Alignments for a candidate for lpd in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Shewanella loihica PV-4

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 5211003 Shew_3429 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__PV4:5211003
          Length = 475

 Score =  828 bits (2140), Expect = 0.0
 Identities = 406/474 (85%), Positives = 447/474 (94%)

Query: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60
           MS EIKTQVVVLGAGPAGYSAAFR ADLGLETVIVER++TLGGVCLNVGCIPSKALLHV+
Sbjct: 1   MSNEIKTQVVVLGAGPAGYSAAFRAADLGLETVIVERFSTLGGVCLNVGCIPSKALLHVS 60

Query: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120
           KVIEEAKA++ HG+VFGEP+ D+DK+R +K+ VI+QLTGGL GM+K RKV VVNGLGKFT
Sbjct: 61  KVIEEAKAISNHGVVFGEPQIDLDKLREFKQSVISQLTGGLGGMSKMRKVNVVNGLGKFT 120

Query: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV 180
           G NT+EV GE+G  V++F+ AIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVP +LLV
Sbjct: 121 GPNTIEVAGEDGVKVVHFEQAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPGKLLV 180

Query: 181 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA 240
           MGGGIIGLEMGTVY +LGS+IDVVEMFDQVIPAADKDIV+V+TK+I  KFNL+LETKVTA
Sbjct: 181 MGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDIVRVYTKKIKNKFNLILETKVTA 240

Query: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300
           VEAKEDGIYV+MEGKKAP EP RYDAVLVAIGR PNGK +DA KAGV +D+RGFI VDKQ
Sbjct: 241 VEAKEDGIYVSMEGKKAPTEPVRYDAVLVAIGRTPNGKLIDADKAGVNIDERGFINVDKQ 300

Query: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360
           +RTNVPHI+AIGDIVGQPMLAHKGVHEGHVAAEVIAG KHYFDPKVIPSIAYT+PEVAWV
Sbjct: 301 MRTNVPHIYAIGDIVGQPMLAHKGVHEGHVAAEVIAGMKHYFDPKVIPSIAYTDPEVAWV 360

Query: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420
           GLTEKEAKE+GI+YETA+FPWAASGRAIASDC++GMTKLIFDKE+HRVIGGAIVG NGGE
Sbjct: 361 GLTEKEAKEQGIAYETASFPWAASGRAIASDCSEGMTKLIFDKETHRVIGGAIVGVNGGE 420

Query: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           LLGEIGLAIEMGCDAED+ALTIHAHPTLHESVGLAAE++EGSITDLPNPKAKKK
Sbjct: 421 LLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEIYEGSITDLPNPKAKKK 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: 837
Number of extensions: 25
Number of successful extensions: 4
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: 475
Length adjustment: 33
Effective length of query: 441
Effective length of database: 442
Effective search space:   194922
Effective search space used:   194922
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 5211003 Shew_3429 (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.391.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.1e-154  500.5   6.3   2.5e-154  500.3   6.3    1.0  1  lcl|FitnessBrowser__PV4:5211003  Shew_3429 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211003  Shew_3429 dihydrolipoamide dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.3   6.3  2.5e-154  2.5e-154       2     453 ..       7     458 ..       6     465 .. 0.97

  Alignments for each domain:
  == domain 1  score: 500.3 bits;  conditional E-value: 2.5e-154
                        TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldle 78 
                                      ++vvv+G+Gp+GY aA raa lgl++++ve+ ++lGG+ClnvGCiP+KalL+ ++v+ee+k ++++g+   + ++dl+
  lcl|FitnessBrowser__PV4:5211003   7 TQVVVLGAGPAGYSAAFRAADLGLETVIVERfSTLGGVCLNVGCIPSKALLHVSKVIEEAKAISNHGVVFGEPQIDLD 84 
                                      579*************************************************************************** PP

                        TIGR01350  79 kllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleedekv 156
                                      kl e k++v+++l+gG+ ++ k  kv+v++G +k+++++++ev++e++ k+++++++iiA Gs+p++lp+ + ++  +
  lcl|FitnessBrowser__PV4:5211003  85 KLREFKQSVISQLTGGLGGMSKMRKVNVVNGLGKFTGPNTIEVAGEDGVKVVHFEQAIIAAGSRPIQLPF-IPHEDPR 161
                                      **********************************************************************.8888889 PP

                        TIGR01350 157 vitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakv 234
                                      +++s++alelkevp +l+++GgG+iG+E+++++++lG+++ v+e+ d+++pa d+++ +v +kk+k+ + +++ ++kv
  lcl|FitnessBrowser__PV4:5211003 162 IWDSTDALELKEVPGKLLVMGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDIVRVYTKKIKN-KFNLILETKV 238
                                      ****************************************************************976.589******* PP

                        TIGR01350 235 tevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvig 310
                                      t+ve++ed + v++++k   +e +++++vLva+Gr+pn + ++ +k gv++derg+i+vd+++rtnvp+iyaiGD++g
  lcl|FitnessBrowser__PV4:5211003 239 TAVEAKEDGIYVSMEGKkaPTEPVRYDAVLVAIGRTPNGKLIDADKAGVNIDERGFINVDKQMRTNVPHIYAIGDIVG 316
                                      ***********988888556899******************************************************* PP

                        TIGR01350 311 klmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleet 388
                                      ++mLAh+ ++eg vaae iag ++  +d k++Ps+ yt+Peva vGlte++ake+gi++++++fp aa+g+a+a++ +
  lcl|FitnessBrowser__PV4:5211003 317 QPMLAHKGVHEGHVAAEVIAGMKH-YFDPKVIPSIAYTDPEVAWVGLTEKEAKEQGIAYETASFPWAASGRAIASDCS 393
                                      *********************665.9**************************************************** PP

                        TIGR01350 389 dGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453
                                      +G+ k+i+dk+t++++G  ivg +  el+ e+ la+e++  +e+la tih+HPtl E +  aa+ 
  lcl|FitnessBrowser__PV4:5211003 394 EGMTKLIFDKETHRVIGGAIVGVNGGELLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEI 458
                                      *********************************************************99888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (475 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: 11.38
//
[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