Alignments for a candidate for lpd in Thermocrinis albus DSM 14484

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Thermocrinis albus DSM 14484

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_012992228.1 THAL_RS06070 dihydrolipoyl dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_000025605.1:WP_012992228.1
          Length = 463

 Score =  266 bits (679), Expect = 1e-75
 Identities = 157/466 (33%), Positives = 254/466 (54%), Gaps = 17/466 (3%)

Query: 4   KFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKALLDS 63
           +FD+V++GAG GGY A + A + G+K A +E          +GG CLN GCIPSK +   
Sbjct: 2   EFDLVIVGAGSGGYEAGLYAHRRGMKVAFVEL-----SPETVGGNCLNRGCIPSKYMRYG 56

Query: 64  SYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEGHGK 123
           +Y         + +GI  KG  + +P +   + N+V+ +        +  G+  F G G 
Sbjct: 57  AYMIERFSHMSR-YGILPKGFHLSMPHLKEGRDNVVRTIRENFKKFAQHLGIPIFYGKGF 115

Query: 124 LLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAVPKK 183
           L     V V G D     L +  V++A+GS  V +         I D+      +  PK+
Sbjct: 116 LKDPNTVVVEGAD---ITLRSRFVLLATGSSTVSVGGMVADGRYIHDTDTIWNLEEFPKR 172

Query: 184 LGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAAD--EQIAKEALKVLTKQGLNIRL 241
           + ++G G +G+E   ++   GA+VT+ E  D+ LP A   E+ ++   + L K G++I+L
Sbjct: 173 VVIVGGGAVGVEFAYIFRMYGADVTLTELKDRLLPMAGIPEESSRFLARKLKKLGIDIKL 232

Query: 242 GARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGFI 301
              V   E  ++ + V+FTD     + T D +++AVGR+P T      ++G+ +DERGF+
Sbjct: 233 KTTVNHYEKTEEGLKVSFTDGT---QLTTDIILLAVGRKPNTEGF--KETGIEMDERGFV 287

Query: 302 YVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKA-QMNYDLIPSVIYTH 360
            VD HC+T++P V+A GD+    MLAHKA  EG +    + G +  + N  L+P +IY+ 
Sbjct: 288 VVDKHCRTNLPSVYACGDITSPLMLAHKAMYEGKVAVSHMLGDEGWEKNDTLMPKIIYSA 347

Query: 361 PEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVI 420
            E+A VG TE   + EG  V VG   F  + +AM   +  G V+V+ + +T R+LG H++
Sbjct: 348 YEVASVGLTEDEAEDEGYHVRVGVVSFVTNPKAMDDGENEGFVRVVVEERTKRILGCHIL 407

Query: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVN 466
           GP+A EL+ Q    M+ G  A+ +   V+SHP+LSEA+ +A++ V+
Sbjct: 408 GPNAGELLHQVIHAMKAGLGADFMSRSVYSHPSLSEAIGQASMEVH 453


Lambda     K      H
   0.316    0.134    0.375 

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: 517
Number of extensions: 25
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: 478
Length of database: 463
Length adjustment: 33
Effective length of query: 445
Effective length of database: 430
Effective search space:   191350
Effective search space used:   191350
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: 51 (24.3 bits)

Align candidate WP_012992228.1 THAL_RS06070 (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.3474354.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-131  425.0   0.0   1.9e-131  424.9   0.0    1.0  1  NCBI__GCF_000025605.1:WP_012992228.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025605.1:WP_012992228.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.9   0.0  1.9e-131  1.9e-131       1     459 [.       2     457 ..       2     459 .. 0.97

  Alignments for each domain:
  == domain 1  score: 424.9 bits;  conditional E-value: 1.9e-131
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek..eklGGtClnvGCiPtKalLksaevveelkeakelgieve 71 
                                           e+d+v++G+G gGY a   a + g+kva ve   e++GG Cln+GCiP+K +   a ++e++++++++gi  +
  NCBI__GCF_000025605.1:WP_012992228.1   2 EFDLVIVGAGSGGYEAGLYAHRRGMKVAFVELspETVGGNCLNRGCIPSKYMRYGAYMIERFSHMSRYGILPK 74 
                                           69*****************************8889************************************** PP

                             TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGsepr 144
                                           +++l++ +l+e +++vv+++++  k   ++ ++  + G++ l+d+++v v++ +   +l+   +++AtGs+  
  NCBI__GCF_000025605.1:WP_012992228.1  75 GFHLSMPHLKEGRDNVVRTIRENFKKFAQHLGIPIFYGKGFLKDPNTVVVEGAD--ITLRSRFVLLATGSSTV 145
                                           *****************************************************9..479************** PP

                             TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpal..daevsk 215
                                           ++ + + +d++++++ +++ +l+e+p+++vivGgG++GvEfa+if+ +G++vt+ el+dr+lp+    +e s+
  NCBI__GCF_000025605.1:WP_012992228.1 146 SVGG-MVADGRYIHDTDTIWNLEEFPKRVVIVGGGAVGVEFAYIFRMYGADVTLTELKDRLLPMAgiPEESSR 217
                                           ****.888889***************************************************9862269**** PP

                             TIGR01350 216 vlkkklkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgvelderga 288
                                           +l++klkk g++i+ +++v++ ek+e+ ++v+  ++  ++l+++ +L+avGrkpn+e  g++++g+e+derg+
  NCBI__GCF_000025605.1:WP_012992228.1 218 FLARKLKKLGIDIKLKTTVNHYEKTEEGLKVSFTDG--TQLTTDIILLAVGRKPNTE--GFKETGIEMDERGF 286
                                           ********************************9999..79*****************..************** PP

                             TIGR01350 289 ikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeq 361
                                           ++vd+++rtn+p++ya+GD++++lmLAh+A++eg va+ +++g+e  e + +++P++iy+  evasvGlte++
  NCBI__GCF_000025605.1:WP_012992228.1 287 VVVDKHCRTNLPSVYACGDITSPLMLAHKAMYEGKVAVSHMLGDEGWEKNDTLMPKIIYSAYEVASVGLTEDE 359
                                           *********************************************99************************** PP

                             TIGR01350 362 akeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveela 434
                                           a +eg++v+vg ++f  n ka+  +e++Gfv+v+v++ t++ilG+hi+g++a el++++  a++++l ++ ++
  NCBI__GCF_000025605.1:WP_012992228.1 360 AEDEGYHVRVGVVSFVTNPKAMDDGENEGFVRVVVEERTKRILGCHILGPNAGELLHQVIHAMKAGLGADFMS 432
                                           ************************************************************************* PP

                             TIGR01350 435 ktihpHPtlsEaikeaalaalgkai 459
                                           ++++ HP+lsEai +a  ++   +i
  NCBI__GCF_000025605.1:WP_012992228.1 433 RSVYSHPSLSEAIGQASMEVHFGPI 457
                                           ***************9988876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (463 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: 18.52
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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