Alignments for a candidate for lpd in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Echinicola vietnamensis KMM 6221, DSM 17526

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Echvi_4609 Echvi_4609 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Cola:Echvi_4609
          Length = 465

 Score =  447 bits (1149), Expect = e-130
 Identities = 232/461 (50%), Positives = 315/461 (68%), Gaps = 2/461 (0%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FD+IV+G GPGGYVAAIRA+QL LK A+VE   LGGICLNWGCIPTK+LL+SA+V+  + 
Sbjct: 6   FDVIVVGSGPGGYVAAIRASQLGLKTAVVEAAELGGICLNWGCIPTKALLKSAQVFEYIN 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
           +A+ YG+T   P  D   ++ RSR VA  ++ G++ LL+KNK+E + G G++   +++ V
Sbjct: 66  HAKDYGITVKDPKADFGGMVKRSRGVADGMSKGIQFLLKKNKIEQLLGWGKVKPGKKVEV 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
           E  +G++    A +IIIATGAR+R+LP +  D K I  Y  A+     PKK++V+GSGAI
Sbjct: 126 EDKDGKKTTYSADNIIIATGARSRELPAIKIDDKKIIGYRKAMTLEKQPKKMVVVGSGAI 185

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244
           G+EFA FYA  G EV++VE   +I+P EDAEVS  + + +KK G+ I+T + + ++    
Sbjct: 186 GVEFAYFYAAIGTEVTVVEFMDRIVPNEDAEVSKALERMYKKAGMNIMTSTEVTSVDTKG 245

Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304
            G    +    G+ T +     + A GVVANVEN GL+ +GI +D+G I VD F +TN+ 
Sbjct: 246 SGCKVTVKTKKGEETID-CDVVLSAAGVVANVENCGLEDVGIVVDKGRIKVDEFYKTNMP 304

Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364
             +AIGDV   P LAH AS +G+I  E IAG D   PL+  NIPGCTY  P++ASVG TE
Sbjct: 305 GYYAIGDVIPGPALAHVASAEGIICVEKIAGHD-PEPLDYNNIPGCTYCVPEIASVGYTE 363

Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424
           EKA++ GY +K+G FPF A+GKA A GA+DGFVK +FDA  G LLGAHM+GA VTEMI  
Sbjct: 364 EKAKEAGYELKVGKFPFSASGKAKAAGASDGFVKLIFDAKYGELLGAHMIGANVTEMIAE 423

Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
               R LETT  E+++T+ PHPT+SEA+ E+  AAY   +H
Sbjct: 424 IVAVRKLETTGHELIKTVHPHPTMSEAVMEAAAAAYDEVIH 464


Lambda     K      H
   0.319    0.135    0.393 

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: 585
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: 466
Length of database: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate Echvi_4609 Echvi_4609 (dihydrolipoamide 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.3545.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.1e-176  574.0  13.4   1.2e-176  573.8  13.4    1.0  1  lcl|FitnessBrowser__Cola:Echvi_4609  Echvi_4609 dihydrolipoamide dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4609  Echvi_4609 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.8  13.4  1.2e-176  1.2e-176       1     460 [.       5     464 ..       5     465 .] 0.97

  Alignments for each domain:
  == domain 1  score: 573.8 bits;  conditional E-value: 1.2e-176
                            TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                          ++dv+v+G+GpgGYvaAira+qlglk+a+ve  +lGG+Cln+GCiPtKalLksa+v+e++++ak++gi+v++ k
  lcl|FitnessBrowser__Cola:Echvi_4609   5 KFDVIVVGSGPGGYVAAIRASQLGLKTAVVEAAELGGICLNWGCIPTKALLKSAQVFEYINHAKDYGITVKDPK 78 
                                          59************************************************************************ PP

                            TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelp 147
                                           d+  +++r++ v + +++G+++Llkknk+e++ G +k++  k+vev++++++ ++++a+niiiAtG++ relp
  lcl|FitnessBrowser__Cola:Echvi_4609  79 ADFGGMVKRSRGVADGMSKGIQFLLKKNKIEQLLGWGKVKPGKKVEVEDKDGKkTTYSADNIIIATGARSRELP 152
                                          *************************************************998867899**************** PP

                            TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkkl 221
                                            ++ d k +i +++a++l+++p+++v+vG+G+iGvEfa+++a +G++vtv+e++dri+p++daevsk+l++++
  lcl|FitnessBrowser__Cola:Echvi_4609 153 A-IKIDDKKIIGYRKAMTLEKQPKKMVVVGSGAIGVEFAYFYAAIGTEVTVVEFMDRIVPNEDAEVSKALERMY 225
                                          *.999999****************************************************************** PP

                            TIGR01350 222 kkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293
                                          kk g++i+t+++vt+v ++    +  v++kk+ +et++ + vL a G+ +n+e+ gle +g+ +d+ g+ikvde
  lcl|FitnessBrowser__Cola:Echvi_4609 226 KKAGMNIMTSTEVTSVDTKGSGCKvtVKTKKG-EETIDCDVVLSAAGVVANVENCGLEDVGIVVDK-GRIKVDE 297
                                          **************988887766622555555.6*******************************9.******* PP

                            TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegi 367
                                           ++tn+pg yaiGDvi ++ LAhvAs+eg++++ekiag+ ++ +dy+ +P ++y+ Pe+asvG+tee+ake+g+
  lcl|FitnessBrowser__Cola:Echvi_4609 298 FYKTNMPGYYAIGDVIPGPALAHVASAEGIICVEKIAGHDPEPLDYNNIPGCTYCVPEIASVGYTEEKAKEAGY 371
                                          ************************************************************************** PP

                            TIGR01350 368 evkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHP 441
                                          e+kvgkfpf+a+gka a++ +dGfvk+i+d k+ge+lGah++ga+++e+i+e++++ +le+t +el kt+hpHP
  lcl|FitnessBrowser__Cola:Echvi_4609 372 ELKVGKFPFSASGKAKAAGASDGFVKLIFDAKYGELLGAHMIGANVTEMIAEIVAVRKLETTGHELIKTVHPHP 445
                                          ************************************************************************** PP

                            TIGR01350 442 tlsEaikeaalaalgkaih 460
                                          t+sEa++eaa+aa+++ ih
  lcl|FitnessBrowser__Cola:Echvi_4609 446 TMSEAVMEAAAAAYDEVIH 464
                                          ****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 11.69
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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