Alignments for a candidate for ilvA in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Acidithiobacillus ferrooxidans ATCC 23270

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_074874168.1 AFE_RS03420 threonine ammonia-lyase, biosynthetic

Query= BRENDA::P04968
         (514 letters)



>NCBI__GCF_000021485.1:WP_074874168.1
          Length = 521

 Score =  526 bits (1354), Expect = e-154
 Identities = 271/498 (54%), Positives = 360/498 (72%), Gaps = 3/498 (0%)

Query: 17  LRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEE 76
           LR VL + VY+ A+ TPL+   KLS+RL   +L KRED QPV SFKLRGAY  +A L++ 
Sbjct: 20  LREVLCSRVYDVARETPLEAAPKLSARLQREVLFKREDLQPVFSFKLRGAYNKIAQLSDA 79

Query: 77  QKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFD 136
           +KA GVITASAGNHAQGVA+++ +LG++A+IVMP  T +IKV+AVR  G EV+LHG ++ 
Sbjct: 80  EKARGVITASAGNHAQGVAYAAQKLGIRAVIVMPGTTPEIKVNAVRARGAEVILHGDSYS 139

Query: 137 EAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGGGLAAG 195
           +A+A    L  + G  ++PPFD P+VIAGQGT+  E+L+Q  A L+ +FVPVGGGGL AG
Sbjct: 140 DAQAHCDALIAESGLVFIPPFDDPLVIAGQGTIGAEILRQRGAGLEAIFVPVGGGGLIAG 199

Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255
           VA  +K ++P+I++I VE  ++  +  +L AG  V LP+VG+FA+GVAV+++G+ TF LC
Sbjct: 200 VAAYLKSIVPEIRIIGVEPFEADAMYQSLQAGERVTLPQVGIFADGVAVRQVGEHTFALC 259

Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILS 315
           ++Y+D+I+ V +D ICAA+KD+F++ R+V EP+GALALAG+K+  A    RG     +LS
Sbjct: 260 RKYVDEIVRVTNDEICAAIKDVFDETRSVMEPAGALALAGLKRMAATDPGRGGAWVALLS 319

Query: 316 GANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADAK 375
           GAN+NF  LR+++ER ELGE REAL AVTIPE  G+F  FC  +G R VTEFNYR     
Sbjct: 320 GANMNFDRLRFIAERAELGEAREALFAVTIPERPGAFRAFCAAIGQRVVTEFNYRLHHRD 379

Query: 376 NACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQERL 435
            A IFVGV + R  E+   +L+ L   G+  +DLSDDEMAKLH+R+MVGG  +    ER+
Sbjct: 380 RAHIFVGVAI-RDREDASALLESLRVTGHEALDLSDDEMAKLHIRHMVGGHAAAAQNERI 438

Query: 436 YSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-PDFETRLNE 494
           Y FEFPE PGAL+ FL+ LG +WNISLFHYR++G D GRVLA FE+ D E   FE+ L  
Sbjct: 439 YRFEFPERPGALMEFLDKLGGHWNISLFHYRNNGVDLGRVLAGFEVPDSEMARFESLLAR 498

Query: 495 LGYDCHDETNNPAFRFFL 512
           L Y    ET NPA+RFFL
Sbjct: 499 LDYPHVAETANPAYRFFL 516


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: 708
Number of extensions: 29
Number of successful extensions: 6
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: 521
Length adjustment: 35
Effective length of query: 479
Effective length of database: 486
Effective search space:   232794
Effective search space used:   232794
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_074874168.1 AFE_RS03420 (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.4661.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-246  803.0   0.1   5.4e-246  802.9   0.1    1.0  1  lcl|NCBI__GCF_000021485.1:WP_074874168.1  AFE_RS03420 threonine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021485.1:WP_074874168.1  AFE_RS03420 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  802.9   0.1  5.4e-246  5.4e-246       2     499 .]      19     516 ..      18     516 .. 1.00

  Alignments for each domain:
  == domain 1  score: 802.9 bits;  conditional E-value: 5.4e-246
                                 TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 
                                               +lr++l +rvy++a etple a kls+rl+ +vl+kredlqpvfsfklrGaynk+aqls+ +ka+Gvi+
  lcl|NCBI__GCF_000021485.1:WP_074874168.1  19 LLREVLCSRVYDVARETPLEAAPKLSARLQREVLFKREDLQPVFSFKLRGAYNKIAQLSDAEKARGVIT 87 
                                               799****************************************************************** PP

                                 TIGR01124  71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltf 139
                                               asaGnhaqGva++a+klG++avivmp ttpeikv+av+a+G+ev+lhG++y++a+a++ +l  e gl f
  lcl|NCBI__GCF_000021485.1:WP_074874168.1  88 ASAGNHAQGVAYAAQKLGIRAVIVMPGTTPEIKVNAVRARGAEVILHGDSYSDAQAHCDALIAESGLVF 156
                                               ********************************************************************* PP

                                 TIGR01124 140 iapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalk 208
                                               i+pfddplviaGqGt++ e+lrq    l+a+fvpvGGGGliaGvaa++k ++pei++igve+ +++a++
  lcl|NCBI__GCF_000021485.1:WP_074874168.1 157 IPPFDDPLVIAGQGTIGAEILRQRGAGLEAIFVPVGGGGLIAGVAAYLKSIVPEIRIIGVEPFEADAMY 225
                                               ********************************************************************* PP

                                 TIGR01124 209 qaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277
                                               q+l+aGerv+l qvG+fadGvav++vG++tf+lc++y+d+iv+v  de+caaikdvf++tr+v+epaGa
  lcl|NCBI__GCF_000021485.1:WP_074874168.1 226 QSLQAGERVTLPQVGIFADGVAVRQVGEHTFALCRKYVDEIVRVTNDEICAAIKDVFDETRSVMEPAGA 294
                                               ********************************************************************* PP

                                 TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevl 346
                                               lalaGlk+ +a++  ++   va+lsGan+nfdrlr+++eraelGe real+avtipe++G+++ f+  +
  lcl|NCBI__GCF_000021485.1:WP_074874168.1 295 LALAGLKRMAATDPGRGGAWVALLSGANMNFDRLRFIAERAELGEAREALFAVTIPERPGAFRAFCAAI 363
                                               ********************************************************************* PP

                                 TIGR01124 347 GeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraak 415
                                               G+r +tefnyrl ++++ahifvGv ++++e+++ ll++l+ +g++ +dl+dde+aklh+r++vGG aa 
  lcl|NCBI__GCF_000021485.1:WP_074874168.1 364 GQRVVTEFNYRLHHRDRAHIFVGVAIRDREDASALLESLRVTGHEALDLSDDEMAKLHIRHMVGGHAAA 432
                                               ********************************************************************* PP

                                 TIGR01124 416 venerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgy 484
                                               ++ner+y+fefperpGal++fl++l ++wnislfhyrn G d Grvl+g+evpd+e+++fe+ la+l+y
  lcl|NCBI__GCF_000021485.1:WP_074874168.1 433 AQNERIYRFEFPERPGALMEFLDKLGGHWNISLFHYRNNGVDLGRVLAGFEVPDSEMARFESLLARLDY 501
                                               ********************************************************************* PP

                                 TIGR01124 485 ryedetenpayrlfl 499
                                                 + et npayr+fl
  lcl|NCBI__GCF_000021485.1:WP_074874168.1 502 PHVAETANPAYRFFL 516
                                               **************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (521 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: 11.24
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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