Alignments for a candidate for lpd in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Shewanella oneidensis MR-1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 199618 SO0426 pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI ptt file)

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__MR1:199618
          Length = 475

 Score =  825 bits (2132), Expect = 0.0
 Identities = 408/475 (85%), Positives = 448/475 (94%), Gaps = 1/475 (0%)

Query: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60
           MS EIKTQVVVLGAGPAGYSAAFR ADLGLETVIVER++TLGGVCLNVGCIPSKALLHVA
Sbjct: 1   MSNEIKTQVVVLGAGPAGYSAAFRAADLGLETVIVERFSTLGGVCLNVGCIPSKALLHVA 60

Query: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120
           KVIEEAKA+A HG+VFGEP  D+DK+R++K+KVI+QLTGGL GM+K RKV VVNG GKF+
Sbjct: 61  KVIEEAKAVAAHGVVFGEPTIDLDKLRSFKQKVISQLTGGLGGMSKMRKVNVVNGFGKFS 120

Query: 121 GANTLEVEGENGK-TVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLL 179
           G N+LEV  E+G  TV+ FD AIIAAGSRPI+LPFIPHEDPRIWDSTDALELKEVP +LL
Sbjct: 121 GPNSLEVTAEDGTVTVVKFDQAIIAAGSRPIKLPFIPHEDPRIWDSTDALELKEVPGKLL 180

Query: 180 VMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVT 239
           VMGGGIIGLEMGTVY +LGS+IDVVEMFDQVIPAADKD+V+VFTK+I KKFNL+LETKVT
Sbjct: 181 VMGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDVVRVFTKQIKKKFNLILETKVT 240

Query: 240 AVEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDK 299
           AVEA+EDGIYV+MEGK APAEP RYDAVLVAIGR PNGK +DA KAGV++D+RGFI VDK
Sbjct: 241 AVEAREDGIYVSMEGKSAPAEPVRYDAVLVAIGRTPNGKLIDAEKAGVKIDERGFINVDK 300

Query: 300 QLRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAW 359
           QLRTNVPHI+AIGDIVGQPMLAHKGVHEGHVAAEVIAG KHYFDPKVIPSIAYT+PEVAW
Sbjct: 301 QLRTNVPHIYAIGDIVGQPMLAHKGVHEGHVAAEVIAGMKHYFDPKVIPSIAYTDPEVAW 360

Query: 360 VGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGG 419
           VGLTEKEAKE+GI+YETATFPWAASGRAIASDC++GMTKLIFDK++HRVIGGAIVG NGG
Sbjct: 361 VGLTEKEAKEQGIAYETATFPWAASGRAIASDCSEGMTKLIFDKDTHRVIGGAIVGVNGG 420

Query: 420 ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           ELLGEIGLAIEMGCDAED+ALTIHAHPTLHESVGLAAE++EGSITDLPNPKAKKK
Sbjct: 421 ELLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEIYEGSITDLPNPKAKKK 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: 829
Number of extensions: 24
Number of successful extensions: 5
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 199618 SO0426 (pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI ptt file))
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.29979.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.1e-153  496.0   5.1     6e-153  495.7   5.1    1.0  1  lcl|FitnessBrowser__MR1:199618  SO0426 pyruvate dehydrogenase co


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199618  SO0426 pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI pt
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.7   5.1    6e-153    6e-153       2     453 ..       7     459 ..       6     466 .. 0.97

  Alignments for each domain:
  == domain 1  score: 495.7 bits;  conditional E-value: 6e-153
                       TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldlek 79 
                                     ++vvv+G+Gp+GY aA raa lgl++++ve+ ++lGG+ClnvGCiP+KalL+ a+v+ee+k ++ +g+   + ++dl+k
  lcl|FitnessBrowser__MR1:199618   7 TQVVVLGAGPAGYSAAFRAADLGLETVIVERfSTLGGVCLNVGCIPSKALLHVAKVIEEAKAVAAHGVVFGEPTIDLDK 85 
                                     579**************************************************************************** PP

                       TIGR01350  80 llerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelplkleedekvv 157
                                     l   k+kv+++l+gG+ ++ k  kv+v++G +k+++++++ev++e+++ ++++++++iiA Gs+p++lp+ + ++  ++
  lcl|FitnessBrowser__MR1:199618  86 LRSFKQKVISQLTGGLGGMSKMRKVNVVNGFGKFSGPNSLEVTAEDGTvTVVKFDQAIIAAGSRPIKLPF-IPHEDPRI 163
                                     **********************************************998999******************.8888889* PP

                       TIGR01350 158 itseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvte 236
                                     ++s++alelkevp +l+++GgG+iG+E+++++++lG+++ v+e+ d+++pa d++v +v +k++kk + +++ ++kvt+
  lcl|FitnessBrowser__MR1:199618 164 WDSTDALELKEVPGKLLVMGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDVVRVFTKQIKK-KFNLILETKVTA 241
                                     ***************************************************************976.689********* PP

                       TIGR01350 237 vekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklm 313
                                     ve++ed + v++++k   +e +++++vLva+Gr+pn + ++ ek gv++derg+i+vd++lrtnvp+iyaiGD++g++m
  lcl|FitnessBrowser__MR1:199618 242 VEAREDGIYVSMEGKsaPAEPVRYDAVLVAIGRTPNGKLIDAEKAGVKIDERGFINVDKQLRTNVPHIYAIGDIVGQPM 320
                                     *********999988656899********************************************************** PP

                       TIGR01350 314 LAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfv 392
                                     LAh+ ++eg vaae iag ++  +d k++Ps+ yt+Peva vGlte++ake+gi+++++ fp aa+g+a+a++ ++G+ 
  lcl|FitnessBrowser__MR1:199618 321 LAHKGVHEGHVAAEVIAGMKH-YFDPKVIPSIAYTDPEVAWVGLTEKEAKEQGIAYETATFPWAASGRAIASDCSEGMT 398
                                     ******************665.9******************************************************** PP

                       TIGR01350 393 kvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453
                                     k+i+dk+t++++G  ivg +  el+ e+ la+e++  +e+la tih+HPtl E +  aa+ 
  lcl|FitnessBrowser__MR1:199618 399 KLIFDKDTHRVIGGAIVGVNGGELLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEI 459
                                     *****************************************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.93
//
[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