Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N1B4

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate Pf1N1B4_3683 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683
          Length = 478

 Score =  852 bits (2201), Expect = 0.0
 Identities = 435/478 (91%), Positives = 452/478 (94%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           MTQKFDVVVIGAGPGGYVAAIKAAQLGL TACIEKYTD EGKLALGGTCLNVGCIPSKAL
Sbjct: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLSTACIEKYTDKEGKLALGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           LDSSWK+ EA++ F +HGI+   V MDV AMVGRKA IVK LT GVATLFKANGVTSIQG
Sbjct: 61  LDSSWKFHEAQDGFAIHGINHAGVTMDVPAMVGRKANIVKGLTSGVATLFKANGVTSIQG 120

Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180
           HGKLLAGKKVEVTK DG+ E+IEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEFQ+V
Sbjct: 121 HGKLLAGKKVEVTKPDGSVEIIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEFQSV 180

Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240
           PKRLGVIGAGVIGLELGSVW+RLGAEVTVLEALDTFLMAAD AVSKEA KTLTKQGLDIK
Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAEVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIK 240

Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300
           LGARVTGSKVNG+EV V YT+A GEQ ITFDKLIVAVGRRPVTTDLLAAD GVT+DERG+
Sbjct: 241 LGARVTGSKVNGDEVVVNYTDANGEQNITFDKLIVAVGRRPVTTDLLAADCGVTLDERGF 300

Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360
           + VDD+CAT+VPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH
Sbjct: 301 VHVDDHCATTVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360

Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420
           PEIAWVGKTEQ LKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI
Sbjct: 361 PEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420

Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478
           GPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIH+ANRKKR
Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHIANRKKR 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: 886
Number of extensions: 17
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: 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 Pf1N1B4_3683 (Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4))
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.24921.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   7.6e-165  535.0  10.3   8.7e-165  534.8  10.3    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683  Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.8  10.3  8.7e-165  8.7e-165       1     461 []       4     472 ..       4     472 .. 0.97

  Alignments for each domain:
  == domain 1  score: 534.8 bits;  conditional E-value: 8.7e-165
                                      TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtKalLksaevv 57 
                                                    ++dvvviG+GpgGYvaAi+aaqlgl++a++ek  +k     lGGtClnvGCiP+KalL s+  +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683   4 KFDVVVIGAGPGGYVAAIKAAQLGLSTACIEKytDKegklaLGGTCLNVGCIPSKALLDSSWKF 67 
                                                    59*****************************95421344449********************** PP

                                      TIGR01350  58 eelke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkeve 120
                                                    +e+++ ++ +gi+ ++v++d+ +++ rk ++vk l++Gv++L+k n+v++i+G++kll  k+ve
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683  68 HEAQDgFAIHGINHAGVTMDVPAMVGRKANIVKGLTSGVATLFKANGVTSIQGHGKLLAGKKVE 131
                                                    **************************************************************** PP

                                      TIGR01350 121 vkkekke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGv 183
                                                    v+k +++ + +ea+n+i+A Gs+p+ +p    +d++v+++s++ale+++vp++l ++G+GviG+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683 132 VTKPDGSvEIIEAENVILAPGSRPIDIPP-APVDQNVIVDSTGALEFQSVPKRLGVIGAGVIGL 194
                                                    ***9988899******************9.8999999*************************** PP

                                      TIGR01350 184 EfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvve 247
                                                    E++s++++lG++vtv+e+ld+ l a da vsk++ k+l+k+g++i+ +a+vt  + + devvv+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683 195 ELGSVWSRLGAEVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIKLGARVTGSKVNGDEVVVN 258
                                                    ****************************************************999999999977 PP

                                      TIGR01350 248 akkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvig 310
                                                      +   +++++ +k++vavGr+p +++l  +  gv+lderg+++vd+++ t+vpg+yaiGDv++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683 259 YTDAnGEQNITFDKLIVAVGRRPVTTDLLAADCGVTLDERGFVHVDDHCATTVPGVYAIGDVVR 322
                                                    66665679******************************************************** PP

                                      TIGR01350 311 klmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkf 374
                                                    ++mLAh+As+eg++++e+i g+++ +++y+++Psviyt+Pe+a vG+te+ +k+eg+ev+vg f
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683 323 GMMLAHKASEEGIMVVERIKGHKA-QMNYDLIPSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTF 385
                                                    *********************665.9************************************** PP

                                      TIGR01350 375 pfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktih 438
                                                    pfaa+g+a+a+++t Gfvkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++e+l ++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683 386 PFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVF 449
                                                    **************************************************************** PP

                                      TIGR01350 439 pHPtlsEaikeaalaalgkaihv 461
                                                     HPtlsEa++eaala++g aih+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683 450 SHPTLSEALHEAALAVNGGAIHI 472
                                                    *********************95 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.59
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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