Alignments for a candidate for tdcB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcB in Pseudomonas fluorescens GW456-L13

Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate PfGW456L13_3031 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= curated2:P37946
         (422 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031
          Length = 337

 Score =  229 bits (584), Expect = 9e-65
 Identities = 134/323 (41%), Positives = 185/323 (57%), Gaps = 7/323 (2%)

Query: 13  VKHILKAHQNVKDVVIHTPLQRNDRLSERYECNIYLKREDLQVVRSFKLRGAYHKMKQLS 72
           VK IL A   V ++ + TPLQ    LSE     I LKREDLQ   SFK+RGAY+K+ QLS
Sbjct: 15  VKKILAAP--VYELAVRTPLQPAPALSEALGNQILLKREDLQPTFSFKIRGAYNKLVQLS 72

Query: 73  SEQTENGVVCASAGNHAQGVAFSCKHLGIHGKIFMPSTTPRQKVSQVELFGKGFIDIILT 132
             Q   GVV ASAGNHAQGVA + + LGI+  I MP TTP+ KV  V   G    D +L 
Sbjct: 73  EVQKARGVVTASAGNHAQGVALAARELGINATIVMPCTTPQLKVIGVRSRGA---DAVLH 129

Query: 133 GDTFDDVYKSAAECCEAESRTFIHPFDDPDVMAGQGTLAVEILNDIDTEPHFLFASVGGG 192
           G++F      A +      RTF+ PFDDP+V+AGQGT+A+EIL         +F  VGGG
Sbjct: 130 GESFPFALACALDLARETGRTFVSPFDDPEVIAGQGTVAMEILRQHQGPLDAIFVPVGGG 189

Query: 193 GLLSGVGTYLKNVSPDTKVIAVEPAGAASYFESNKAGHVVTLDKIDKFVDGAAVKKIGEE 252
           GL++G+  Y+K + P+ +VI VE   +A    +  AG  V L  +  F DG AV +IG  
Sbjct: 190 GLIAGIAAYVKYLRPEVRVIGVESEHSACLQAAMHAGERVVLPSVGTFADGVAVAQIGAY 249

Query: 253 TFRTLETVVDDILLVPEGKVCTSILELYNECAVVAEPAGALSVAALDLYKDQ--IKGKNV 310
            F      VDD++ V   ++C +I  +Y++   + EP+GAL+VA +  Y  Q    G+ +
Sbjct: 250 GFEVCRFCVDDVVTVSNDELCAAIKNIYDDTRSITEPSGALAVAGIKRYVAQTGALGQTL 309

Query: 311 VCVVSGGNNDIGRMQEMKERSLI 333
           V + SG N +   +  + ER+ +
Sbjct: 310 VAIDSGANINFDSLGHVAERAAL 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: 311
Number of extensions: 12
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: 337
Length adjustment: 30
Effective length of query: 392
Effective length of database: 307
Effective search space:   120344
Effective search space used:   120344
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 PfGW456L13_3031 (Threonine dehydratase biosynthetic (EC 4.3.1.19))
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.18034.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.3e-150  487.4   2.0   2.8e-150  487.1   2.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031  Threonine dehydratase biosynthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031  Threonine dehydratase biosynthetic (EC 4.3.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.1   2.0  2.8e-150  2.8e-150       2     320 ..      14     332 ..      13     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 487.1 bits;  conditional E-value: 2.8e-150
                                               TIGR01124   2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkm 56 
                                                             y+++il a vye av tpl++a  lse l+n++llkredlqp fsfk+rGaynk+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031  14 YVKKILAAPVYELAVRTPLQPAPALSEALGNQILLKREDLQPTFSFKIRGAYNKL 68 
                                                             899**************************************************** PP

                                               TIGR01124  57 aqlsaeqkakGviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafG 111
                                                              qls+ qka+Gv++asaGnhaqGval+a++lG++a+ivmp+ttp++kv  v+++G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031  69 VQLSEVQKARGVVTASAGNHAQGVALAARELGINATIVMPCTTPQLKVIGVRSRG 123
                                                             ******************************************************* PP

                                               TIGR01124 112 gevvlhGenydeakakalelaqekgltfiapfddplviaGqGtvalellrqveed 166
                                                             ++ vlhGe++  a a al+la+e g tf++pfddp viaGqGtva+e+lrq++ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031 124 ADAVLHGESFPFALACALDLARETGRTFVSPFDDPEVIAGQGTVAMEILRQHQGP 178
                                                             ******************************************************* PP

                                               TIGR01124 167 ldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldq 221
                                                             lda+fvpvGGGGliaG+aa+vk l+pe++vigve+e sa+l++a++aGerv l +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031 179 LDAIFVPVGGGGLIAGIAAYVKYLRPEVRVIGVESEHSACLQAAMHAGERVVLPS 233
                                                             ******************************************************* PP

                                               TIGR01124 222 vGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaG 276
                                                             vG fadGvav ++G++ f++c+  +dd+v+v  de+caaik++++dtr+++ep+G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031 234 VGTFADGVAVAQIGAYGFEVCRFCVDDVVTVSNDELCAAIKNIYDDTRSITEPSG 288
                                                             ******************************************************* PP

                                               TIGR01124 277 alalaGlkkyvakkgiedktlvailsGanlnfdrlryvserael 320
                                                             ala+aG+k+yva+ g+ ++tlvai sGan+nfd+l +v+era l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3031 289 ALAVAGIKRYVAQTGALGQTLVAIDSGANINFDSLGHVAERAAL 332
                                                             *****************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (499 nodes)
Target sequences:                          1  (337 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.38
//
[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