GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Echinicola vietnamensis KMM 6221, DSM 17526

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Echvi_3354 Echvi_3354 threonine dehydratase

Query= BRENDA::Q04513
         (436 letters)



>FitnessBrowser__Cola:Echvi_3354
          Length = 416

 Score =  378 bits (971), Expect = e-109
 Identities = 186/392 (47%), Positives = 262/392 (66%), Gaps = 7/392 (1%)

Query: 29  AQARISSVIAPTPLQYCPRLSEETGAEIYLKREDLQDVRSYKIRGALNSGAQLTQEQRDA 88
           A   +  V+ PTPLQ+  +LSEE G  +YLKREDLQ VRSYKIRGA +  + L++E++  
Sbjct: 12  ASEALQEVLHPTPLQFNEQLSEEYGCRVYLKREDLQAVRSYKIRGAYHKISSLSEEEKSR 71

Query: 89  GIVAASAGNHAQGVAYVCKSLGVQGRIYVPVQTPKQKRDRIMVHGGEFVSLVVTGNNFDE 148
           G+V ASAGNHAQGVA+ CK LG++G I++P  T  QK +R+ + G E V +V++G+ +D+
Sbjct: 72  GVVCASAGNHAQGVAFACKKLGIKGTIFIPSTTSAQKINRMKLFGKEMVEIVLSGDTYDD 131

Query: 149 ASAAAHEDAERTGATLIEPFDARNTVIGQGTVAAEILSQLTSMGKSADHVMVPVGGGGLL 208
           A   A E  E  GA  + PFD    + GQGT+A EIL          D++ +P+GGGG+ 
Sbjct: 132 AYQTAAEYCEERGAVFVHPFDDPKVIEGQGTIAKEILDDAEF---PVDYLFLPIGGGGMA 188

Query: 209 AGVVSYMADMAPRTAIVGIEPAGAASMQAALHNGGPITLETVDPFVDGAAVKRVGDLNYT 268
           AGV +Y    +P T ++G EP GA SM  ++ N     L+ +D FVDGAAVK+VG++ + 
Sbjct: 189 AGVSTYFEQSSPETKLIGTEPKGAPSMLTSIQNLKNTVLDEIDGFVDGAAVKKVGNITFE 248

Query: 269 IVEKNQGRVHMMSATEGAVCTEMLDLYQNEGIIAEPAGALSIAGLK--EMSFAPGSVVVC 326
           I  K+     M+   EG +CT +L+LY NEGI+ EPAGA+++A L   +     G  VVC
Sbjct: 249 ICRKSLD--EMLLVPEGRICTTILNLYNNEGIVVEPAGAMTLAALSLYDKEKLKGKNVVC 306

Query: 327 IISGGNNDVLRYAEIAERSLVHRGLKHYFLVNFPQKPGQLRHFLEDILGPDDDITLFEYL 386
           ++SGGNND++R AEI ERSL++ GLKHYF+V FPQ+PG L+ F+  ILGPDDDI  F++ 
Sbjct: 307 VVSGGNNDIMRTAEIKERSLLYEGLKHYFMVQFPQRPGALKDFVSKILGPDDDIAYFQFT 366

Query: 387 KRNNRETGTALVGIHLSEASGLDSLLERMEES 418
           K+NNRE G A+VGI L +   L  + +R++E+
Sbjct: 367 KKNNRENGPAVVGIELKDPQNLPGIFDRLKEN 398


Lambda     K      H
   0.316    0.133    0.373 

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: 449
Number of extensions: 20
Number of successful extensions: 4
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: 436
Length of database: 416
Length adjustment: 32
Effective length of query: 404
Effective length of database: 384
Effective search space:   155136
Effective search space used:   155136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate Echvi_3354 Echvi_3354 (threonine dehydratase)
to HMM TIGR02079 (ilvA: threonine dehydratase (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/TIGR02079.hmm
# target sequence database:        /tmp/gapView.8503.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02079  [M=410]
Accession:   TIGR02079
Description: THD1: threonine dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.3e-188  612.0   0.0   2.6e-188  611.9   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3354  Echvi_3354 threonine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3354  Echvi_3354 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.9   0.0  2.6e-188  2.6e-188       3     409 ..       9     415 ..       7     416 .] 0.99

  Alignments for each domain:
  == domain 1  score: 611.9 bits;  conditional E-value: 2.6e-188
                            TIGR02079   3 iekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynklkqlsdeelekgvvcasaGnha 76 
                                          i +a + l+ev+++tPlq ne+lse+y++ +ylkredlq vrsyk+rGay+k+++ls+ee+++gvvcasaGnha
  lcl|FitnessBrowser__Cola:Echvi_3354   9 IIEASEALQEVLHPTPLQFNEQLSEEYGCRVYLKREDLQAVRSYKIRGAYHKISSLSEEEKSRGVVCASAGNHA 82 
                                          889*********************************************************************** PP

                            TIGR02079  77 qGvayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekegktlipPfddkdi 150
                                          qGva+ac+klg+kgt+f+P tt  qk++++klfG+e++e++l Gdt+d+a++ a + +e++g+ +++Pfdd+++
  lcl|FitnessBrowser__Cola:Echvi_3354  83 QGVAFACKKLGIKGTIFIPSTTSAQKINRMKLFGKEMVEIVLSGDTYDDAYQTAAEYCEERGAVFVHPFDDPKV 156
                                          ************************************************************************** PP

                            TIGR02079 151 ieGqgtvaveileqleeekidlvlvpvGGGGlisGvtsylkekskktkiigvePeGapslkaslkagevvtldk 224
                                          ieGqgt+a eil++ e + +d++++p+GGGG+++Gv++y+++ s++tk+ig eP+Gaps+ +s+++ +   ld+
  lcl|FitnessBrowser__Cola:Echvi_3354 157 IEGQGTIAKEILDDAEFP-VDYLFLPIGGGGMAAGVSTYFEQSSPETKLIGTEPKGAPSMLTSIQNLKNTVLDE 229
                                          ***************998.******************************************************* PP

                            TIGR02079 225 idkfvdGaavkrvGdlnfkalkkvvdevtlveegavcstildlynkegivaePaGalsiaaleels.eeikgkt 297
                                          id fvdGaavk+vG+++f++++k +de+ lv+eg++c+til+lyn+egiv+ePaGa+++aal  ++ e++kgk+
  lcl|FitnessBrowser__Cola:Echvi_3354 230 IDGFVDGAAVKKVGNITFEICRKSLDEMLLVPEGRICTTILNLYNNEGIVVEPAGAMTLAALSLYDkEKLKGKN 303
                                          *****************************************************************9799***** PP

                            TIGR02079 298 vvcvvsGgnndierleeikersllyeGlkhyflvkfpqraGalreflndvlGPndditkfeyvkksnretGevl 371
                                          vvcvvsGgnndi r+ eikersllyeGlkhyf+v+fpqr+Gal++f++++lGP+ddi++f+++kk+nre+G+++
  lcl|FitnessBrowser__Cola:Echvi_3354 304 VVCVVSGGNNDIMRTAEIKERSLLYEGLKHYFMVQFPQRPGALKDFVSKILGPDDDIAYFQFTKKNNRENGPAV 377
                                          ************************************************************************** PP

                            TIGR02079 372 iGielsdkedfeGllerlkaadieyeainenetlyell 409
                                          +Giel+d +++ G+++rlk    +y+++nen +l +ll
  lcl|FitnessBrowser__Cola:Echvi_3354 378 VGIELKDPQNLPGIFDRLKENRFKYNYLNENLDLLTLL 415
                                          *********************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (410 nodes)
Target sequences:                          1  (416 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.26
//
[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