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; EC 1.8.1.4 (characterized)
to candidate PP_4187 PP_4187 dihydrolipoyl dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__Putida:PP_4187
          Length = 478

 Score =  927 bits (2396), Expect = 0.0
 Identities = 477/478 (99%), Positives = 478/478 (100%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL
Sbjct: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG
Sbjct: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120

Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180
           HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV
Sbjct: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180

Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240
           PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK
Sbjct: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240

Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300
           LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLA+DSGVTIDERGY
Sbjct: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLASDSGVTIDERGY 300

Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360
           IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH
Sbjct: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360

Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420
           PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI
Sbjct: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420

Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478
           GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR
Sbjct: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478


Lambda     K      H
   0.316    0.133    0.374 

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: 939
Number of extensions: 16
Number of successful extensions: 1
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate PP_4187 PP_4187 (dihydrolipoyl dehydrogenase)
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.27779.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-167  543.8  14.4   1.7e-167  543.7  14.4    1.0  1  lcl|FitnessBrowser__Putida:PP_4187  PP_4187 dihydrolipoyl dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4187  PP_4187 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.7  14.4  1.7e-167  1.7e-167       1     461 []       4     472 ..       4     472 .. 0.95

  Alignments for each domain:
  == domain 1  score: 543.7 bits;  conditional E-value: 1.7e-167
                           TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.e......klGGtClnvGCiPtKalLksaevveelke.akelg 67 
                                         ++dvvviG+GpgGYvaAi+aaqlglk+a++ek         lGGtClnvGCiP+KalL s+  ++e+ke ++ +g
  lcl|FitnessBrowser__Putida:PP_4187   4 KFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKyTdaegklALGGTCLNVGCIPSKALLDSSWKYKEAKEsFNVHG 78 
                                         59*****************************95223333359***************************9***** PP

                           TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGs 141
                                         i++ +vk+d+++++ rk  +vk+l+gGv++L+k n+v++i+G++kll  k+vev+k +++ +++ea+n+i+A+Gs
  lcl|FitnessBrowser__Putida:PP_4187  79 ISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQGHGKLLAGKKVEVTKADGTtEVIEAENVILASGS 153
                                         ********************************************************998889************* PP

                           TIGR01350 142 eprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                         +p+ +p    +d++v+++s++ale++ vp++l ++G+GviG+E++s++a+lG++vtv+e+ld+ l a d+ vsk+
  lcl|FitnessBrowser__Putida:PP_4187 154 RPIDIPP-APVDQNVIVDSTGALEFQAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKE 227
                                         ******9.8999999************************************************************ PP

                           TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergai 289
                                         ++k+l+k+g++i+ +a+vt  + + +ev+  +++ ++ +++++ +k++vavGr+p +++l     gv++derg+i
  lcl|FitnessBrowser__Putida:PP_4187 228 AQKTLTKQGLDIKLGARVTGSKVNGNEVEvtYTNAEG-EQKITFDKLIVAVGRRPVTTDLLASDSGVTIDERGYI 301
                                         *******************655555555521554444.69*********************************** PP

                           TIGR01350 290 kvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqake 364
                                          vd+++ t+vpg+yaiGDv++++mLAh+As+eg++++e+i g+++ +++y+++Psviyt+Pe+a vG+te+ +k+
  lcl|FitnessBrowser__Putida:PP_4187 302 FVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKA-QMNYDLIPSVIYTHPEIAWVGKTEQALKA 375
                                         ******************************************665.9**************************** PP

                           TIGR01350 365 egievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439
                                         eg+ev+vg fpfaa+g+a+a+++t Gfvkvi+d kt+++lG+h++g++a+el+++ a+a+e+++++e+l ++++ 
  lcl|FitnessBrowser__Putida:PP_4187 376 EGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFS 450
                                         *************************************************************************** PP

                           TIGR01350 440 HPtlsEaikeaalaalgkaihv 461
                                         HPtlsEa++eaala++g aihv
  lcl|FitnessBrowser__Putida:PP_4187 451 HPTLSEALHEAALAVNGGAIHV 472
                                         ********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (478 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.10
//
[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