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; Dihydrolipoamide dehydrogenase; E3 component of branched-chain alpha-keto acid dehydrogenase complex; LPD-Val (uncharacterized)
to candidate WP_050655902.1 C1M55_RS30485 dihydrolipoyl dehydrogenase

Query= curated2:P54533
         (474 letters)



>NCBI__GCF_002893965.1:WP_050655902.1
          Length = 459

 Score =  326 bits (836), Expect = 9e-94
 Identities = 179/468 (38%), Positives = 275/468 (58%), Gaps = 20/468 (4%)

Query: 6   DVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRTARE 65
           DVVILGGG+GGY  AIRAAQLGL   ++E +K+GGTCLH+GCIP+KALL SAEV  +AR 
Sbjct: 9   DVVILGGGSGGYACAIRAAQLGLSVTLIEADKVGGTCLHRGCIPTKALLHSAEVADSART 68

Query: 66  ADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGKIDVYTGYGRILGPSIFSPL 125
           ++QFGV  +   ++  +V   K   V++L +G+  L+ + KI +  GYG  +G       
Sbjct: 69  SEQFGVRASFAGIDVAQVHDYKNGTVERLYSGLQGLLAQHKITIVNGYGTYVG------- 121

Query: 126 PGTISVERGNGEENDMLIPKQVIIATGSRPRMLPGLEVDGKSVLTSDEALQMEELPQSII 185
                  R    +        +++ATGS PR LPG+E+ G+ ++TSD+AL+++ +P S  
Sbjct: 122 ------GRSIDVDGTRYTGTSLVLATGSYPRELPGIEL-GRRIVTSDQALELDRVPTSAT 174

Query: 186 IVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFITGAKV 245
           ++GGGVIG+E+AS+   FG +VT++E   R++  ED   SK++E   +K+GI   T  KV
Sbjct: 175 VLGGGVIGVEFASLWRSFGAEVTIVEALPRLIAAEDPWSSKQLERAYRKRGIVCKTDTKV 234

Query: 246 LPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDIVTENGMISVN 305
             D+  + +  + I+   DG  +    + +LV++GR    +G G     I  + G +  +
Sbjct: 235 --DSAKEAAGSVRIEL-SDGTIL--DTDLLLVAVGRGPRTDGNGFAENGISLDKGFVVTD 289

Query: 306 ESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYSSPEA 365
           E  +T    +YA+GD++ GL LAH    +GI   E  AG +P P+   L+P+  YS PE 
Sbjct: 290 ERLRTSVDGVYAVGDIVPGLALAHRGFQQGIFVAEQIAGKDPIPVAEHLIPRVTYSHPEV 349

Query: 366 ASVGLTEDEAKANGHNVKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVHMIGPH 425
           ASVGL E+ A+    +V    +     GK+ +   + G +K++       ++GVH++G  
Sbjct: 350 ASVGLGEEVARTQYADVSTVIYDLAGNGKSQIL-RTTGGIKVIRSGTKGPVVGVHLVGDR 408

Query: 426 VTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIGEAALAADGKAIH 473
           V ++I EA LA   +A P EVG+ IH HP+ +EA+GEA LA  G  +H
Sbjct: 409 VGELIGEAQLAVAWEALPDEVGRFIHAHPSQNEALGEAMLALAGTPLH 456


Lambda     K      H
   0.315    0.135    0.382 

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: 630
Number of extensions: 42
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: 459
Length adjustment: 33
Effective length of query: 441
Effective length of database: 426
Effective search space:   187866
Effective search space used:   187866
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_050655902.1 C1M55_RS30485 (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.2485630.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-141  457.2   0.0   3.3e-141  457.0   0.0    1.0  1  NCBI__GCF_002893965.1:WP_050655902.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050655902.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.0   0.0  3.3e-141  3.3e-141       2     460 ..       8     456 ..       7     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 457.0 bits;  conditional E-value: 3.3e-141
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                            dvv++GgG gGY +Airaaqlgl+v+l+e +k+GGtCl++GCiPtKalL+saev++++++ +++g++++   
  NCBI__GCF_002893965.1:WP_050655902.1   8 SDVVILGGGSGGYACAIRAAQLGLSVTLIEADKVGGTCLHRGCIPTKALLHSAEVADSARTSEQFGVRASFAG 80 
                                           69******************************************************************999** PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           +d++++++ k+ +v++l +G+++Ll ++k++ ++G+++ ++ +++ v+++++    +  ++++AtGs prelp
  NCBI__GCF_002893965.1:WP_050655902.1  81 IDVAQVHDYKNGTVERLYSGLQGLLAQHKITIVNGYGTYVGGRSIDVDGTRY----TGTSLVLATGSYPRELP 149
                                           **************************************************95....699************** PP

                             TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                           + +e  + +++ts++alel++vp+s  ++GgGviGvEfas+++++G++vt++e+l+r+++a+d   sk+l+++
  NCBI__GCF_002893965.1:WP_050655902.1 150 G-IELGR-RIVTSDQALELDRVPTSATVLGGGVIGVEFASLWRSFGAEVTIVEALPRLIAAEDPWSSKQLERA 220
                                           *.99998.7**************************************************************** PP

                             TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293
                                           ++k+g+  +t++kv + ++ + +v++e +++  + l+++ +LvavGr p++++ g+++ g++ld+ g++++de
  NCBI__GCF_002893965.1:WP_050655902.1 221 YRKRGIVCKTDTKVDSAKEAAGSVRIELSDG--TILDTDLLLVAVGRGPRTDGNGFAENGISLDK-GFVVTDE 290
                                           ***************************9999..89******************************.******* PP

                             TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366
                                           +lrt+v+g+ya+GD++ +l LAh+ +++g+ +ae+iagk +  + ++++P+v+y++PevasvGl ee a+ ++
  NCBI__GCF_002893965.1:WP_050655902.1 291 RLRTSVDGVYAVGDIVPGLALAHRGFQQGIFVAEQIAGKDPIPVAEHLIPRVTYSHPEVASVGLGEEVARTQY 363
                                           ************************************************************************* PP

                             TIGR01350 367 ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439
                                            +v ++ +++a ngk+ +l   +G +kvi   ++g ++G+h+vg ++ eli e+ lav++e+  +e+ ++ih+
  NCBI__GCF_002893965.1:WP_050655902.1 364 ADVSTVIYDLAGNGKSQILRT-TGGIKVIRSGTKGPVVGVHLVGDRVGELIGEAQLAVAWEALPDEVGRFIHA 435
                                           ****************98875.5779*********************************************** PP

                             TIGR01350 440 HPtlsEaikeaalaalgkaih 460
                                           HP+ +Ea+ ea+la+ g+++h
  NCBI__GCF_002893965.1:WP_050655902.1 436 HPSQNEALGEAMLALAGTPLH 456
                                           ****************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (459 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.84
//
[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