Alignments for a candidate for lpd in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Escherichia coli BW25113

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 14262 b0116 dihydrolipoamide dehydrogenase (NCBI)

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__Keio:14262
          Length = 474

 Score =  941 bits (2433), Expect = 0.0
 Identities = 474/474 (100%), Positives = 474/474 (100%)

Query: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60
           MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA
Sbjct: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60

Query: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120
           KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT
Sbjct: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120

Query: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV 180
           GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV
Sbjct: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV 180

Query: 181 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA 240
           MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA
Sbjct: 181 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA 240

Query: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300
           VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ
Sbjct: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300

Query: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360
           LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV
Sbjct: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360

Query: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420
           GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE
Sbjct: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420

Query: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK
Sbjct: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474


Lambda     K      H
   0.317    0.137    0.396 

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: 943
Number of extensions: 23
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: 474
Length of database: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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 14262 b0116 (dihydrolipoamide dehydrogenase (NCBI))
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.5549.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.1e-154  501.5   6.2   1.3e-154  501.2   6.2    1.0  1  lcl|FitnessBrowser__Keio:14262  b0116 dihydrolipoamide dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14262  b0116 dihydrolipoamide dehydrogenase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.2   6.2  1.3e-154  1.3e-154       2     455 ..       7     460 ..       6     465 .. 0.97

  Alignments for each domain:
  == domain 1  score: 501.2 bits;  conditional E-value: 1.3e-154
                       TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldlek 79 
                                     ++vvv+G+Gp+GY aA r+a lgl++++ve+ ++lGG+ClnvGCiP+KalL+ a+v+ee+k ++e+gi   + k d++k
  lcl|FitnessBrowser__Keio:14262   7 TQVVVLGAGPAGYSAAFRCADLGLETVIVERyNTLGGVCLNVGCIPSKALLHVAKVIEEAKALAEHGIVFGEPKTDIDK 85 
                                     579****************************9*********************************************** PP

                       TIGR01350  80 llerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleedekvvi 158
                                     +  +kekv+++l+gG++++ k  kv+v++G +k+++++++ev++e+++++++++n+iiA Gs+p++lp+ + ++  +++
  lcl|FitnessBrowser__Keio:14262  86 IRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVEGENGKTVINFDNAIIAAGSRPIQLPF-IPHEDPRIW 163
                                     *********************************************************************.8888889** PP

                       TIGR01350 159 tseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtev 237
                                     +s++alelkevpe+l+++GgG+iG+E++++++ lG+++ v+e+ d+++pa d+++ kv +k+++k + +++ ++kvt+v
  lcl|FitnessBrowser__Keio:14262 164 DSTDALELKEVPERLLVMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISK-KFNLMLETKVTAV 241
                                     **************************************************************986.58*********** PP

                       TIGR01350 238 ekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmL 314
                                     e++ed + v++++k   +e  ++++vLva+Gr pn ++l+  k gve+d+rg+i vd++lrtnvp+i+aiGD++g++mL
  lcl|FitnessBrowser__Keio:14262 242 EAKEDGIYVTMEGKkaPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPHIFAIGDIVGQPML 320
                                     ******9988887744578999********************************************************* PP

                       TIGR01350 315 AhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvk 393
                                     Ah+ ++eg vaae iagk++  +d k++Ps+ ytePeva vGlte++ake+gi+++++ fp aa+g+a+a++ +dG+ k
  lcl|FitnessBrowser__Keio:14262 321 AHKGVHEGHVAAEVIAGKKH-YFDPKVIPSIAYTEPEVAWVGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTK 398
                                     *****************776.9********************************************************* PP

                       TIGR01350 394 vivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455
                                     +i+dk++++++G  ivg++  el+ e+ la+e++  +e++a tih+HPtl E +  aa+   
  lcl|FitnessBrowser__Keio:14262 399 LIFDKESHRVIGGAIVGTNGGELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFE 460
                                     *****************************************************998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (474 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: 7.91
//
[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