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.19844.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: 12.71
//
[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:

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:

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:

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:

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