Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E2

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate Pf6N2E2_5857 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857
          Length = 481

 Score =  836 bits (2160), Expect = 0.0
 Identities = 432/481 (89%), Positives = 449/481 (93%), Gaps = 3/481 (0%)

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

Query: 61  LDSSWKYKEAKESFNVHGI---STGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTS 117
           LDSSWK+ EA++   +HGI   +   V +DV AMVGRKA IVK LT GVATLFKANGVTS
Sbjct: 61  LDSSWKFHEAQDGLAIHGIGGVNRENVTIDVPAMVGRKANIVKGLTSGVATLFKANGVTS 120

Query: 118 IQGHGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEF 177
           IQGHGKLL GKKVEVTK DG+ EVIEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEF
Sbjct: 121 IQGHGKLLMGKKVEVTKPDGSVEVIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEF 180

Query: 178 QAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGL 237
           Q+VPKRLGVIGAGVIGLELGSVW+RLGA+VTVLEALDTFLMAAD AVSKEA KTLTKQGL
Sbjct: 181 QSVPKRLGVIGAGVIGLELGSVWSRLGAQVTVLEALDTFLMAADAAVSKEALKTLTKQGL 240

Query: 238 DIKLGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDE 297
           DIKLGARVTGSKVNG EV V YT+A GEQ ITFDKLIVAVGRRPVTTDLLAADSGV +DE
Sbjct: 241 DIKLGARVTGSKVNGEEVVVNYTDANGEQTITFDKLIVAVGRRPVTTDLLAADSGVELDE 300

Query: 298 RGYIFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVI 357
           RG+I VDD+CAT+VPGV+AIGDVVRGMMLAHKASEEGIMVVERIKGHKAQ+NYDLIPSVI
Sbjct: 301 RGFIKVDDFCATTVPGVFAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQINYDLIPSVI 360

Query: 358 YTHPEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGV 417
           YTHPEIAWVGKTEQ LKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGV
Sbjct: 361 YTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGV 420

Query: 418 HVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKK 477
           HVIGPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKK
Sbjct: 421 HVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKK 480

Query: 478 R 478
           R
Sbjct: 481 R 481


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: 901
Number of extensions: 20
Number of successful extensions: 3
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: 481
Length adjustment: 34
Effective length of query: 444
Effective length of database: 447
Effective search space:   198468
Effective search space used:   198468
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 Pf6N2E2_5857 (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.24893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   4.3e-162  525.9  11.0   4.8e-162  525.7  11.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857  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 !  525.7  11.0  4.8e-162  4.8e-162       1     461 []       4     475 ..       4     475 .. 0.96

  Alignments for each domain:
  == domain 1  score: 525.7 bits;  conditional E-value: 4.8e-162
                                      TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtKalLksaevv 57 
                                                    ++dvvviG+GpgGYvaAi+aaqlgl +a++ek  +k     lGGtClnvGCiP+KalL s+  +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857   4 KFDVVVIGAGPGGYVAAIKAAQLGLTTACIEKytDKegklaLGGTCLNVGCIPSKALLDSSWKF 67 
                                                    59*****************************85421344449********************** PP

                                      TIGR01350  58 eelke.akelgie...venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkk 117
                                                    +e+++ ++ +gi     env++d+ +++ rk ++vk l++Gv++L+k n+v++i+G++kll  k
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857  68 HEAQDgLAIHGIGgvnRENVTIDVPAMVGRKANIVKGLTSGVATLFKANGVTSIQGHGKLLMGK 131
                                                    *****99988875322677********************************************* PP

                                      TIGR01350 118 evevkkekke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGv 180
                                                    +vev+k +++ +++ea+n+i+A Gs+p+ +p    +d++v+++s++ale+++vp++l ++G+Gv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857 132 KVEVTKPDGSvEVIEAENVILAPGSRPIDIPP-APVDQNVIVDSTGALEFQSVPKRLGVIGAGV 194
                                                    ******998889*******************9.8999999************************ PP

                                      TIGR01350 181 iGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedev 244
                                                    iG+E++s++++lG++vtv+e+ld+ l a da vsk++ k+l+k+g++i+ +a+vt  + + +ev
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857 195 IGLELGSVWSRLGAQVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIKLGARVTGSKVNGEEV 258
                                                    *******************************************************988888888 PP

                                      TIGR01350 245 vveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGD 307
                                                    vv+  +   ++t++ +k++vavGr+p +++l  +  gvelderg+ikvd+ + t+vpg++aiGD
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857 259 VVNYTDAnGEQTITFDKLIVAVGRRPVTTDLLAADSGVELDERGFIKVDDFCATTVPGVFAIGD 322
                                                    86666655679***************************************************** PP

                                      TIGR01350 308 vigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkv 371
                                                    v++++mLAh+As+eg++++e+i g+++ +i+y+++Psviyt+Pe+a vG+te+ +k+eg+ev+v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857 323 VVRGMMLAHKASEEGIMVVERIKGHKA-QINYDLIPSVIYTHPEIAWVGKTEQTLKAEGVEVNV 385
                                                    ************************665.9*********************************** PP

                                      TIGR01350 372 gkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelak 435
                                                    g fpfaa+g+a+a+++t Gfvkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++e+l +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857 386 GTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGM 449
                                                    **************************************************************** PP

                                      TIGR01350 436 tihpHPtlsEaikeaalaalgkaihv 461
                                                    +++ HPtlsEa++eaala++g aihv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857 450 MVFSHPTLSEALHEAALAVNGGAIHV 475
                                                    ************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (481 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: 10.47
//
[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