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_050654705.1 C1M55_RS23120 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_002893965.1:WP_050654705.1
          Length = 465

 Score =  494 bits (1272), Expect = e-144
 Identities = 248/461 (53%), Positives = 327/461 (70%), Gaps = 6/461 (1%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           +D++V+GGGPGGYVAAIRAAQL L VALVER  LGGICLNWGCIPTK++L  A+V H + 
Sbjct: 10  YDVLVIGGGPGGYVAAIRAAQLGLSVALVERDRLGGICLNWGCIPTKAMLHGADVAHTLS 69

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
             + YG +S    FD+ K+++ SR V+ +L+ GV  L++KN V+VISG  +L     + V
Sbjct: 70  ELDTYGFSSASVQFDISKLVSFSRGVSEKLSGGVAYLMKKNGVDVISGTAKLVDKGVVSV 129

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
           E      +   A  +IIATGAR R +P V  DG  +WTY  AL P  +PK LLVIGSGAI
Sbjct: 130 EG-----QTYRADHVIIATGARPRSIPGVAPDGDRVWTYFDALVPKELPKSLLVIGSGAI 184

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244
           G+EFAS Y D G EV+IVE AP I+P+ED E+SA+V K F+KRGI I T +++  +T  D
Sbjct: 185 GVEFASLYRDLGTEVTIVEMAPHIMPVEDEEISAFVRKQFEKRGITIHTGASVSAVTVGD 244

Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304
           + V   +  +DG V        +VA G+  NVE++GL+ LG++++RG I  D + RT+  
Sbjct: 245 DAVQVNVQTSDG-VESLTVDRVLVAAGITGNVEDLGLEALGVEIERGAIVTDQWCRTSAF 303

Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364
            ++AIGDVAGAPCLAHKASH+ V+  E +AG   VHPL+   +PGCTYARPQVAS+GLTE
Sbjct: 304 GIYAIGDVAGAPCLAHKASHEAVLCVEKLAGVPDVHPLDRDYVPGCTYARPQVASLGLTE 363

Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424
           ++    G  +++G+F   ANGKA+A G  +GFVKT+FDAD+G LLGAHMVG +VTE IQG
Sbjct: 364 KQCAGTGRALRVGHFDLQANGKALAIGEAEGFVKTIFDADTGELLGAHMVGPDVTEQIQG 423

Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           + +AR+LE T  ++ E +F HPTLSEAMHESVL+A GR L+
Sbjct: 424 FGIARSLEATGEDLAEVVFAHPTLSEAMHESVLSALGRPLN 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: 637
Number of extensions: 26
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 WP_050654705.1 C1M55_RS23120 (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.2802286.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-171  557.1   0.3   1.6e-171  557.0   0.3    1.0  1  NCBI__GCF_002893965.1:WP_050654705.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050654705.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  557.0   0.3  1.6e-171  1.6e-171       1     460 [.       9     464 ..       9     465 .] 0.98

  Alignments for each domain:
  == domain 1  score: 557.0 bits;  conditional E-value: 1.6e-171
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           +ydv+viGgGpgGYvaAiraaqlgl+valve+++lGG+Cln+GCiPtKa+L+ a+v+++l+e++++g+++++v
  NCBI__GCF_002893965.1:WP_050654705.1   9 KYDVLVIGGGPGGYVAAIRAAQLGLSVALVERDRLGGICLNWGCIPTKAMLHGADVAHTLSELDTYGFSSASV 81 
                                           59*********************************************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprel 146
                                           ++d++kl+  ++ v++kl+gGv++L+kkn+v+vi+G+akl+dk+ v+v++++    ++a+++iiAtG++pr++
  NCBI__GCF_002893965.1:WP_050654705.1  82 QFDISKLVSFSRGVSEKLSGGVAYLMKKNGVDVISGTAKLVDKGVVSVEGQT----YRADHVIIATGARPRSI 150
                                           *************************************************998....56*************** PP

                             TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219
                                           p+ ++ d+++v+t+ +al  ke+p+sl+++G+G+iGvEfas++++lG++vt++e++++i+p++d+e+s +++k
  NCBI__GCF_002893965.1:WP_050654705.1 151 PG-VAPDGDRVWTYFDALVPKELPKSLLVIGSGAIGVEFASLYRDLGTEVTIVEMAPHIMPVEDEEISAFVRK 222
                                           **.9********************************************************************* PP

                             TIGR01350 220 klkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikv 291
                                           +++k+g++i+t+a+v++v+  +d+v+v+ + +  ve+l++++vLva G + n+e+lgle+lgve+++ gai++
  NCBI__GCF_002893965.1:WP_050654705.1 223 QFEKRGITIHTGASVSAVTVGDDAVQVNVQTSdGVESLTVDRVLVAAGITGNVEDLGLEALGVEIER-GAIVT 294
                                           *************************9777776679*****************************988.***** PP

                             TIGR01350 292 deelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvGlteeqak 363
                                           d+ +rt++ giyaiGDv+g + LAh+As+e+v+++ek+ag  +   +d+++vP ++y++P+vas+Glte+q+ 
  NCBI__GCF_002893965.1:WP_050654705.1 295 DQWCRTSAFGIYAIGDVAGAPCLAHKASHEAVLCVEKLAGVPDVhPLDRDYVPGCTYARPQVASLGLTEKQCA 367
                                           ****************************************988779*************************** PP

                             TIGR01350 364 eegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelakt 436
                                             g +++vg+f+++angkala++e++Gfvk+i+d +tge+lGah+vg++++e i+ + +a +le+t e+la++
  NCBI__GCF_002893965.1:WP_050654705.1 368 GTGRALRVGHFDLQANGKALAIGEAEGFVKTIFDADTGELLGAHMVGPDVTEQIQGFGIARSLEATGEDLAEV 440
                                           ************************************************************************* PP

                             TIGR01350 437 ihpHPtlsEaikeaalaalgkaih 460
                                           +++HPtlsEa++e++l+alg++++
  NCBI__GCF_002893965.1:WP_050654705.1 441 VFAHPTLSEAMHESVLSALGRPLN 464
                                           *******************99876 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: 18.83
//
[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