GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Herbaspirillum seropedicae SmR1

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate HSERO_RS19510 HSERO_RS19510 threonine dehydratase

Query= SwissProt::A0FKE6
         (606 letters)



>FitnessBrowser__HerbieS:HSERO_RS19510
          Length = 508

 Score =  531 bits (1368), Expect = e-155
 Identities = 276/505 (54%), Positives = 358/505 (70%), Gaps = 7/505 (1%)

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

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

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

Query: 287 AGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEETYR 346
           AG+A+Y+K V PDIKIIGV+  D++A+A SL  G+RV L  VG F+DG AVK+VGEET+R
Sbjct: 184 AGVASYVKAVRPDIKIIGVQTTDSDAMARSLKAGRRVALPDVGLFSDGTAVKLVGEETFR 243

Query: 347 LCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAY-----CKYYGLKGE 401
           + +EL+D V++V  DA+C +IKD+F++ RSI+EPAGALA+AGA+AY          +KGE
Sbjct: 244 IAKELVDEVIIVDTDAVCTAIKDIFQDTRSIVEPAGALAVAGAKAYVERAKASKKPIKGE 303

Query: 402 NVVAITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFK 461
           +++ I  GANMNFDRLR V E+AD G  REAV A  +PE+ GSF++F E VGP N+TEF 
Sbjct: 304 SLITIACGANMNFDRLRFVAEMADAGEAREAVFAVTIPEERGSFRRFCETVGPRNVTEFN 363

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

Query: 522 V-HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVE 580
           +  +ELL RF FPE+PGALMKFL + +P WNISLFHYR QG     +L+G+QVP  E+ E
Sbjct: 423 LTGDELLYRFEFPERPGALMKFLSSMNPGWNISLFHYRNQGGDVGRILIGLQVPKKEMKE 482

Query: 581 FEGRADSLGYEYAMESLNEAYQLIM 605
           F      LGY +  ES N  Y+L +
Sbjct: 483 FRAFLAQLGYRHWDESKNPLYKLFL 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: 703
Number of extensions: 32
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 HSERO_RS19510 HSERO_RS19510 (threonine dehydratase)
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.11464.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     2e-249  814.2   0.3   2.3e-249  814.0   0.3    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS19510  HSERO_RS19510 threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS19510  HSERO_RS19510 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.0   0.3  2.3e-249  2.3e-249       1     499 []       4     507 ..       4     507 .. 0.99

  Alignments for each domain:
  == domain 1  score: 814.0 bits;  conditional E-value: 2.3e-249
                                  TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGv 68 
                                                dyl++il+arvy++a+etple a++ls+r++nr+++kred+q vfsfklrGaynkma+l++ q  +Gv
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510   4 DYLKKILTARVYDVAQETPLELANTLSQRIDNRIYFKREDMQSVFSFKLRGAYNKMAHLTPAQLKRGV 71 
                                                89****************************************************************** PP

                                  TIGR01124  69 iaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekg 136
                                                i+asaGnhaqGvalsa++lG++avivmp+ttp++k+davka+Ggevvl G+++ +a+++al l++++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510  72 ICASAGNHAQGVALSAARLGCRAVIVMPTTTPQVKIDAVKARGGEVVLFGDSFTDAYEHALTLEKKQK 139
                                                ******************************************************************** PP

                                  TIGR01124 137 ltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaeds 204
                                                ltf++pfddp viaGqGtv++e+lrq+ ++++a+fv++GGGGliaGva++vk+++p+ik+igv+++ds
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 140 LTFVHPFDDPYVIAGQGTVGMEILRQHPDPIHAIFVAIGGGGLIAGVASYVKAVRPDIKIIGVQTTDS 207
                                                ******************************************************************** PP

                                  TIGR01124 205 aalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravl 272
                                                +a++++l+aG+rv l +vGlf+dG+avk vG+etfr++ke++d+++ vdtd+vc+aikd+f+dtr+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 208 DAMARSLKAGRRVALPDVGLFSDGTAVKLVGEETFRIAKELVDEVIIVDTDAVCTAIKDIFQDTRSIV 275
                                                ******************************************************************** PP

                                  TIGR01124 273 epaGalalaGlkkyvak.....kgiedktlvailsGanlnfdrlryvseraelGeqreallavtipee 335
                                                epaGala+aG k+yv++     k i++++l++i++Gan+nfdrlr+v+e a+ Ge rea++avtipee
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 276 EPAGALAVAGAKAYVERakaskKPIKGESLITIACGANMNFDRLRFVAEMADAGEAREAVFAVTIPEE 343
                                                **************97522222568999**************************************** PP

                                  TIGR01124 336 kGsllkfvevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelakl 403
                                                +Gs+++f+e +G r++tefnyr++d+++ah+fvG+q++  +e+ ++++++e+ag+ v+dlt+delak+
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 344 RGSFRRFCETVGPRNVTEFNYRISDAKAAHVFVGIQVSAADEAGKIARNFEKAGFGVLDLTHDELAKV 411
                                                ******************************************************************** PP

                                  TIGR01124 404 hvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdee 471
                                                h+r+lvGG+++ + +e ly+fefperpGal+kfl+++++ wnislfhyrn G+d Gr+l+gl+vp++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 412 HIRHLVGGKSDLTGDELLYRFEFPERPGALMKFLSSMNPGWNISLFHYRNQGGDVGRILIGLQVPKKE 479
                                                ******************************************************************** PP

                                  TIGR01124 472 aeefeqflaelgyryedetenpayrlfl 499
                                                ++ef  fla+lgyr +de++np y+lfl
  lcl|FitnessBrowser__HerbieS:HSERO_RS19510 480 MKEFRAFLAQLGYRHWDESKNPLYKLFL 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.28
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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