GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Burkholderia phytofirmans PsJN

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate BPHYT_RS03145 BPHYT_RS03145 threonine dehydratase

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__BFirm:BPHYT_RS03145
          Length = 507

 Score =  525 bits (1352), Expect = e-153
 Identities = 268/504 (53%), Positives = 359/504 (71%), Gaps = 6/504 (1%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +YL+  L A VY+ A+ T L++   LS+RL N + +KRED QPV SFK+RGAY  MA ++
Sbjct: 5   DYLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHIS 64

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGG---EVLLH 131
            E    GVITASAGNHAQGVA S+AR+GVKA+IV+P  T  +KVDAVR  GG   EV+  
Sbjct: 65  AEALERGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQF 124

Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGG 190
           G ++ +A   A++L +++  T+V PFD P VIAGQGT+A+E+L Q    +  +FVP+GGG
Sbjct: 125 GESYSDAYEHAVKLQKERDLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGG 184

Query: 191 GLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250
           GLAAGVA  +K + P+IKVI V+ +DS  + A+L AG  V L  VGLF++G AVK +G+E
Sbjct: 185 GLAAGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEE 244

Query: 251 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERL 310
           TFRLC EYLDD++ V++DA+CAA+KD+F+D R+V EP+G+LA+AG K+Y     I  + L
Sbjct: 245 TFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQYAEREGIENQTL 304

Query: 311 AHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYR 370
             I SGAN+NF  +R+V+ER E+GE REA+ AVTIPEE+GSF +FC+L+G RSVTEFNYR
Sbjct: 305 IAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSVTEFNYR 364

Query: 371 FADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHP 430
            ADA +A IFVGV++ R   E  +I       G++ VDL+ DE++K H+RYMVGGR    
Sbjct: 365 IADANSAHIFVGVQI-RNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLA 423

Query: 431 LQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPD-FE 489
             ERL+ FEFPE PGAL++FL+++   WNISLFHYR+ G DY  +L   ++ D E + F 
Sbjct: 424 HDERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFN 483

Query: 490 TRLNELGYDCHDETNNPAFRFFLA 513
             L  LGY   +ET NP +R FLA
Sbjct: 484 KFLATLGYPNWEETQNPVYRLFLA 507


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: 650
Number of extensions: 27
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: 507
Length adjustment: 35
Effective length of query: 479
Effective length of database: 472
Effective search space:   226088
Effective search space used:   226088
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 BPHYT_RS03145 BPHYT_RS03145 (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.carbon/TIGR01124.hmm
# target sequence database:        /tmp/gapView.5377.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.8e-251  820.9   0.4     2e-251  820.8   0.4    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS03145  BPHYT_RS03145 threonine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS03145  BPHYT_RS03145 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.8   0.4    2e-251    2e-251       1     499 []       5     506 ..       5     506 .. 1.00

  Alignments for each domain:
  == domain 1  score: 820.8 bits;  conditional E-value: 2e-251
                                TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 
                                              dyl++ l+arvy++a et le+a +ls+rl+n v+lkred+qpvfsfk+rGaynkma++sae+  +Gvi+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145   5 DYLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHISAEALERGVIT 74 
                                              89******************************************************************** PP

                                TIGR01124  71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakalelaqekgl 137
                                              asaGnhaqGvalsa+++Gvka+iv+p ttp++kvdav+a+Gg   evv  Ge+y++a+++a++l++e++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145  75 ASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGptvEVVQFGESYSDAYEHAVKLQKERDL 144
                                              *****************************************877789*********************** PP

                                TIGR01124 138 tfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaal 207
                                              tf++pfddp viaGqGtva+e+l+q++ +++a+fvp+GGGGl+aGvaa+vk ++peikvigv+++ds+a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 145 TFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGGLAAGVAAYVKSVRPEIKVIGVQTDDSCAM 214
                                              ********************************************************************** PP

                                TIGR01124 208 kqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277
                                              +++l+aGerv+l++vGlf+dG+avk vG+etfrlc eyldd++lv+td++caaikdvf+dtr+vlepaG+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 215 AASLKAGERVTLNEVGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGS 284
                                              ********************************************************************** PP

                                TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlG 347
                                              la+aG k+y++++gie++tl+ai+sGan+nfdr+r+v+erae+Ge rea++avtipee+Gs+++f+e++G
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 285 LAVAGAKQYAEREGIENQTLIAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVG 354
                                              ********************************************************************** PP

                                TIGR01124 348 eraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakve 417
                                               r++tefnyr+ad+++ahifvGvq+++++e ++++  +e +g+++vdlt del+k h+ry+vGGr+  ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 355 TRSVTEFNYRIADANSAHIFVGVQIRNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLAH 424
                                              ********************************************************************** PP

                                TIGR01124 418 nerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyrye 487
                                              +erl++fefperpGal+kfl+++ ++wnislfhyrn Gady  +lvg++vpd+e+e+f++fla+lgy  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 425 DERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFNKFLATLGYPNW 494
                                              ********************************************************************** PP

                                TIGR01124 488 detenpayrlfl 499
                                              +et+np+yrlfl
  lcl|FitnessBrowser__BFirm:BPHYT_RS03145 495 EETQNPVYRLFL 506
                                              ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (507 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: 7.57
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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