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

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.17667.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: 11.44
//
[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