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_478 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)

Query= reanno::pseudo6_N2E2:Pf6N2E2_478
         (461 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478
          Length = 461

 Score =  909 bits (2349), Expect = 0.0
 Identities = 461/461 (100%), Positives = 461/461 (100%)

Query: 1   MQQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60
           MQQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE
Sbjct: 1   MQQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60

Query: 61  QFHQTRHHSQGSALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120
           QFHQTRHHSQGSALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK
Sbjct: 61  QFHQTRHHSQGSALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120

Query: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVDLPMLPVGGPIISSTEALAPTSVPKHLVVVGG 180
           VIDGKTVEVGDTRIQCEHLLLATGSKSVDLPMLPVGGPIISSTEALAPTSVPKHLVVVGG
Sbjct: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVDLPMLPVGGPIISSTEALAPTSVPKHLVVVGG 180

Query: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240
           GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD
Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240

Query: 241 AQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVKIDQRCQTSM 300
           AQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVKIDQRCQTSM
Sbjct: 241 AQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVKIDQRCQTSM 300

Query: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360
           RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD
Sbjct: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360

Query: 361 EAKAAGLDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420
           EAKAAGLDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF
Sbjct: 361 EAKAAGLDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420

Query: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461
           GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461


Lambda     K      H
   0.318    0.135    0.394 

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: 836
Number of extensions: 14
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: 461
Length of database: 461
Length adjustment: 33
Effective length of query: 428
Effective length of database: 428
Effective search space:   183184
Effective search space used:   183184
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate Pf6N2E2_478 (Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid 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.25495.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.7e-148  481.1   0.8   1.9e-148  480.9   0.8    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478  Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.9   0.8  1.9e-148  1.9e-148       3     460 ..       8     460 ..       6     461 .] 0.98

  Alignments for each domain:
  == domain 1  score: 480.9 bits;  conditional E-value: 1.9e-148
                                     TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...ak 64 
                                                    +++iGgGpgGYvaAira+qlg  ++lve + lGGtCln GCiP+Kal++ ae +++ ++    +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478   8 TLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAEQFHQTRHhsqGS 72 
                                                   578*******************************************************9953335 PP

                                     TIGR01350  65 elgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekk 129
                                                    lgi+v+  +ld+ k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak+ d k+vev +++    
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478  73 ALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAKVIDGKTVEVGDTR---- 133
                                                   79*******************************************************9998.... PP

                                     TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGv 194
                                                   ++ +++++AtGs+   lp+ l + +  +i+s+eal+ ++vp++lv+vGgG+iG+E++ +++klG+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 134 IQCEHLLLATGSKSVDLPM-LPVGG-PIISSTEALAPTSVPKHLVVVGGGYIGLELGIAYRKLGA 196
                                                   89*****************.99998.69************************************* PP

                                     TIGR01350 195 kvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevetleae 259
                                                   +v+v+e+++rilpa d e+++ ++++lk+ gvk++ +++v+   +++ +++v+   +++ +l+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 197 EVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFDAQASTLQVRDPAGDTLNLDTD 261
                                                   ***************************************************99999999****** PP

                                     TIGR01350 260 kvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvv 324
                                                   +vLvavGrkpn+++ +le+l++ ++   a+k+d++++t++ +++aiGD+ g++mLAh+A+++g +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 262 RVLVAVGRKPNTQGWNLEALNLAMNG-AAVKIDQRCQTSMRNVWAIGDLSGEPMLAHRAMAQGEM 325
                                                   *************************9.78************************************ PP

                                     TIGR01350 325 aaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetd 389
                                                   +ae iag+++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfaang+a++le ++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 326 VAELIAGQHR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGLDCIVSSFPFAANGRAMTLESKS 389
                                                   *******998.9***************************************************** PP

                                     TIGR01350 390 GfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaa 454
                                                   Gfv+v++ ++ + i+G + vg  +sel + +   +e+++++e++a tih+HPtl+Ea++eaal a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 390 GFVRVVARRDNHLIVGWQAVGVGVSELSTAFGQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRA 454
                                                   ***************************************************************** PP

                                     TIGR01350 455 lgkaih 460
                                                   lg+a+h
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 455 LGHALH 460
                                                   ***999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (461 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.05
//
[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