Alignments for a candidate for lpd in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Desulfobacter vibrioformis DSM 8776

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_035242564.1 Q366_RS19535 dihydrolipoyl dehydrogenase

Query= SwissProt::P80647
         (53 letters)



>NCBI__GCF_000745975.1:WP_035242564.1
          Length = 479

 Score = 62.4 bits (150), Expect = 3e-15
 Identities = 29/48 (60%), Positives = 37/48 (77%), Gaps = 1/48 (2%)

Query: 6  KDLVVIGSGPGGYVAAIKAAQLGMLTVCIEKYPTFGGTCLNVGCIPSK 53
          +++++IG+GPGGYVAA++AA LG     IEK    GGTCLN GCIPSK
Sbjct: 3  ENIIIIGAGPGGYVAALRAAGLGARVTLIEK-ENLGGTCLNHGCIPSK 49


Lambda     K      H
   0.319    0.140    0.428 

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: 100
Number of extensions: 4
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: 53
Length of database: 479
Length adjustment: 16
Effective length of query: 37
Effective length of database: 463
Effective search space:    17131
Effective search space used:    17131
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: 42 (20.8 bits)

Align candidate WP_035242564.1 Q366_RS19535 (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.1973163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-148  479.6   8.3   5.4e-148  479.4   8.3    1.0  1  NCBI__GCF_000745975.1:WP_035242564.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745975.1:WP_035242564.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.4   8.3  5.4e-148  5.4e-148       3     460 ..       4     478 ..       2     479 .] 0.96

  Alignments for each domain:
  == domain 1  score: 479.4 bits;  conditional E-value: 5.4e-148
                             TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieven.vk 74 
                                           ++++iG+GpgGYvaA raa lg +v+l+eke+lGGtCln GCiP+K + +sa+++ ++ +a ++gi++++ v+
  NCBI__GCF_000745975.1:WP_035242564.1   4 NIIIIGAGPGGYVAALRAAGLGARVTLIEKENLGGTCLNHGCIPSKIMKNSADLLLDCLKAGSMGIKISGtVS 76 
                                           79*****************************************************************9998** PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprel 146
                                            d+++l++rke+v ++ ++G+++Ll+k++v+ ++G+ak++ +++v v ++++   ++ ++++iiA G+ p ++
  NCBI__GCF_000745975.1:WP_035242564.1  77 PDIRALMQRKETVLESQRKGLAGLLEKAGVNIVMGRAKIVCPGKVAVVSDREPpISVAYDKLIIAAGTVPMNV 149
                                           *********************************************9988875568999*************** PP

                             TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp..aldaevskvl 217
                                           p  + +d++ +++s+++l+l+ +p+sl ivGgGviG Efa+if+ lG++vt++e++dr+lp   +da  sk+l
  NCBI__GCF_000745975.1:WP_035242564.1 150 PA-FPFDHEKILSSNDILSLDYIPTSLTIVGGGVIGSEFAFIFSALGCQVTIVEAMDRVLPlpGVDASCSKLL 221
                                           **.9*******************************************************852279******** PP

                             TIGR01350 218 kkklkkkgvkiltnakvtevekeedevv........veakkk.evetleaekvLvavGrkpnleelgleklgv 281
                                            +++kk+ +k+lt++ vt+ e+++  +         ++  +k +++ ++++++ v++Gr++  +elgle++g+
  NCBI__GCF_000745975.1:WP_035242564.1 222 LREMKKRRIKVLTDTIVTRAENKSSGLDiflgaspfTQSAGKlKTQIVQSDAMAVCIGRSSLAKELGLENIGL 294
                                           ******************99999988777788888778888899***************************** PP

                             TIGR01350 282 eldergaikvdeelrtnvpgiyaiGDvig..klmLAhvAskegvvaaekiagkeks...eidykavPsviyte 349
                                           e+d++g i v+e+++t v+++yaiGD+ g  ++mLAhvA++eg+vaa++++g++ +   ++ y+avP +i+t 
  NCBI__GCF_000745975.1:WP_035242564.1 295 ETDKAGWIAVNEYMQTCVDNVYAIGDILGpaHVMLAHVAYHEGLVAAANACGQTGTskiAMSYDAVPGAIFTM 367
                                           ***************************972257******************998877889************* PP

                             TIGR01350 350 PevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselal 422
                                           Pe+ +vGlte+qa+e+g+e++++ ++f+  gka a+++  G +k+iv+k +g++lG+h+ g++a++li+e+al
  NCBI__GCF_000745975.1:WP_035242564.1 368 PEIGTVGLTEQQAREQGKEIETAVVNFRVLGKAHAIDQIAGEAKMIVEKGSGKVLGVHMTGPHATDLIAEAAL 440
                                           ************************************************************************* PP

                             TIGR01350 423 aveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                           a++ +lt+++la+tih+HPtl+E++ e+al++lg ++h
  NCBI__GCF_000745975.1:WP_035242564.1 441 AIRKGLTAKDLAHTIHAHPTLAEIMGETALKILGIPLH 478
                                           *******************************9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (479 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: 00:00:00.01
# Mc/sec: 21.17
//
[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