Alignments for a candidate for tdcB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Pseudomonas simiae WCS417

Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate GFF2483 PS417_12665 hypothetical protein

Query= curated2:P37946
         (422 letters)



>FitnessBrowser__WCS417:GFF2483
          Length = 340

 Score =  235 bits (599), Expect = 2e-66
 Identities = 132/320 (41%), Positives = 188/320 (58%), Gaps = 7/320 (2%)

Query: 13  VKHILKAHQNVKDVVIHTPLQRNDRLSERYECNIYLKREDLQVVRSFKLRGAYHKMKQLS 72
           VK IL A   V D+ + TPLQ    LS      + LKREDLQ   SFK+RGAY+K+ QL+
Sbjct: 19  VKKILAAP--VYDLAVRTPLQAAPALSALLGNQVLLKREDLQPTFSFKIRGAYNKLVQLT 76

Query: 73  SEQTENGVVCASAGNHAQGVAFSCKHLGIHGKIFMPSTTPRQKVSQVELFGKGFIDIILT 132
            EQ   GVV ASAGNHAQGVA + + LGI  +I MP++TP  KV  V   G      +L 
Sbjct: 77  PEQRARGVVTASAGNHAQGVALAARELGIKARIVMPASTPELKVLGVRSRGA---QAVLH 133

Query: 133 GDTFDDVYKSAAECCEAESRTFIHPFDDPDVMAGQGTLAVEILNDIDTEPHFLFASVGGG 192
           G +F      A +  E+   TF+ PFDDPDV+AGQGT+A+EIL         +F  VGGG
Sbjct: 134 GASFPFALAYALQLAESSGCTFVSPFDDPDVIAGQGTVAMEILRQQQGPLDAIFVPVGGG 193

Query: 193 GLLSGVGTYLKNVSPDTKVIAVEPAGAASYFESNKAGHVVTLDKIDKFVDGAAVKKIGEE 252
           GL++GV  Y+K + PD ++I VEP G++    + +AG  V L  +D F DG AV ++G  
Sbjct: 194 GLIAGVAAYVKYLRPDVRIIGVEPEGSSCLLAALRAGERVVLPSVDGFADGTAVAQVGAH 253

Query: 253 TFRTLETVVDDILLVPEGKVCTSILELYNECAVVAEPAGALSVAALDLY--KDQIKGKNV 310
            F      VD+++ V    +C++I  +Y++   + EP+GAL+VA +  Y     ++G+ +
Sbjct: 254 GFEICRDWVDEVITVSNDALCSAIKLIYDDTRSITEPSGALAVAGIRQYVATHNLRGQTL 313

Query: 311 VCVVSGGNNDIGRMQEMKER 330
           V + SG N +   ++ + ER
Sbjct: 314 VAINSGANINFDSLRHVAER 333


Lambda     K      H
   0.318    0.137    0.397 

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: 330
Number of extensions: 9
Number of successful extensions: 2
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: 422
Length of database: 340
Length adjustment: 30
Effective length of query: 392
Effective length of database: 310
Effective search space:   121520
Effective search space used:   121520
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: 50 (23.9 bits)

Align candidate GFF2483 PS417_12665 (hypothetical protein)
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.4349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.7e-150  486.7   0.7   4.5e-150  486.4   0.7    1.0  1  lcl|FitnessBrowser__WCS417:GFF2483  PS417_12665 hypothetical protein


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2483  PS417_12665 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.4   0.7  4.5e-150  4.5e-150       2     318 ..      18     334 ..      17     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: 486.4 bits;  conditional E-value: 4.5e-150
                           TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnh 76 
                                         y+++il a vy+ av tpl+ a  ls+ l+n+vllkredlqp fsfk+rGaynk+ ql++eq+a+Gv++asaGnh
  lcl|FitnessBrowser__WCS417:GFF2483  18 YVKKILAAPVYDLAVRTPLQAAPALSALLGNQVLLKREDLQPTFSFKIRGAYNKLVQLTPEQRARGVVTASAGNH 92 
                                         899************************************************************************ PP

                           TIGR01124  77 aqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaG 151
                                         aqGval+a++lG+ka ivmp++tpe+kv  v+++G++ vlhG+++  a a+al+la+  g tf++pfddp+viaG
  lcl|FitnessBrowser__WCS417:GFF2483  93 AQGVALAARELGIKARIVMPASTPELKVLGVRSRGAQAVLHGASFPFALAYALQLAESSGCTFVSPFDDPDVIAG 167
                                         *************************************************************************** PP

                           TIGR01124 152 qGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfa 226
                                         qGtva+e+lrq++ +lda+fvpvGGGGliaGvaa+vk l+p++++igve+e s++l +al aGerv l +v  fa
  lcl|FitnessBrowser__WCS417:GFF2483 168 QGTVAMEILRQQQGPLDAIFVPVGGGGLIAGVAAYVKYLRPDVRIIGVEPEGSSCLLAALRAGERVVLPSVDGFA 242
                                         *************************************************************************** PP

                           TIGR01124 227 dGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvail 301
                                         dG+av +vG++ f++c++++d++++v  d++c+aik +++dtr+++ep+Gala+aG+++yva+++++++tlvai+
  lcl|FitnessBrowser__WCS417:GFF2483 243 DGTAVAQVGAHGFEICRDWVDEVITVSNDALCSAIKLIYDDTRSITEPSGALAVAGIRQYVATHNLRGQTLVAIN 317
                                         *************************************************************************** PP

                           TIGR01124 302 sGanlnfdrlryvsera 318
                                         sGan+nfd+lr+v+er 
  lcl|FitnessBrowser__WCS417:GFF2483 318 SGANINFDSLRHVAERV 334
                                         ****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (340 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.60
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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