Alignments for a candidate for ilvA in Geobacter uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Geobacter uraniireducens Rf4

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_011940816.1 GURA_RS20520 threonine ammonia-lyase

Query= BRENDA::Q74FW6
         (402 letters)



>NCBI__GCF_000016745.1:WP_011940816.1
          Length = 402

 Score =  647 bits (1668), Expect = 0.0
 Identities = 327/402 (81%), Positives = 370/402 (92%)

Query: 1   MLPYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMT 60
           ML Y LI EA DRL+KRVRRTELIHSHHFSEKLGIPI+FKCENLQRTGAFKIRGALNFMT
Sbjct: 1   MLTYNLIHEAADRLKKRVRRTELIHSHHFSEKLGIPIFFKCENLQRTGAFKIRGALNFMT 60

Query: 61  SQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLT 120
           +QPRE L  GVITASAGNHAQGVAFSADLLGV S VFMPESTPPQKVFATRDYGAEVVLT
Sbjct: 61  AQPRENLRNGVITASAGNHAQGVAFSADLLGVKSMVFMPESTPPQKVFATRDYGAEVVLT 120

Query: 121 GRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGG 180
           G+NFDEAYAAA++AQ+E GALFVHPFDDPLVMAGQGTIGLE+L ELPD+ANILVPIGGGG
Sbjct: 121 GKNFDEAYAAALKAQKETGALFVHPFDDPLVMAGQGTIGLEILDELPDLANILVPIGGGG 180

Query: 181 LIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNT 240
           LIAGIATAI++T P VRIIGVE+AAAPS H+SL+KGKI + P++VTLADGIAVK+ G NT
Sbjct: 181 LIAGIATAIKQTRPRVRIIGVESAAAPSMHFSLEKGKITETPLSVTLADGIAVKRVGKNT 240

Query: 241 FPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCV 300
           FPI+R+LVDEVVLVEEEEIA AIVALLER+KLLVEGAGAV LAAL+N +V  ++GKTVC+
Sbjct: 241 FPIVRELVDEVVLVEEEEIAQAIVALLERSKLLVEGAGAVTLAALMNGKVEHVTGKTVCL 300

Query: 301 LSGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHDR 360
           LSGGNIDVKTI++VVERGL+AAGRYLKLKVELDD+PG+LA+L+T+IA   ANIS+ITHDR
Sbjct: 301 LSGGNIDVKTIAIVVERGLLAAGRYLKLKVELDDVPGSLAKLSTDIAATNANISLITHDR 360

Query: 361 RSKSLPIGKTEVLIELETRGFEHIQEVISHLQGVGYLVDVLK 402
           RSK+LPIG+ EVL+ELETRGF+HI+EV+ +L   GY V+VLK
Sbjct: 361 RSKALPIGRAEVLLELETRGFDHIREVVGYLGERGYEVEVLK 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: 496
Number of extensions: 11
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: 402
Length adjustment: 31
Effective length of query: 371
Effective length of database: 371
Effective search space:   137641
Effective search space used:   137641
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_011940816.1 GURA_RS20520 (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.19712.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-153  496.0   1.3   4.2e-153  495.8   1.3    1.0  1  lcl|NCBI__GCF_000016745.1:WP_011940816.1  GURA_RS20520 threonine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016745.1:WP_011940816.1  GURA_RS20520 threonine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.8   1.3  4.2e-153  4.2e-153       1     380 []      21     400 ..      21     400 .. 0.99

  Alignments for each domain:
  == domain 1  score: 495.8 bits;  conditional E-value: 4.2e-153
                                 TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakv 69 
                                               t l++s+ +s+  g  +++k enlq+tG+fkirGaln ++    e+ ++Gv++asaGnhaqGva++a+ 
  lcl|NCBI__GCF_000016745.1:WP_011940816.1  21 TELIHSHHFSEKLGIPIFFKCENLQRTGAFKIRGALNFMTAQPRENLRNGVITASAGNHAQGVAFSADL 89 
                                               7899***************************************************************** PP

                                 TIGR01127  70 fgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtl 138
                                                g+k+++ mPes+p++kv at+ yGaev+L G++fDeay++a + ++e+g+ fvh+fdD+ v+aGqGt+
  lcl|NCBI__GCF_000016745.1:WP_011940816.1  90 LGVKSMVFMPESTPPQKVFATRDYGAEVVLTGKNFDEAYAAALKAQKETGALFVHPFDDPLVMAGQGTI 158
                                               ********************************************************************* PP

                                 TIGR01127 139 gleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvkti 207
                                               gleil++lpd+  ++vP+GGGGLi+G+a+a+k++ p v++iGve+ aaps+  sl++gki+++    t+
  lcl|NCBI__GCF_000016745.1:WP_011940816.1 159 GLEILDELPDLANILVPIGGGGLIAGIATAIKQTRPRVRIIGVESAAAPSMHFSLEKGKITETPLSVTL 227
                                               ********************************************************************* PP

                                 TIGR01127 208 aDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvd.vkgk 275
                                               aDGiavk++g+ tf+iv+elvDevv v+eeeia+ai+ Ller+k+++egaGav++aa+++ kv+ v g 
  lcl|NCBI__GCF_000016745.1:WP_011940816.1 228 ADGIAVKRVGKNTFPIVRELVDEVVLVEEEEIAQAIVALLERSKLLVEGAGAVTLAALMNGKVEhVTG- 295
                                               ****************************************************************5555. PP

                                 TIGR01127 276 kvavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlske 344
                                               k++ ++sGGnid++ + +++e+gL   gr++k+++ l D PG+L kl   ia ++ani  i+hdr sk 
  lcl|NCBI__GCF_000016745.1:WP_011940816.1 296 KTVCLLSGGNIDVKTIAIVVERGLLAAGRYLKLKVELDDVPGSLAKLSTDIAATNANISLITHDRRSKA 364
                                               88899**************************************************************** PP

                                 TIGR01127 345 ialgaakvelelevkgkehleellktlrdkgyevkv 380
                                               +++g a+v lele++g +h+ e+   l ++gyev+v
  lcl|NCBI__GCF_000016745.1:WP_011940816.1 365 LPIGRAEVLLELETRGFDHIREVVGYLGERGYEVEV 400
                                               *********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (402 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: 6.99
//
[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