Alignments for a candidate for lpd in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Klebsiella michiganensis M5al

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate BWI76_RS04890 BWI76_RS04890 dihydrolipoyl dehydrogenase

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__Koxy:BWI76_RS04890
          Length = 474

 Score =  919 bits (2374), Expect = 0.0
 Identities = 461/474 (97%), Positives = 469/474 (98%)

Query: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60
           MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERY+TLGGVCLNVGCIPSKALLHVA
Sbjct: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYSTLGGVCLNVGCIPSKALLHVA 60

Query: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120
           KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVI QLTGGLAGMAKGRKVKVVNGLGKFT
Sbjct: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVITQLTGGLAGMAKGRKVKVVNGLGKFT 120

Query: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV 180
           GANTLEVEGENGKTVINFDNAIIAAGSRPI+LPFIPHEDPR+WDSTDALELK VP+RLLV
Sbjct: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIELPFIPHEDPRVWDSTDALELKTVPKRLLV 180

Query: 181 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA 240
           MGGGIIGLEMGTVYHALGS+IDVVEMFDQVIPAADKD+VKVFTKRISKKFNLMLETKVTA
Sbjct: 181 MGGGIIGLEMGTVYHALGSEIDVVEMFDQVIPAADKDVVKVFTKRISKKFNLMLETKVTA 240

Query: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300
           VEAKEDGIYV+MEGKKAPAE QRYDAVLVAIGRVPNGKNLDAGKAGVEVD+RGFIRVDKQ
Sbjct: 241 VEAKEDGIYVSMEGKKAPAEAQRYDAVLVAIGRVPNGKNLDAGKAGVEVDERGFIRVDKQ 300

Query: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360
           LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAG KHYFDPKVIPSIAYTEPEVAWV
Sbjct: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGMKHYFDPKVIPSIAYTEPEVAWV 360

Query: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420
           GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE
Sbjct: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420

Query: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPN KAKKK
Sbjct: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNAKAKKK 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: 924
Number of extensions: 25
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 BWI76_RS04890 BWI76_RS04890 (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.10693.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.2e-154  499.2   7.3   6.3e-154  499.0   7.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04890  BWI76_RS04890 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04890  BWI76_RS04890 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  499.0   7.3  6.3e-154  6.3e-154       2     455 ..       7     460 ..       6     465 .. 0.97

  Alignments for each domain:
  == domain 1  score: 499.0 bits;  conditional E-value: 6.3e-154
                               TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgieve 71 
                                             ++vvv+G+Gp+GY aA r+a lgl++++ve+ ++lGG+ClnvGCiP+KalL+ a+v+ee+k ++e+gi   
  lcl|FitnessBrowser__Koxy:BWI76_RS04890   7 TQVVVLGAGPAGYSAAFRCADLGLETVIVERySTLGGVCLNVGCIPSKALLHVAKVIEEAKALAEHGIVFG 77 
                                             579****************************99************************************** PP

                               TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGse 142
                                             + k d++k+  +kekv+++l+gG++++ k  kv+v++G +k+++++++ev++e+++++++++n+iiA Gs+
  lcl|FitnessBrowser__Koxy:BWI76_RS04890  78 EPKTDIDKIRTWKEKVITQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVEGENGKTVINFDNAIIAAGSR 148
                                             *********************************************************************** PP

                               TIGR01350 143 prelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaev 213
                                             p+elp+ + ++  +v++s++alelk+vp++l+++GgG+iG+E++++++ lG+++ v+e+ d+++pa d++v
  lcl|FitnessBrowser__Koxy:BWI76_RS04890 149 PIELPF-IPHEDPRVWDSTDALELKTVPKRLLVMGGGIIGLEMGTVYHALGSEIDVVEMFDQVIPAADKDV 218
                                             ******.8888889********************************************************* PP

                               TIGR01350 214 skvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgve 282
                                              kv +k+++k + +++ ++kvt+ve++ed + v++++k   +e  ++++vLva+Gr pn ++l+  k gve
  lcl|FitnessBrowser__Koxy:BWI76_RS04890 219 VKVFTKRISK-KFNLMLETKVTAVEAKEDGIYVSMEGKkaPAEAQRYDAVLVAIGRVPNGKNLDAGKAGVE 288
                                             *******986.58*******************99888844579999************************* PP

                               TIGR01350 283 ldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePeva 353
                                             +derg+i vd++lrtnvp+i+aiGD++g++mLAh+ ++eg vaae iag ++  +d k++Ps+ ytePeva
  lcl|FitnessBrowser__Koxy:BWI76_RS04890 289 VDERGFIRVDKQLRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGMKH-YFDPKVIPSIAYTEPEVA 358
                                             *************************************************665.9***************** PP

                               TIGR01350 354 svGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalav 424
                                              vGlte++ake+gi+++++ fp aa+g+a+a++ +dG+ k+i+dk++++++G  ivg++  el+ e+ la+
  lcl|FitnessBrowser__Koxy:BWI76_RS04890 359 WVGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGLAI 429
                                             *********************************************************************** PP

                               TIGR01350 425 eleltveelaktihpHPtlsEaikeaalaal 455
                                             e++  +e++a tih+HPtl E +  aa+   
  lcl|FitnessBrowser__Koxy:BWI76_RS04890 430 EMGCDAEDIALTIHAHPTLHESVGLAAEVFE 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: 00:00:00.01
# Mc/sec: 11.96
//
[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