Alignments for a candidate for lpd in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Shewanella amazonensis SB2B

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 6936188 Sama_0377 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__SB2B:6936188
          Length = 476

 Score =  844 bits (2181), Expect = 0.0
 Identities = 419/475 (88%), Positives = 450/475 (94%), Gaps = 1/475 (0%)

Query: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60
           MS +IKTQVVVLGAGPAGYSAAFR ADLGLETVI+ER++TLGGVCLNVGCIPSKALLH+A
Sbjct: 1   MSNQIKTQVVVLGAGPAGYSAAFRAADLGLETVIIERFSTLGGVCLNVGCIPSKALLHIA 60

Query: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120
           KVIEEAK  AEHG+VFGEP  DIDK+R +KEKVI QLTGGL GMAK RKV+VVNGLGKFT
Sbjct: 61  KVIEEAKTAAEHGVVFGEPSIDIDKLRGYKEKVIGQLTGGLGGMAKMRKVQVVNGLGKFT 120

Query: 121 GANTLEVEGENGK-TVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLL 179
           G N++EV G +G  TVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVP++LL
Sbjct: 121 GPNSIEVTGADGAATVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPKKLL 180

Query: 180 VMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVT 239
           VMGGGIIGLEMGTVYHALGS IDVVEMFDQVIPAADKD+VKV+T++ISKKFNLMLETKVT
Sbjct: 181 VMGGGIIGLEMGTVYHALGSDIDVVEMFDQVIPAADKDVVKVYTRKISKKFNLMLETKVT 240

Query: 240 AVEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDK 299
           AVEAKEDGIYV+MEGKKAP EP RYDAVLVAIGR PNGK +DA KAG+ VD+RGFI+VDK
Sbjct: 241 AVEAKEDGIYVSMEGKKAPTEPVRYDAVLVAIGRTPNGKLIDADKAGINVDERGFIKVDK 300

Query: 300 QLRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAW 359
           QLRTNVPHIFA+GDIVGQPMLAHKGVHEGHVAAEVI+G KH+FDPKVIPSIAYT+PEVAW
Sbjct: 301 QLRTNVPHIFAVGDIVGQPMLAHKGVHEGHVAAEVISGLKHFFDPKVIPSIAYTDPEVAW 360

Query: 360 VGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGG 419
           VGLTEKEAKEKGI+YETATFPWAASGRAIASD +DGMTKLIFDKE+HRVIGGAIVG NGG
Sbjct: 361 VGLTEKEAKEKGIAYETATFPWAASGRAIASDASDGMTKLIFDKETHRVIGGAIVGVNGG 420

Query: 420 ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEV+EGSITDLPNPKAKKK
Sbjct: 421 ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVYEGSITDLPNPKAKKK 475


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: 858
Number of extensions: 23
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: 474
Length of database: 476
Length adjustment: 33
Effective length of query: 441
Effective length of database: 443
Effective search space:   195363
Effective search space used:   195363
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 6936188 Sama_0377 (dihydrolipoamide dehydrogenase (RefSeq))
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.20060.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     4e-152  493.0   6.5   4.8e-152  492.8   6.5    1.0  1  lcl|FitnessBrowser__SB2B:6936188  Sama_0377 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936188  Sama_0377 dihydrolipoamide dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.8   6.5  4.8e-152  4.8e-152       2     455 ..       7     461 ..       6     466 .. 0.97

  Alignments for each domain:
  == domain 1  score: 492.8 bits;  conditional E-value: 4.8e-152
                         TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldl 77 
                                       ++vvv+G+Gp+GY aA raa lgl+++++e+ ++lGG+ClnvGCiP+KalL+ a+v+ee+k+a+e+g+   + ++d+
  lcl|FitnessBrowser__SB2B:6936188   7 TQVVVLGAGPAGYSAAFRAADLGLETVIIERfSTLGGVCLNVGCIPSKALLHIAKVIEEAKTAAEHGVVFGEPSIDI 83 
                                       579************************************************************************** PP

                         TIGR01350  78 ekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelplkleed 153
                                       +kl   kekv+ +l+gG+ ++ k  kv+v++G +k+++++++ev++ +++ ++++++n+iiA Gs+p++lp+ + ++
  lcl|FitnessBrowser__SB2B:6936188  84 DKLRGYKEKVIGQLTGGLGGMAKMRKVQVVNGLGKFTGPNSIEVTGADGAaTVINFDNAIIAAGSRPIQLPF-IPHE 159
                                       **********************************************998878999*****************.8888 PP

                         TIGR01350 154 ekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkilt 230
                                         ++++s++alelkevp++l+++GgG+iG+E++++++ lG+++ v+e+ d+++pa d++v kv ++k++k + +++ 
  lcl|FitnessBrowser__SB2B:6936188 160 DPRIWDSTDALELKEVPKKLLVMGGGIIGLEMGTVYHALGSDIDVVEMFDQVIPAADKDVVKVYTRKISK-KFNLML 235
                                       889****************************************************************986.58**** PP

                         TIGR01350 231 nakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyai 305
                                       ++kvt+ve++ed + v++++k   +e +++++vLva+Gr+pn + ++ +k g+++derg+ikvd++lrtnvp+i+a+
  lcl|FitnessBrowser__SB2B:6936188 236 ETKVTAVEAKEDGIYVSMEGKkaPTEPVRYDAVLVAIGRTPNGKLIDADKAGINVDERGFIKVDKQLRTNVPHIFAV 312
                                       ***************988888556899************************************************** PP

                         TIGR01350 306 GDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangka 382
                                       GD++g++mLAh+ ++eg vaae i g ++  +d k++Ps+ yt+Peva vGlte++ake+gi+++++ fp aa+g+a
  lcl|FitnessBrowser__SB2B:6936188 313 GDIVGQPMLAHKGVHEGHVAAEVISGLKH-FFDPKVIPSIAYTDPEVAWVGLTEKEAKEKGIAYETATFPWAASGRA 388
                                       **************************665.9********************************************** PP

                         TIGR01350 383 laleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455
                                       +a++ +dG+ k+i+dk+t++++G  ivg +  el+ e+ la+e++  +e++a tih+HPtl E +  aa+   
  lcl|FitnessBrowser__SB2B:6936188 389 IASDASDGMTKLIFDKETHRVIGGAIVGVNGGELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVYE 461
                                       ****************************************************************998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (476 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.00
//
[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