Alignments for a candidate for lpd in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Desulfobulbus mediterraneus DSM 13871

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_028584055.1 G494_RS0107595 dihydrolipoyl dehydrogenase

Query= BRENDA::P0A9P0
         (474 letters)



>NCBI__GCF_000429965.1:WP_028584055.1
          Length = 473

 Score =  389 bits (1000), Expect = e-113
 Identities = 207/466 (44%), Positives = 302/466 (64%), Gaps = 8/466 (1%)

Query: 5   IKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIE 64
           + TQV+V+G+GP GY AAFR ADLGLE  +V+     GGVCL  GCIPSK  L ++++I+
Sbjct: 6   VDTQVLVIGSGPGGYGAAFRAADLGLEVTLVDPAPRPGGVCLFQGCIPSKTFLFLSELID 65

Query: 65  EAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANT 124
           +A+  +  G+ F EP  D+ ++R W+E+V++ +  GL  +   R +++++G  +F  A+T
Sbjct: 66  DARRASAMGVSFAEPSIDLARVRAWREQVVDSMAKGLTTLCARRGIELISGKARFESADT 125

Query: 125 LEVEGENGKTVINFDNAIIAAGSRPIQLPFIPH-EDPRIWDSTDALELKEVPERLLVMGG 183
           + VE    +  I F  AIIA GS P+ LP +P   D RI DS+ AL L ++PERLLV+GG
Sbjct: 126 VFVEDAAVRR-IQFRQAIIATGSHPLALPGVPLVADGRIMDSSGALALADIPERLLVIGG 184

Query: 184 GIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFN-LMLETKVTAVE 242
           G IGLE+G++Y  LGS++ +VE+ D+++   D+D+V    +R+ + F+ + L+T+VT ++
Sbjct: 185 GYIGLELGSLYAGLGSRVRLVELSDRLLGGVDRDLVLPLQRRLEQAFDSIRLQTRVTGLK 244

Query: 243 AKEDGIYVTME--GKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300
              D + V++E  G+ +    +R   VLVAIGR  N   L   +AGV V   G I VD+Q
Sbjct: 245 ECADQVEVSLEIDGRTSTESVER---VLVAIGRAANSDGLGLDRAGVRVGPGGEIVVDEQ 301

Query: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360
            RTNV  IFA+GD+ G  MLAH    +G VAAEVIAG+   FD + +P++ YT+P+VAW 
Sbjct: 302 QRTNVAQIFAVGDVCGGMMLAHTATRQGKVAAEVIAGQASAFDVRAVPAVVYTDPQVAWC 361

Query: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420
           GL+E++A++  +      FPW  SGRA      DG+TKL+ D ES R++G  I G +   
Sbjct: 362 GLSEEQARQNKLPVRVERFPWKYSGRAATMGATDGLTKLLVDPESGRILGLGITGRDAEG 421

Query: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDL 466
           L+ E  LAIEMG  AED+AL+IH HPTL E+   AAE++ GS T L
Sbjct: 422 LIAEGVLAIEMGALAEDLALSIHPHPTLSETEAEAAELYSGSATHL 467


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: 558
Number of extensions: 24
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: 473
Length adjustment: 33
Effective length of query: 441
Effective length of database: 440
Effective search space:   194040
Effective search space used:   194040
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 WP_028584055.1 G494_RS0107595 (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.8978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-142  459.4   0.0   7.1e-142  459.2   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028584055.1  G494_RS0107595 dihydrolipoyl deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028584055.1  G494_RS0107595 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.2   0.0  7.1e-142  7.1e-142       3     460 ..       9     466 ..       7     467 .. 0.97

  Alignments for each domain:
  == domain 1  score: 459.2 bits;  conditional E-value: 7.1e-142
                                 TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                               +v+viG+GpgGY aA raa lgl+v+lv+   + GG+Cl +GCiP+K++L  +e++++++ a+ +g++ 
  lcl|NCBI__GCF_000429965.1:WP_028584055.1   9 QVLVIGSGPGGYGAAFRAADLGLEVTLVDPaPRPGGVCLFQGCIPSKTFLFLSELIDDARRASAMGVSF 77 
                                               799**************************9899************************************ PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAt 139
                                               ++ ++dl+++ +++e+vv+++++G+++L+ + ++e i+G+a+++++++v v++ +  + +++ ++iiAt
  lcl|NCBI__GCF_000429965.1:WP_028584055.1  78 AEPSIDLARVRAWREQVVDSMAKGLTTLCARRGIELISGKARFESADTVFVEDAAV-RRIQFRQAIIAT 145
                                               ******************************************************96.5*********** PP

                                 TIGR01350 140 Gseprelplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207
                                               Gs+p +lp+  l +d+ ++++s++al+l  +pe+l+++GgG+iG+E++s++a lG+ v ++el+dr+l 
  lcl|NCBI__GCF_000429965.1:WP_028584055.1 146 GSHPLALPGVpLVADG-RIMDSSGALALADIPERLLVIGGGYIGLELGSLYAGLGSRVRLVELSDRLLG 213
                                               *********8755665.7*************************************************** PP

                                 TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelg 275
                                                +d+++   l+++l++   +i  +++vt +++ +d+v+v+ + +  ++t ++e+vLva+Gr +n ++lg
  lcl|NCBI__GCF_000429965.1:WP_028584055.1 214 GVDRDLVLPLQRRLEQAFDSIRLQTRVTGLKECADQVEVSLEIDgRTSTESVERVLVAIGRAANSDGLG 282
                                               **************************************87776667999******************** PP

                                 TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPs 344
                                               l++ gv++   g i+vde+ rtnv++i+a+GDv g++mLAh+A+++g vaae iag+++ ++d +avP+
  lcl|NCBI__GCF_000429965.1:WP_028584055.1 283 LDRAGVRVGPGGEIVVDEQQRTNVAQIFAVGDVCGGMMLAHTATRQGKVAAEVIAGQAS-AFDVRAVPA 350
                                               ********************************************************886.9******** PP

                                 TIGR01350 345 viytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaea 413
                                               v+yt+P+va  Gl+eeqa++++  v+v +fp + +g+a +++ tdG+ k++vd+++g+ilG+ i g +a
  lcl|NCBI__GCF_000429965.1:WP_028584055.1 351 VVYTDPQVAWCGLSEEQARQNKLPVRVERFPWKYSGRAATMGATDGLTKLLVDPESGRILGLGITGRDA 419
                                               ********************************************************************* PP

                                 TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                                 li+e +la+e+++ +e+la +ihpHPtlsE+ +eaa+  +g+a h
  lcl|NCBI__GCF_000429965.1:WP_028584055.1 420 EGLIAEGVLAIEMGALAEDLALSIHPHPTLSETEAEAAELYSGSATH 466
                                               ***************************************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (473 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: 9.35
//
[ok]

This GapMind analysis is from Sep 24 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