Alignments for a candidate for lpd in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Saccharomonospora cyanea NA-134

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_005454512.1 SACCYDRAFT_RS05990 dihydrolipoyl dehydrogenase

Query= BRENDA::Q9M5K2
         (507 letters)



>NCBI__GCF_000244975.1:WP_005454512.1
          Length = 457

 Score =  335 bits (858), Expect = 3e-96
 Identities = 193/465 (41%), Positives = 283/465 (60%), Gaps = 18/465 (3%)

Query: 45  DVVIIGGGPGGYVAAIKAAQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           D+VI+GGG GGY AA +AA+LGL  T IEK   LGGTCL+ GCIP+KALLH++ +   A+
Sbjct: 7   DLVILGGGSGGYAAAFRAAELGLSVTLIEK-DKLGGTCLHRGCIPTKALLHAAEVADSAR 65

Query: 105 HVFANHGVKVSSVEVDLPAMLAQKDTAVKNLTRGVEGLFKKNKVNYVKGYGKFLSPSEVS 164
                 GVK +   VD+  +   KD+ +  L +G++GL K NKVNYV+G G F+  +   
Sbjct: 66  DG-EQFGVKTTFEGVDIAGVHKYKDSVITRLYKGLQGLAKANKVNYVEGTGTFVGGT--- 121

Query: 165 VDTIDGENVVVKGKHIIVATGSDVKSLPGITIDEKKIVSSTGALSLTEIPKKLIVIGAGY 224
             T+D E     GK++++ATGS  K+LP + +  + I++S  AL+L  +PKK +V+G G 
Sbjct: 122 --TVDVEGTRYTGKNLVLATGSYSKTLPDLELGGR-IITSDDALTLDFVPKKAVVLGGGV 178

Query: 225 IGLEMGSVWGRLGSEVTVVEFAADIVPAMDGEIRKQFQRSLEKQKMKFMLKTKVVGVDSS 284
           IG+E  SVW   G+EVT+VE    +VPA D    KQ +R+  ++K+ F    K  G    
Sbjct: 179 IGVEFASVWASFGTEVTIVEALPRLVPAEDEFSSKQLERAFRRRKIAFKTGVKFTGAKQD 238

Query: 285 GDGVKLIVEPAEGGEQTTLEADVVLVSAGRTPFTSGLDLEKIGVETDKGGRILVNERFST 344
             GV + +E  E     TLEADV+LV+ GR P T+G   ++ G+  D+ G +L +ER  T
Sbjct: 239 AGGVTVSLESGE-----TLEADVLLVAVGRGPNTAGHGYDEAGLRMDR-GFVLTDERLRT 292

Query: 345 NVSGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGH-VDYDKVPGVVYTYPEVASVGK 403
           N+ GVYA+GD++PG  LAH+  + G+   E IAG     +D   +P V Y++PEVASVG 
Sbjct: 293 NLPGVYAVGDIVPGLQLAHRGFQQGIFVAEDIAGLDPKPIDESGIPRVTYSHPEVASVGL 352

Query: 404 TEEQLK-KEGVSYNVGKFPFMANSRAKAIDTAEGMVKILADKETDKILGVHIMSPNAGEL 462
           TE Q K K G       +    N +++ + T+ G VK++   +   ++G+H++    GEL
Sbjct: 353 TEAQAKEKYGPDITTFTYDLAGNGKSQILKTS-GAVKLIKAPD-GPVVGLHLVGDRVGEL 410

Query: 463 IHEAVLAINYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHM 507
           I EA L  N++A  ED+A + HAHPT +EA+ EA +A   KP+H+
Sbjct: 411 IGEAQLIYNWEAFPEDVAPLIHAHPTQTEALGEAHLALAGKPLHV 455


Lambda     K      H
   0.315    0.134    0.376 

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: 600
Number of extensions: 28
Number of successful extensions: 9
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: 507
Length of database: 457
Length adjustment: 34
Effective length of query: 473
Effective length of database: 423
Effective search space:   200079
Effective search space used:   200079
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: 52 (24.6 bits)

Align candidate WP_005454512.1 SACCYDRAFT_RS05990 (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.6812.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-142  461.1   0.0   2.2e-142  460.9   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454512.1  SACCYDRAFT_RS05990 dihydrolipoyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454512.1  SACCYDRAFT_RS05990 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.9   0.0  2.2e-142  2.2e-142       2     461 .]       6     455 ..       5     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 460.9 bits;  conditional E-value: 2.2e-142
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                                d+v++GgG gGY aA raa+lgl+v+l+ek+klGGtCl++GCiPtKalL++aev++++++ +++g+++
  lcl|NCBI__GCF_000244975.1:WP_005454512.1   6 ADLVILGGGSGGYAAAFRAAELGLSVTLIEKDKLGGTCLHRGCIPTKALLHAAEVADSARDGEQFGVKT 74 
                                               69*****************************************************************99 PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAt 139
                                               +   +d++ +++ k++v+++l +G+++L k nkv+ ++G++++++ ++v v++++    ++ kn+++At
  lcl|NCBI__GCF_000244975.1:WP_005454512.1  75 TFEGVDIAGVHKYKDSVITRLYKGLQGLAKANKVNYVEGTGTFVGGTTVDVEGTR----YTGKNLVLAT 139
                                               9999**************************************************9....56******** PP

                                 TIGR01350 140 GseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpa 208
                                               Gs  ++lp  le  + ++its++al+l+ vp++ v++GgGviGvEfas++a++G++vt++e+l+r++pa
  lcl|NCBI__GCF_000244975.1:WP_005454512.1 140 GSYSKTLPD-LELGG-RIITSDDALTLDFVPKKAVVLGGGVIGVEFASVWASFGTEVTIVEALPRLVPA 206
                                               *********.99999.7**************************************************** PP

                                 TIGR01350 209 ldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgle 277
                                               +d+  sk+l+++++++++ ++t+ k t  ++++  v+v+ +++  etlea+ +LvavGr pn+ + g +
  lcl|NCBI__GCF_000244975.1:WP_005454512.1 207 EDEFSSKQLERAFRRRKIAFKTGVKFTGAKQDAGGVTVSLESG--ETLEADVLLVAVGRGPNTAGHGYD 273
                                               ****************************************999..8*********************** PP

                                 TIGR01350 278 klgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsvi 346
                                               + g+++d+ g++ +de+lrtn+pg+ya+GD++ +l+LAh+ +++g+ +ae iag  ++ id++ +P+v+
  lcl|NCBI__GCF_000244975.1:WP_005454512.1 274 EAGLRMDR-GFVLTDERLRTNLPGVYAVGDIVPGLQLAHRGFQQGIFVAEDIAGLDPKPIDESGIPRVT 341
                                               *****998.************************************************************ PP

                                 TIGR01350 347 ytePevasvGlteeqakeeg.ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeas 414
                                               y++PevasvGlte+qake++  ++ +  +++a ngk+ +l +t+G vk+i  + +g ++G+h+vg ++ 
  lcl|NCBI__GCF_000244975.1:WP_005454512.1 342 YSHPEVASVGLTEAQAKEKYgPDITTFTYDLAGNGKSQIL-KTSGAVKLIKAP-DGPVVGLHLVGDRVG 408
                                               ******************96479*************9876.689*****9776.689************ PP

                                 TIGR01350 415 eliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               eli e+ l+ ++e+  e++a +ih+HPt +Ea+ ea la+ gk++hv
  lcl|NCBI__GCF_000244975.1:WP_005454512.1 409 ELIGEAQLIYNWEAFPEDVAPLIHAHPTQTEALGEAHLALAGKPLHV 455
                                               ********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (457 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: 00:00:00.02
# Mc/sec: 7.69
//
[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