Alignments for a candidate for ilvA in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Herbaspirillum autotrophicum IAM 14942

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate WP_050462793.1 AKL27_RS10590 threonine ammonia-lyase, biosynthetic

Query= SwissProt::A0FKE6
         (606 letters)



>NCBI__GCF_001189915.1:WP_050462793.1
          Length = 508

 Score =  523 bits (1347), Expect = e-153
 Identities = 274/505 (54%), Positives = 358/505 (70%), Gaps = 7/505 (1%)

Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166
           +YL  IL+++VYDVA ETPL+ A  LSER+   ++ KRED+Q VFSFK+RGAYN MA L 
Sbjct: 4   DYLQKILTARVYDVAIETPLELANTLSERMENRIYFKREDMQSVFSFKLRGAYNKMAHLT 63

Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGATVVLVGDS 226
             QL++GVIC+SAGNHAQGVALSA +LGC AVIVMP TTP +K ++VK  G  VVL GDS
Sbjct: 64  PAQLKRGVICASAGNHAQGVALSAAKLGCRAVIVMPTTTPTVKIEAVKARGGEVVLHGDS 123

Query: 227 YDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGGGLI 286
           + +A  +A    +    TF+ PFD P VI GQGTVGMEI RQ  D IHAIFV +GGGGLI
Sbjct: 124 FTDAYNHALTLEKKLKLTFVHPFDDPYVIAGQGTVGMEILRQHADPIHAIFVAIGGGGLI 183

Query: 287 AGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEETYR 346
           +GIAAY+K V PDIKIIGV+  D++A+A SL  G+R+ L  VG F+DG AVK+VGEET+R
Sbjct: 184 SGIAAYVKAVRPDIKIIGVQTADSDAMARSLKAGRRITLPDVGLFSDGTAVKLVGEETFR 243

Query: 347 LCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCK-----YYGLKGE 401
           + +  +D +++V  DA+C +IKD+F++ RSI+EPAGALA+AGA+AY +        +K E
Sbjct: 244 MAKLYVDDIIIVDTDAVCTAIKDIFQDTRSIVEPAGALAVAGAKAYIERAKNSKKPIKNE 303

Query: 402 NVVAITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFK 461
            ++ I  GANMNFDRLR V E+ADVG+ REAV A  +PE+ GSFK+F E VGP N+TEF 
Sbjct: 304 ALITIACGANMNFDRLRFVAEMADVGQSREAVFAVTIPEEHGSFKRFCETVGPRNVTEFN 363

Query: 462 YRYNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRTN 521
           YR  SD++ A +   +   +  E   +    E     T++LT ++L K H+RHL+GG++ 
Sbjct: 364 YRI-SDEKSAHIFVGIQTDSQDESAKIARNFEKQGFATLDLTHDELAKVHIRHLVGGKSL 422

Query: 522 V-HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVE 580
           +  NELL RF FPE+PGALM+FL+A +P WNISLFHYR QG     +LVG+QVP  E+  
Sbjct: 423 LAQNELLYRFEFPERPGALMRFLNAMNPNWNISLFHYRNQGSDVGRILVGLQVPKKEMKT 482

Query: 581 FEGRADSLGYEYAMESLNEAYQLIM 605
           F     +LGY +  ES N  Y+L +
Sbjct: 483 FRLFLSNLGYRHWDESKNPLYKLFL 507


Lambda     K      H
   0.318    0.136    0.393 

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: 683
Number of extensions: 31
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: 606
Length of database: 508
Length adjustment: 36
Effective length of query: 570
Effective length of database: 472
Effective search space:   269040
Effective search space used:   269040
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_050462793.1 AKL27_RS10590 (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.25932.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-249  813.1   0.3   4.9e-249  812.9   0.3    1.0  1  lcl|NCBI__GCF_001189915.1:WP_050462793.1  AKL27_RS10590 threonine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001189915.1:WP_050462793.1  AKL27_RS10590 threonine ammonia-lyase, biosynthetic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  812.9   0.3  4.9e-249  4.9e-249       1     499 []       4     507 ..       4     507 .. 0.99

  Alignments for each domain:
  == domain 1  score: 812.9 bits;  conditional E-value: 4.9e-249
                                 TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvi 69 
                                               dyl++il+arvy++a+etple a++lser++nr+++kred+q vfsfklrGaynkma+l++ q  +Gvi
  lcl|NCBI__GCF_001189915.1:WP_050462793.1   4 DYLQKILTARVYDVAIETPLELANTLSERMENRIYFKREDMQSVFSFKLRGAYNKMAHLTPAQLKRGVI 72 
                                               89******************************************************************* PP

                                 TIGR01124  70 aasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekglt 138
                                               +asaGnhaqGvalsa+klG++avivmp+ttp +k++avka+GgevvlhG+++ +a+++al l+++  lt
  lcl|NCBI__GCF_001189915.1:WP_050462793.1  73 CASAGNHAQGVALSAAKLGCRAVIVMPTTTPTVKIEAVKARGGEVVLHGDSFTDAYNHALTLEKKLKLT 141
                                               ********************************************************************* PP

                                 TIGR01124 139 fiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaal 207
                                               f++pfddp viaGqGtv++e+lrq++++++a+fv++GGGGli+G+aa+vk+++p+ik+igv++ ds+a+
  lcl|NCBI__GCF_001189915.1:WP_050462793.1 142 FVHPFDDPYVIAGQGTVGMEILRQHADPIHAIFVAIGGGGLISGIAAYVKAVRPDIKIIGVQTADSDAM 210
                                               ********************************************************************* PP

                                 TIGR01124 208 kqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaG 276
                                               +++l+aG+r++l +vGlf+dG+avk vG+etfr++k y+ddi+ vdtd+vc+aikd+f+dtr+++epaG
  lcl|NCBI__GCF_001189915.1:WP_050462793.1 211 ARSLKAGRRITLPDVGLFSDGTAVKLVGEETFRMAKLYVDDIIIVDTDAVCTAIKDIFQDTRSIVEPAG 279
                                               ********************************************************************* PP

                                 TIGR01124 277 alalaGlkkyva.....kkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsll 340
                                               ala+aG k+y++     kk i+++ l++i++Gan+nfdrlr+v+e a++G+ rea++avtipee+Gs++
  lcl|NCBI__GCF_001189915.1:WP_050462793.1 280 ALAVAGAKAYIEraknsKKPIKNEALITIACGANMNFDRLRFVAEMADVGQSREAVFAVTIPEEHGSFK 348
                                               ***********72222245699*********************************************** PP

                                 TIGR01124 341 kfvevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylv 409
                                               +f+e +G r++tefnyr++d+++ahifvG+q+ +++e +++++++e++g++++dlt+delak+h+r+lv
  lcl|NCBI__GCF_001189915.1:WP_050462793.1 349 RFCETVGPRNVTEFNYRISDEKSAHIFVGIQTDSQDESAKIARNFEKQGFATLDLTHDELAKVHIRHLV 417
                                               ********************************************************************* PP

                                 TIGR01124 410 GGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqf 478
                                               GG++  ++ne ly+fefperpGal++fl+ ++++wnislfhyrn G+d Gr+lvgl+vp++e+++f  f
  lcl|NCBI__GCF_001189915.1:WP_050462793.1 418 GGKSLLAQNELLYRFEFPERPGALMRFLNAMNPNWNISLFHYRNQGSDVGRILVGLQVPKKEMKTFRLF 486
                                               ********************************************************************* PP

                                 TIGR01124 479 laelgyryedetenpayrlfl 499
                                               l++lgyr +de++np y+lfl
  lcl|NCBI__GCF_001189915.1:WP_050462793.1 487 LSNLGYRHWDESKNPLYKLFL 507
                                               ********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (508 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: 00:00:00.03
# Mc/sec: 7.45
//
[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