAAQADSNQHGTVFIHPFDDPLVMAGQGTI 162
                                               ********************************************************************* PP

                                 TIGR01127 139 gleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvkti 207
                                               gleil+dlpdv  ++vP+GGGGL++G+a+a+k++np+v++iGve+ aap + ++++++ i +v   +ti
  lcl|NCBI__GCF_000020385.1:WP_012468564.1 163 GLEILKDLPDVANLLVPIGGGGLLAGIATAIKEHNPQVRIIGVESAAAPCMFRAVHDNAIAEVPLGTTI 231
                                               ********************************************************************* PP

                                 TIGR01127 208 aDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvd.vkgk 275
                                               aDGiavkk+g++t +i+++lvD++v v+eeeia ai+ Lle++k+++egaGav +aa+l+ + +   g 
  lcl|NCBI__GCF_000020385.1:WP_012468564.1 232 ADGIAVKKAGQITTPIIQNLVDDLVLVEEEEIALAIVALLEKSKLLVEGAGAVPLAALLNGRAKgIRG- 299
                                               ****************************************************************6666. PP

                                 TIGR01127 276 kvavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlske 344
                                               k++ ++sGGnid++ l  ++e+gL   gr++k++  ++D+PGaL +l+  +ae++ani +i+hdr +k 
  lcl|NCBI__GCF_000020385.1:WP_012468564.1 300 KTVCLLSGGNIDVRTLALVVERGLLAAGRYLKLRIEMQDTPGALAHLATDLAEAKANIHDITHDRRTKG 368
                                               88899**************************************************************** PP

                                 TIGR01127 345 ialgaakvelelevkgkehleellktlrdkgyevk 379
                                               + +g++ v+l le++g+eh +e+l  l ++gy+v+
  lcl|NCBI__GCF_000020385.1:WP_012468564.1 369 LVMGTTAVQLLLETRGQEHAHEVLGLLAKRGYSVT 403
                                               ********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (406 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.94
//
[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