Alignments for a candidate for tdcB in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Dyella japonica UNC79MFTsu3.2

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate N515DRAFT_0565 N515DRAFT_0565 threonine dehydratase

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0565
          Length = 523

 Score =  532 bits (1371), Expect = e-155
 Identities = 276/503 (54%), Positives = 357/503 (70%), Gaps = 6/503 (1%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           + LR  L A VYE A+ T L+    LS+RL   +L+KRED+QPV SFKLRGAY  M GL 
Sbjct: 17  DLLRRTLAARVYEVARETALESAPLLSARLGQRVLLKREDQQPVFSFKLRGAYNKMVGLD 76

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGG---EVLLH 131
             Q+A GVI ASAGNHAQGVA ++A+LG++A+IVMP     +K+DAVR  GG   EV+L 
Sbjct: 77  AAQRARGVIAASAGNHAQGVALAAAKLGLRAVIVMPVTAPQVKIDAVRRLGGAWVEVVLA 136

Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGG 190
           G ++ +A+A+A  L QQ G+T+V PFD P VIAGQ T+ +E+L+Q    L  VFVPVGGG
Sbjct: 137 GDSYSDAQAEAARLEQQHGYTFVHPFDDPAVIAGQATVGMEILRQHPGPLHAVFVPVGGG 196

Query: 191 GLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250
           GL AGVA  IK L P++KVI V+  DS  +  +L+ G  V L  VGLFA+G AVKR+G E
Sbjct: 197 GLLAGVAAYIKALRPEVKVIGVQTVDSDAMAQSLEQGERVTLDEVGLFADGTAVKRVGAE 256

Query: 251 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERL 310
           TF LCQ ++D ++ VD+DAICAA++D+F++ R+V EPSGALALAG+K+Y A H +    L
Sbjct: 257 TFALCQRHVDAMLRVDTDAICAAIRDVFQETRSVPEPSGALALAGLKQYAATHQLDDATL 316

Query: 311 AHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYR 370
             I+SGAN+NF  LR+V+ER E+GEQREA+ AVTIPEE+GSF +FC  LG RS+TEFNYR
Sbjct: 317 VAIVSGANLNFDRLRFVAERAEVGEQREAVFAVTIPEERGSFRRFCATLGQRSITEFNYR 376

Query: 371 FADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHP 430
             DA +A IFVG+++ R  +ER+ +       G+ V+DL+DDE+AKLH+R+M+GGR    
Sbjct: 377 IGDAASAHIFVGIQI-RQRDEREALTAAFAAEGFGVLDLTDDELAKLHLRHMIGGRSPLA 435

Query: 431 LQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFE 489
             E LY FEFPE PGAL RFL  +   WNISLFHYR+HG DYGR+L   ++       FE
Sbjct: 436 HDELLYRFEFPERPGALTRFLGHMHPDWNISLFHYRNHGADYGRILVGIQVPAGERAMFE 495

Query: 490 TRLNELGYDCHDETNNPAFRFFL 512
             L +LGY C DE+ NPA+R  L
Sbjct: 496 QFLAQLGYPCRDESGNPAYRLLL 518


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: 737
Number of extensions: 40
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: 523
Length adjustment: 35
Effective length of query: 479
Effective length of database: 488
Effective search space:   233752
Effective search space used:   233752
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 N515DRAFT_0565 N515DRAFT_0565 (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.17257.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.4e-250  815.6   0.3   8.5e-250  815.4   0.3    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565  N515DRAFT_0565 threonine dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0565  N515DRAFT_0565 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  815.4   0.3  8.5e-250  8.5e-250       1     499 []      17     518 ..      17     518 .. 0.99

  Alignments for each domain:
  == domain 1  score: 815.4 bits;  conditional E-value: 8.5e-250
                                    TIGR01124   1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkak 66 
                                                  d+lr+ l arvye+a et le a  ls+rl+ rvllkred+qpvfsfklrGaynkm  l a q+a+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565  17 DLLRRTLAARVYEVARETALESAPLLSARLGQRVLLKREDQQPVFSFKLRGAYNKMVGLDAAQRAR 82 
                                                  789*************************************************************** PP

                                    TIGR01124  67 GviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakal 129
                                                  GviaasaGnhaqGval+a+klG++avivmp t+p++k+dav+  Gg   evvl G++y++a+a+a 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565  83 GVIAASAGNHAQGVALAAAKLGLRAVIVMPVTAPQVKIDAVRRLGGawvEVVLAGDSYSDAQAEAA 148
                                                  ********************************************986668**************** PP

                                    TIGR01124 130 elaqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeik 195
                                                  +l+q++g tf++pfddp viaGq tv++e+lrq+  +l+avfvpvGGGGl+aGvaa++k+l+pe+k
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 149 RLEQQHGYTFVHPFDDPAVIAGQATVGMEILRQHPGPLHAVFVPVGGGGLLAGVAAYIKALRPEVK 214
                                                  ****************************************************************** PP

                                    TIGR01124 196 vigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaai 261
                                                  vigv++ ds+a++q+le+Gerv+ld+vGlfadG+avk+vG+etf+lc++++d +++vdtd++caai
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 215 VIGVQTVDSDAMAQSLEQGERVTLDEVGLFADGTAVKRVGAETFALCQRHVDAMLRVDTDAICAAI 280
                                                  ****************************************************************** PP

                                    TIGR01124 262 kdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreal 327
                                                  +dvf++tr+v ep+GalalaGlk+y+a+++++d tlvai+sGanlnfdrlr+v+erae+Geqrea+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 281 RDVFQETRSVPEPSGALALAGLKQYAATHQLDDATLVAIVSGANLNFDRLRFVAERAEVGEQREAV 346
                                                  ****************************************************************** PP

                                    TIGR01124 328 lavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvv 393
                                                  +avtipee+Gs+++f+  lG+r+itefnyr++d+ +ahifvG+q+++++er+ l+a +  +g+ v+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 347 FAVTIPEERGSFRRFCATLGQRSITEFNYRIGDAASAHIFVGIQIRQRDEREALTAAFAAEGFGVL 412
                                                  ****************************************************************** PP

                                    TIGR01124 394 dltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyG 459
                                                  dltddelaklh+r+++GGr+  +++e ly+fefperpGal++fl +++++wnislfhyrnhGadyG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 413 DLTDDELAKLHLRHMIGGRSPLAHDELLYRFEFPERPGALTRFLGHMHPDWNISLFHYRNHGADYG 478
                                                  ****************************************************************** PP

                                    TIGR01124 460 rvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499
                                                  r+lvg++vp  e + feqfla+lgy + de+ npayrl+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 479 RILVGIQVPAGERAMFEQFLAQLGYPCRDESGNPAYRLLL 518
                                                  *************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (523 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: 9.78
//
[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:

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

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 catabolism of small carbon sources