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.19802.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.27
//
[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