GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2C3

Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate AO356_27710 AO356_27710 threonine dehydratase

Query= curated2:P37946
         (422 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27710
          Length = 333

 Score =  230 bits (586), Expect = 5e-65
 Identities = 133/331 (40%), Positives = 193/331 (58%), Gaps = 9/331 (2%)

Query: 7   ENSLIQ--VKHILKAHQNVKDVVIHTPLQRNDRLSERYECNIYLKREDLQVVRSFKLRGA 64
           E +L++  VK IL A   V ++ + TPLQ    LSE     I LKREDLQ   SFK+RGA
Sbjct: 7   EQTLLEHYVKKILAAP--VYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGA 64

Query: 65  YHKMKQLSSEQTENGVVCASAGNHAQGVAFSCKHLGIHGKIFMPSTTPRQKVSQVELFGK 124
           Y+K+  L+ EQ   GV+ ASAGNHAQGVA + + LGI  +I MP TTP+ KV  V   G 
Sbjct: 65  YNKLVHLTPEQRARGVITASAGNHAQGVALAARELGISARIVMPVTTPQLKVLGVRNRGA 124

Query: 125 GFIDIILTGDTFDDVYKSAAECCEAESRTFIHPFDDPDVMAGQGTLAVEILNDIDTEPHF 184
              + +L GD+F      A E  E   R F+ PFDDPDV+AGQGT+A+EIL         
Sbjct: 125 ---EALLHGDSFPFALAHALELAEQTGREFVSPFDDPDVIAGQGTVAMEILRQHPGRLDA 181

Query: 185 LFASVGGGGLLSGVGTYLKNVSPDTKVIAVEPAGAASYFESNKAGHVVTLDKIDKFVDGA 244
           +F  VGGGGL++G+  Y+K + P+ ++I VE   +A    +  AG  VTL ++  F DG 
Sbjct: 182 IFVPVGGGGLIAGIAAYVKYLRPEVRIIGVESQHSACLQAALAAGERVTLPEVGTFADGV 241

Query: 245 AVKKIGEETFRTLETVVDDILLVPEGKVCTSILELYNECAVVAEPAGALSVAALDLY--K 302
           AV +IG          VD+++ V   ++C +I ++Y++   + EP+GAL+VA +  Y   
Sbjct: 242 AVAQIGAHGLDICRFCVDEVMTVSNDQLCAAIKDIYDDTRSITEPSGALAVAGIKQYVAH 301

Query: 303 DQIKGKNVVCVVSGGNNDIGRMQEMKERSLI 333
              +G+ +V + SG N +   ++ + ER+ +
Sbjct: 302 TGARGETLVAIDSGANINFDSLRHVAERAAV 332


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: 329
Number of extensions: 15
Number of successful extensions: 3
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: 333
Length adjustment: 30
Effective length of query: 392
Effective length of database: 303
Effective search space:   118776
Effective search space used:   118776
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 AO356_27710 AO356_27710 (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.6939.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   5.4e-152  492.8   1.0   6.2e-152  492.6   1.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710  AO356_27710 threonine dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710  AO356_27710 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.6   1.0  6.2e-152  6.2e-152       2     321 ..      14     333 .]      13     333 .] 1.00

  Alignments for each domain:
  == domain 1  score: 492.6 bits;  conditional E-value: 6.2e-152
                                       TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqk 64 
                                                     y+++il a vye av tpl+ a  lse l+nr+llkredlqp fsfk+rGaynk+ +l++eq+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710  14 YVKKILAAPVYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVHLTPEQR 76 
                                                     899************************************************************ PP

                                       TIGR01124  65 akGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakak 127
                                                     a+Gvi+asaGnhaqGval+a++lG++a ivmp ttp++kv  v+++G+e +lhG+++  a a+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710  77 ARGVITASAGNHAQGVALAARELGISARIVMPVTTPQLKVLGVRNRGAEALLHGDSFPFALAH 139
                                                     *************************************************************** PP

                                       TIGR01124 128 alelaqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkql 190
                                                     alela++ g  f++pfddp+viaGqGtva+e+lrq+   lda+fvpvGGGGliaG+aa+vk l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 140 ALELAEQTGREFVSPFDDPDVIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLIAGIAAYVKYL 202
                                                     *************************************************************** PP

                                       TIGR01124 191 lpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvd 253
                                                     +pe+++igve++ sa+l++al+aGerv+l +vG fadGvav ++G++ +++c+  +d++++v 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 203 RPEVRIIGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVDEVMTVS 265
                                                     *************************************************************** PP

                                       TIGR01124 254 tdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvse 316
                                                      d++caaikd+++dtr+++ep+Gala+aG+k+yva+ g++++tlvai sGan+nfd+lr+v+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 266 NDQLCAAIKDIYDDTRSITEPSGALAVAGIKQYVAHTGARGETLVAIDSGANINFDSLRHVAE 328
                                                     *************************************************************** PP

                                       TIGR01124 317 raelG 321
                                                     ra +G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27710 329 RAAVG 333
                                                     **998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (333 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: 7.89
//
[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