GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Rhodococcus qingshengii djl-6-2

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_047269781.1 C1M55_RS25440 dihydrolipoyl dehydrogenase

Query= BRENDA::P9WHH8
         (464 letters)



>NCBI__GCF_002893965.1:WP_047269781.1
          Length = 467

 Score =  729 bits (1881), Expect = 0.0
 Identities = 360/464 (77%), Positives = 408/464 (87%), Gaps = 2/464 (0%)

Query: 2   THYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHI 61
           +HYDVVVLGAGPGGYVAAIRAAQLGLSTAI+E KYWGGVCLNVGCIPSKALLRNAEL HI
Sbjct: 3   SHYDVVVLGAGPGGYVAAIRAAQLGLSTAIIEQKYWGGVCLNVGCIPSKALLRNAELAHI 62

Query: 62  FTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANTL 121
           FTK+AK FG+SG+V+FD+G A+DRSRKVA+GRV G+HFLMKKNKI E  G GTF DANT+
Sbjct: 63  FTKEAKTFGMSGDVSFDFGSAFDRSRKVADGRVKGIHFLMKKNKIPEYDGKGTFVDANTI 122

Query: 122 LVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAGA 181
            V+L+ GGTE++TFDNAIIATGS T+L+PGTSLS NVVTYEEQIL+R+LP SI+I GAGA
Sbjct: 123 SVELSKGGTETITFDNAIIATGSYTKLLPGTSLSENVVTYEEQILTRDLPGSILIVGAGA 182

Query: 182 IGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADG 241
           IGMEFGYVLKNYGVDVTIVEFL RALPNEDADVSKEI KQ+KKLGVTI T   V+SI+D 
Sbjct: 183 IGMEFGYVLKNYGVDVTIVEFLDRALPNEDADVSKEIAKQYKKLGVTIKTGAAVQSISDD 242

Query: 242 GSQVTVTV--TKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRT 299
           GS+VTV++   K G  + +  +KVLQ++GFAP VEG+GL+  GVALTDR AI +DDYMRT
Sbjct: 243 GSKVTVSIKDNKSGEIETVVVDKVLQSVGFAPRVEGFGLENTGVALTDRGAIAIDDYMRT 302

Query: 300 NVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFG 359
           NV HI+AIGDV   LQLAHVAEAQ VVAAETI GAET TLGD+RM+PRATFCQP VASFG
Sbjct: 303 NVPHIFAIGDVTAKLQLAHVAEAQAVVAAETIGGAETQTLGDYRMMPRATFCQPQVASFG 362

Query: 360 LTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAEL 419
           LTE+QA+ EGYDV VA FPF AN KAHG+GDP+GFVKL+AD K+GELLGGHL+G DV+EL
Sbjct: 363 LTEEQAKAEGYDVKVANFPFAANGKAHGLGDPTGFVKLIADKKYGELLGGHLIGPDVSEL 422

Query: 420 LPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMIN 463
           LPELTLAQ+WDLT +ELARNVHTHPT+SEALQE  HGL GHMIN
Sbjct: 423 LPELTLAQKWDLTVNELARNVHTHPTLSEALQEAIHGLAGHMIN 466


Lambda     K      H
   0.318    0.136    0.390 

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: 744
Number of extensions: 19
Number of successful extensions: 2
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: 464
Length of database: 467
Length adjustment: 33
Effective length of query: 431
Effective length of database: 434
Effective search space:   187054
Effective search space used:   187054
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_047269781.1 C1M55_RS25440 (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.2619273.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-171  556.6   1.5   2.3e-171  556.4   1.5    1.0  1  NCBI__GCF_002893965.1:WP_047269781.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_047269781.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  556.4   1.5  2.3e-171  2.3e-171       1     460 [.       4     466 ..       4     467 .] 0.97

  Alignments for each domain:
  == domain 1  score: 556.4 bits;  conditional E-value: 2.3e-171
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke.akelgieven 72 
                                           +ydvvv+G+GpgGYvaAiraaqlgl++a++e++++GG+ClnvGCiP+KalL++ae+++ +++ ak++g+ + +
  NCBI__GCF_002893965.1:WP_047269781.1   4 HYDVVVLGAGPGGYVAAIRAAQLGLSTAIIEQKYWGGVCLNVGCIPSKALLRNAELAHIFTKeAKTFGM-SGD 75 
                                           69********************************************************99988*****9.668 PP

                             TIGR01350  73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsepr 144
                                           v++d+ ++ +r++kv +  v+G+++L+kknk+ ++ G+++++d+++++v+ +k+  ++++++n+iiAtGs  +
  NCBI__GCF_002893965.1:WP_047269781.1  76 VSFDFGSAFDRSRKVADGRVKGIHFLMKKNKIPEYDGKGTFVDANTISVELSKGGtETITFDNAIIATGSYTK 148
                                           **************************************************9887669**************** PP

                             TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvl 217
                                            lp+  + +e  v+t+ee++  + +p s++ivG+G+iG+Ef+++++++Gv+vt++e+ldr lp++da+vsk++
  NCBI__GCF_002893965.1:WP_047269781.1 149 LLPG-TSLSE-NVVTYEEQILTRDLPGSILIVGAGAIGMEFGYVLKNYGVDVTIVEFLDRALPNEDADVSKEI 219
                                           ****.66665.5999999999**************************************************** PP

                             TIGR01350 218 kkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgvelderg 287
                                           +k++kk gv+i+t+a v++++++  +v+  ++ +k+ e+et+ ++kvL +vG+ p++e++gle++gv l++rg
  NCBI__GCF_002893965.1:WP_047269781.1 220 AKQYKKLGVTIKTGAAVQSISDDGSKVTvsIKDNKSgEIETVVVDKVLQSVGFAPRVEGFGLENTGVALTDRG 292
                                           ***************************955555555799********************************** PP

                             TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvGlte 359
                                           ai +d+++rtnvp+i+aiGDv++kl+LAhvA++++vvaae+i g+e++   dy+++P++++++P+vas+Glte
  NCBI__GCF_002893965.1:WP_047269781.1 293 AIAIDDYMRTNVPHIFAIGDVTAKLQLAHVAEAQAVVAAETIGGAETQtLGDYRMMPRATFCQPQVASFGLTE 365
                                           ********************************************9988788********************** PP

                             TIGR01350 360 eqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltvee 432
                                           eqak+eg++vkv++fpfaangka  l++ +Gfvk+i+dkk+ge+lG h++g+++sel+ el+la +++ltv+e
  NCBI__GCF_002893965.1:WP_047269781.1 366 EQAKAEGYDVKVANFPFAANGKAHGLGDPTGFVKLIADKKYGELLGGHLIGPDVSELLPELTLAQKWDLTVNE 438
                                           ************************************************************************* PP

                             TIGR01350 433 laktihpHPtlsEaikeaalaalgkaih 460
                                           la+ +h+HPtlsEa++ea++ + g++i+
  NCBI__GCF_002893965.1:WP_047269781.1 439 LARNVHTHPTLSEALQEAIHGLAGHMIN 466
                                           **********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (467 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.14
//
[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:

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:

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:

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:

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