Alignments for a candidate for lpd in Thermomonospora curvata DSM 43183

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Thermomonospora curvata DSM 43183

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_012854130.1 TCUR_RS18775 dihydrolipoyl dehydrogenase

Query= BRENDA::P9WHH8
         (464 letters)



>NCBI__GCF_000024385.1:WP_012854130.1
          Length = 468

 Score =  650 bits (1677), Expect = 0.0
 Identities = 326/467 (69%), Positives = 385/467 (82%), Gaps = 5/467 (1%)

Query: 2   THYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHI 61
           TH+DVVVLGAGPGGYVAAIRAAQLGL T IVE +YWGGVCLNVGCIPSKALLRNAEL ++
Sbjct: 3   THFDVVVLGAGPGGYVAAIRAAQLGLRTGIVEERYWGGVCLNVGCIPSKALLRNAELAYL 62

Query: 62  FTKDAKAFGIS--GEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADAN 119
           F  + K FGI   G+V FD+  A  RSR+VA+GRV GVH+LMKKN ITE HG G F D +
Sbjct: 63  FNNERKLFGIEVDGQVRFDFAAAVQRSRQVADGRVKGVHYLMKKNGITEFHGRGVFTDPH 122

Query: 120 TLLVDLNDGG-TESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAG 178
           TL V   DGG  ++VTFD+ IIATG+  RL+PGTSLS  VVTYEEQIL+ ELP+SI+IAG
Sbjct: 123 TLQVTPTDGGQAQTVTFDHCIIATGAHPRLLPGTSLSERVVTYEEQILAEELPESIVIAG 182

Query: 179 AGAIGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESI 238
           AGAIG+EFGYVL NYG  VTIVEFL R +P ED +VSKE+ ++++KLG+ +LT+T+VE+I
Sbjct: 183 AGAIGVEFGYVLHNYGTKVTIVEFLDRMVPGEDEEVSKELARRYRKLGIDVLTSTRVEAI 242

Query: 239 ADGGSQVTVTVT-KDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYM 297
            D G +V VTVT  DG  + L+A+KVLQAIGFAPNVEGYGL+K GV LTDR AI VD   
Sbjct: 243 DDSGEKVKVTVTGSDGQPKTLEADKVLQAIGFAPNVEGYGLEKTGVRLTDRGAIDVDARC 302

Query: 298 RTNVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVAS 357
           RT+V HI+AIGDV   L LAH AEA G+VAAETIAGAET+ + D+RM+PRAT+CQP +AS
Sbjct: 303 RTSVPHIFAIGDVTAKLMLAHTAEAMGIVAAETIAGAETMEI-DYRMVPRATYCQPQIAS 361

Query: 358 FGLTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVA 417
           FGLTE QAR EGYDV VAKFPFTAN K+HG+GDP+GFVKL+ADAK+GELLGGH++G DV 
Sbjct: 362 FGLTEAQARAEGYDVKVAKFPFTANGKSHGLGDPNGFVKLIADAKYGELLGGHMIGPDVT 421

Query: 418 ELLPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF 464
           ELLPELTLAQ+WDLT  E+ARN+H HPT+SEA++E  HGL GHMINF
Sbjct: 422 ELLPELTLAQQWDLTVHEVARNIHAHPTLSEAVKEAVHGLAGHMINF 468


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: 702
Number of extensions: 23
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: 464
Length of database: 468
Length adjustment: 33
Effective length of query: 431
Effective length of database: 435
Effective search space:   187485
Effective search space used:   187485
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_012854130.1 TCUR_RS18775 (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.29726.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-174  565.6   0.1   4.5e-174  565.4   0.1    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012854130.1  TCUR_RS18775 dihydrolipoyl dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012854130.1  TCUR_RS18775 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.4   0.1  4.5e-174  4.5e-174       1     460 [.       4     467 ..       4     468 .] 0.97

  Alignments for each domain:
  == domain 1  score: 565.4 bits;  conditional E-value: 4.5e-174
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke.akelgi 68 
                                               ++dvvv+G+GpgGYvaAiraaqlgl++ +ve++++GG+ClnvGCiP+KalL++ae+++ +++  k +gi
  lcl|NCBI__GCF_000024385.1:WP_012854130.1   4 HFDVVVLGAGPGGYVAAIRAAQLGLRTGIVEERYWGGVCLNVGCIPSKALLRNAELAYLFNNeRKLFGI 72 
                                               59*********************************************************999899**** PP

                                 TIGR01350  69 even.vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke..kkleakn 134
                                               ev++ v++d++++++r+++v +  v+Gv++L+kkn++++++G++ ++d+++++v+ +++   +++++++
  lcl|NCBI__GCF_000024385.1:WP_012854130.1  73 EVDGqVRFDFAAAVQRSRQVADGRVKGVHYLMKKNGITEFHGRGVFTDPHTLQVTPTDGGqaQTVTFDH 141
                                               ***99*************************************************988765679****** PP

                                 TIGR01350 135 iiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielld 203
                                               +iiAtG++pr lp+  + +e +v+t+ee++  +e+pes+vi G+G+iGvEf+++++++G+kvt++e+ld
  lcl|NCBI__GCF_000024385.1:WP_012854130.1 142 CIIATGAHPRLLPG-TSLSE-RVVTYEEQILAEELPESIVIAGAGAIGVEFGYVLHNYGTKVTIVEFLD 208
                                               **************.55554.799********************************************* PP

                                 TIGR01350 204 rilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpn 270
                                               r++p +d+evsk+l+++++k g+++lt+++v+++ ++ ++v+v+  ++  + +tlea+kvL a+G+ pn
  lcl|NCBI__GCF_000024385.1:WP_012854130.1 209 RMVPGEDEEVSKELARRYRKLGIDVLTSTRVEAIDDSGEKVKVTVTGSdgQPKTLEADKVLQAIGFAPN 277
                                               *************************************9999966655544789**************** PP

                                 TIGR01350 271 leelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidy 339
                                               +e+ glek+gv+l++rgai vd+++rt+vp+i+aiGDv++klmLAh+A+++g+vaae+iag+e+ eidy
  lcl|NCBI__GCF_000024385.1:WP_012854130.1 278 VEGYGLEKTGVRLTDRGAIDVDARCRTSVPHIFAIGDVTAKLMLAHTAEAMGIVAAETIAGAETMEIDY 346
                                               ********************************************************************* PP

                                 TIGR01350 340 kavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahi 408
                                               ++vP+++y++P++as+Glte+qa++eg++vkv+kfpf+angk+  l++ +Gfvk+i+d k+ge+lG h+
  lcl|NCBI__GCF_000024385.1:WP_012854130.1 347 RMVPRATYCQPQIASFGLTEAQARAEGYDVKVAKFPFTANGKSHGLGDPNGFVKLIADAKYGELLGGHM 415
                                               ********************************************************************* PP

                                 TIGR01350 409 vgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                               +g++++el+ el+la +++ltv+e+a+ ih+HPtlsEa+kea++ + g++i+
  lcl|NCBI__GCF_000024385.1:WP_012854130.1 416 IGPDVTELLPELTLAQQWDLTVHEVARNIHAHPTLSEAVKEAVHGLAGHMIN 467
                                               ***********************************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (468 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.71
//
[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