Alignments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2E3

Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate AO353_25960 AO353_25960 threonine dehydratase

Query= curated2:P37946
         (422 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25960
          Length = 336

 Score =  234 bits (598), Expect = 2e-66
 Identities = 133/323 (41%), Positives = 191/323 (59%), Gaps = 7/323 (2%)

Query: 13  VKHILKAHQNVKDVVIHTPLQRNDRLSERYECNIYLKREDLQVVRSFKLRGAYHKMKQLS 72
           VK IL A   V ++ + TPLQ    LSE     I LKREDLQ   SFK+RGAY+K+ QLS
Sbjct: 19  VKKILAAP--VYELAVRTPLQVAPALSEVLGNQILLKREDLQPTFSFKIRGAYNKLAQLS 76

Query: 73  SEQTENGVVCASAGNHAQGVAFSCKHLGIHGKIFMPSTTPRQKVSQVELFGKGFIDIILT 132
           +EQ   GV+ ASAGNHAQGVA + + LGI   I MP++TP  KV  V   G    + +L 
Sbjct: 77  AEQKARGVITASAGNHAQGVALAARELGIEASIVMPTSTPELKVIGVRSRGA---NAVLH 133

Query: 133 GDTFDDVYKSAAECCEAESRTFIHPFDDPDVMAGQGTLAVEILNDIDTEPHFLFASVGGG 192
           G++F    + A        RTF+ PFDDPDV+AGQGT+A+EIL         +F  VGGG
Sbjct: 134 GESFPFALEYALNLARQTGRTFVSPFDDPDVIAGQGTVAMEILRQHQGALDAIFVPVGGG 193

Query: 193 GLLSGVGTYLKNVSPDTKVIAVEPAGAASYFESNKAGHVVTLDKIDKFVDGAAVKKIGEE 252
           GL++G+  Y+K + P+ +++ VE   +A    +  AG  V L K+  F DG AV +IGE 
Sbjct: 194 GLIAGIAAYVKYLRPEIRIVGVESEHSACLQAAMLAGERVVLPKVGTFADGVAVAQIGEY 253

Query: 253 TFRTLETVVDDILLVPEGKVCTSILELYNECAVVAEPAGALSVAALDLYKDQ--IKGKNV 310
            F      VD++L V   ++C +I  +Y++   + EP+GAL+VA +  Y  Q  ++G+ +
Sbjct: 254 GFEICRHHVDEVLTVSNDELCAAIKNIYDDTRSITEPSGALAVAGIKKYVAQTGVRGQTL 313

Query: 311 VCVVSGGNNDIGRMQEMKERSLI 333
           V + SG N +   ++ + ER+ +
Sbjct: 314 VAIDSGANINFDSLRHVAERAAL 336


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: 310
Number of extensions: 13
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: 336
Length adjustment: 30
Effective length of query: 392
Effective length of database: 306
Effective search space:   119952
Effective search space used:   119952
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 AO353_25960 AO353_25960 (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.26516.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.2e-153  497.3   2.3   2.5e-153  497.2   2.3    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960  AO353_25960 threonine dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960  AO353_25960 threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.2   2.3  2.5e-153  2.5e-153       2     319 ..      18     335 ..      17     336 .] 0.99

  Alignments for each domain:
  == domain 1  score: 497.2 bits;  conditional E-value: 2.5e-153
                                     TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkak 66 
                                                   y+++il a vye av tpl+ a  lse l+n++llkredlqp fsfk+rGaynk+aqlsaeqka+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960  18 YVKKILAAPVYELAVRTPLQVAPALSEVLGNQILLKREDLQPTFSFKIRGAYNKLAQLSAEQKAR 82 
                                                   899************************************************************** PP

                                     TIGR01124  67 GviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalel 131
                                                   Gvi+asaGnhaqGval+a++lG++a ivmp++tpe+kv  v+++G++ vlhGe++  a ++al+l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960  83 GVITASAGNHAQGVALAARELGIEASIVMPTSTPELKVIGVRSRGANAVLHGESFPFALEYALNL 147
                                                   ***************************************************************** PP

                                     TIGR01124 132 aqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikv 196
                                                   a++ g tf++pfddp+viaGqGtva+e+lrq++  lda+fvpvGGGGliaG+aa+vk l+pei++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 148 ARQTGRTFVSPFDDPDVIAGQGTVAMEILRQHQGALDAIFVPVGGGGLIAGIAAYVKYLRPEIRI 212
                                                   ***************************************************************** PP

                                     TIGR01124 197 igveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaai 261
                                                   +gve+e sa+l++a+ aGerv l +vG fadGvav ++G++ f++c++++d++++v  de+caai
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 213 VGVESEHSACLQAAMLAGERVVLPKVGTFADGVAVAQIGEYGFEICRHHVDEVLTVSNDELCAAI 277
                                                   ***************************************************************** PP

                                     TIGR01124 262 kdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvserae 319
                                                   k++++dtr+++ep+Gala+aG+kkyva+ g++++tlvai sGan+nfd+lr+v+era 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25960 278 KNIYDDTRSITEPSGALAVAGIKKYVAQTGVRGQTLVAIDSGANINFDSLRHVAERAA 335
                                                   ********************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (336 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: 8.96
//
[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