Alignments for a candidate for lpd in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas putida KT2440

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of branched-chain alpha-keto acid dehydrogenase complex; LPD-Val; EC 1.8.1.4 (characterized)
to candidate PP_4404 PP_4404 dihydrolipoyl dehydrogenase component of branched-chain alpha-keto acid dehydrogenase complex

Query= SwissProt::P09063
         (459 letters)



>FitnessBrowser__Putida:PP_4404
          Length = 459

 Score =  889 bits (2296), Expect = 0.0
 Identities = 451/459 (98%), Positives = 454/459 (98%)

Query: 1   MQQTIQTTLLIIGGGPGGYVAAIRAGQLGIPTVLVEGQALGGTCLNIGCIPSKALIHVAE 60
           MQQ IQTTLLIIGGGPGGYVAAIRAGQLGIPTVLVEGQALGGTCLNIGCIPSKALIHVAE
Sbjct: 1   MQQIIQTTLLIIGGGPGGYVAAIRAGQLGIPTVLVEGQALGGTCLNIGCIPSKALIHVAE 60

Query: 61  QFHQASRFTEPSPLGISVASPRLDIGQSVAWKDGIVDRLTTGVAALLKKHGVKVVHGWAK 120
           QFHQASRFTEPSPLGISVASPRLDIGQSV WKDGIVDRLTTGVAALLKKHGVKVVHGWAK
Sbjct: 61  QFHQASRFTEPSPLGISVASPRLDIGQSVTWKDGIVDRLTTGVAALLKKHGVKVVHGWAK 120

Query: 121 VLDGKQVEVDGQRIQCEHLLLATGSSSVELPMLPLGGPVISSTEALAPKALPQHLVVVGG 180
           VLDGKQVEVDGQRIQCEHLLLATGSSSVELPMLPLGGPVISSTEALAPK LPQHLVVVGG
Sbjct: 121 VLDGKQVEVDGQRIQCEHLLLATGSSSVELPMLPLGGPVISSTEALAPKTLPQHLVVVGG 180

Query: 181 GYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESLKKLGIALHLGHSVEGYE 240
           GYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESLKKLGIALHLGHSVEGYE
Sbjct: 181 GYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESLKKLGIALHLGHSVEGYE 240

Query: 241 NGCLLANDGKGGQLRLEADRVLVAVGRRPRTKGFNLECLDLKMNGAAIAIDERCQTSMHN 300
           NGCLLA+DGKGGQLRLEAD+VLVAVGRRPRTKGFNLECLDLKMNGAAIAIDERC TSMHN
Sbjct: 241 NGCLLASDGKGGQLRLEADQVLVAVGRRPRTKGFNLECLDLKMNGAAIAIDERCHTSMHN 300

Query: 301 VWAIGDVAGEPMLAHRAMAQGEMVAEIIAGKARRFEPAAIAAVCFTDPEVVVVGKTPEQA 360
           VWAIGDVAGEPMLAHRAMAQGEMVAEIIAGKARRFEP AIAAVCFTDPEVVVVGKTPEQA
Sbjct: 301 VWAIGDVAGEPMLAHRAMAQGEMVAEIIAGKARRFEPTAIAAVCFTDPEVVVVGKTPEQA 360

Query: 361 SQQGLDCIVAQFPFAANGRAMSLESKSGFVRVVARRDNHLILGWQAVGVAVSELSTAFAQ 420
           SQQGLDCIVAQFPFAANGRAMSLESKSGFVRVVARRDNHLI+GWQAVGVAVSELSTAFAQ
Sbjct: 361 SQQGLDCIVAQFPFAANGRAMSLESKSGFVRVVARRDNHLIVGWQAVGVAVSELSTAFAQ 420

Query: 421 SLEMGACLEDVAGTIHAHPTLGEAVQEAALRALGHALHI 459
           SLEMGACLEDVAGTIHAHPTLGEAVQEAALRALGHALHI
Sbjct: 421 SLEMGACLEDVAGTIHAHPTLGEAVQEAALRALGHALHI 459


Lambda     K      H
   0.319    0.136    0.398 

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: 880
Number of extensions: 22
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: 459
Length of database: 459
Length adjustment: 33
Effective length of query: 426
Effective length of database: 426
Effective search space:   181476
Effective search space used:   181476
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate PP_4404 PP_4404 (dihydrolipoyl dehydrogenase component of branched-chain alpha-keto acid dehydrogenase complex)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

# 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/TIGR01350.hmm
# target sequence database:        /tmp/gapView.4226.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01350  [M=461]
Accession:   TIGR01350
Description: lipoamide_DH: dihydrolipoyl dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.7e-145  469.4   0.6   6.5e-145  469.3   0.6    1.0  1  lcl|FitnessBrowser__Putida:PP_4404  PP_4404 dihydrolipoyl dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4404  PP_4404 dihydrolipoyl dehydrogenase component of branched-chain alpha-keto acid d
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.3   0.6  6.5e-145  6.5e-145       4     461 .]       9     459 .]       6     459 .] 0.96

  Alignments for each domain:
  == domain 1  score: 469.3 bits;  conditional E-value: 6.5e-145
                           TIGR01350   4 vvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeake...lgievenvkl 75 
                                         +++iGgGpgGYvaAira+qlg  ++lve + lGGtCln GCiP+Kal++ ae +++++ + e   lgi+v++ +l
  lcl|FitnessBrowser__Putida:PP_4404   9 LLIIGGGPGGYVAAIRAGQLGIPTVLVEGQALGGTCLNIGCIPSKALIHVAEQFHQASRFTEpspLGISVASPRL 83 
                                         78*****************************************************99885433339********* PP

                           TIGR01350  76 dlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkl 150
                                         d+ + + +k+ +v++l++Gv+aLlkk++v+v++G ak+ld k+vev++++    ++ +++++AtGs+  elp+ l
  lcl|FitnessBrowser__Putida:PP_4404  84 DIGQSVTWKDGIVDRLTTGVAALLKKHGVKVVHGWAKVLDGKQVEVDGQR----IQCEHLLLATGSSSVELPM-L 153
                                         ***********************************************998....89*****************.8 PP

                           TIGR01350 151 eedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkg 225
                                            +  vi+s+eal+ k++p++lv+vGgG+iG+E++ +++klG++v+v+e+ +rilp+ d+e++  ++++lkk g
  lcl|FitnessBrowser__Putida:PP_4404 154 PLGG-PVISSTEALAPKTLPQHLVVVGGGYIGLELGIAYRKLGAQVSVVEARERILPTYDSELTAPVAESLKKLG 227
                                         8888.6********************************************************************* PP

                           TIGR01350 226 vkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvp 300
                                         + ++ +++v+  e  +  + ++  k+ +  lea++vLvavGr+p++++++le l+++++   ai +de+++t+++
  lcl|FitnessBrowser__Putida:PP_4404 228 IALHLGHSVEGYE--NGCLLASDGKGGQLRLEADQVLVAVGRRPRTKGFNLECLDLKMNG-AAIAIDERCHTSMH 299
                                         **********443..33444444444789******************************9.78************ PP

                           TIGR01350 301 giyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfp 375
                                         +++aiGDv+g++mLAh+A+++g ++ae iagk++  ++ +a+ +v +t+Pev +vG+t eqa ++g ++ v++fp
  lcl|FitnessBrowser__Putida:PP_4404 300 NVWAIGDVAGEPMLAHRAMAQGEMVAEIIAGKAR-RFEPTAIAAVCFTDPEVVVVGKTPEQASQQGLDCIVAQFP 373
                                         *******************************887.9*************************************** PP

                           TIGR01350 376 faangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikea 450
                                         faang+a++le ++Gfv+v++ ++ + i+G + vg ++sel + +a  +e+++ +e++a tih+HPtl+Ea++ea
  lcl|FitnessBrowser__Putida:PP_4404 374 FAANGRAMSLESKSGFVRVVARRDNHLIVGWQAVGVAVSELSTAFAQSLEMGACLEDVAGTIHAHPTLGEAVQEA 448
                                         *************************************************************************** PP

                           TIGR01350 451 alaalgkaihv 461
                                         al alg+a+h+
  lcl|FitnessBrowser__Putida:PP_4404 449 ALRALGHALHI 459
                                         ********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (459 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: 12.28
//
[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