Alignments for a candidate for lpd in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Derxia gummosa DSM 723

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_028312512.1 H566_RS0117905 dihydrolipoyl dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>NCBI__GCF_000482785.1:WP_028312512.1
          Length = 611

 Score =  871 bits (2251), Expect = 0.0
 Identities = 452/608 (74%), Positives = 502/608 (82%), Gaps = 16/608 (2%)

Query: 3   VIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVK 62
           +IEV VPDIGDFDAVEVIEVLVK GD +  EQSLI LESDKASM+VPS AAG V E+KVK
Sbjct: 4   IIEVTVPDIGDFDAVEVIEVLVKPGDKIAKEQSLITLESDKASMEVPSDAAGVVKEIKVK 63

Query: 63  VGDKVGQGAVICTIEAQQAAA------APAPAQAPAPAQA----PAPA-AAAPAPAP--- 108
           VGDKV +G+VI   E+  AAA      APA A  P PA A    PAP  AAAPAPA    
Sbjct: 64  VGDKVSKGSVILLAESDGAAAPATAPAAPASAATPVPAPAVQSSPAPVPAAAPAPASVPA 123

Query: 109 --AAASHSGGADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIP 166
             AA +++G  D  C MLVLGAGPGGYSAAFR+ADLGM+T++VERY+TLGGVCLNVGCIP
Sbjct: 124 PNAAPAYTGKVDHTCRMLVLGAGPGGYSAAFRSADLGMDTIIVERYATLGGVCLNVGCIP 183

Query: 167 SKALLHNAAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQV 226
           SKALLH AAV+DEA   A  G+ F   KID+D LR +K +VVGKLTGGLAGMAKARKV+ 
Sbjct: 184 SKALLHVAAVMDEASHFADLGVEFAAPKIDIDKLRAHKEKVVGKLTGGLAGMAKARKVRT 243

Query: 227 VRGIGNFLDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDS 286
           VRG+G F+D HH+EV +  G G+  TG+K VI+FE+AIIAAGSQ VKLPF+PEDPRIVDS
Sbjct: 244 VRGVGRFIDSHHLEVSVASGTGQELTGEKQVIKFEQAIIAAGSQPVKLPFVPEDPRIVDS 303

Query: 287 TGALELPEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKK 346
           TGALEL +VP KMLVIGGGIIGLEMATVYSTLGA IDVVEM+DGLM G DRDLV VW+K 
Sbjct: 304 TGALELRQVPKKMLVIGGGIIGLEMATVYSTLGARIDVVEMMDGLMVGPDRDLVNVWQKY 363

Query: 347 NKDRFGKVMLKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEK 406
           N  RF KVMLKTKTVGVEAKP+GI V FEGE APAEPQ YDLVLV+VGRSPNGK+I AE 
Sbjct: 364 NAKRFDKVMLKTKTVGVEAKPEGIAVTFEGEQAPAEPQLYDLVLVAVGRSPNGKKIGAEA 423

Query: 407 AGVAVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDA 466
           AGVAV++RGFI VD+QMRTNVPHIFAIGD+VGQPMLAHKAVHEAHVAAEAA GEKA+FDA
Sbjct: 424 AGVAVTDRGFIPVDRQMRTNVPHIFAIGDLVGQPMLAHKAVHEAHVAAEAAAGEKAFFDA 483

Query: 467 KQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEE 526
           + IP VA+TDPEVAW G TEDE K+ GIK   G FPWAASGRAIAN RDEGFTKLIFDE 
Sbjct: 484 RVIPGVAYTDPEVAWVGTTEDEAKKAGIKVKVGKFPWAASGRAIANTRDEGFTKLIFDEA 543

Query: 527 THRVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCT 586
           +H++IGGGIVGTHAGD I EV LAIEMGAD VDI KTIHPHPTLGESIGMAAE+ EG CT
Sbjct: 544 SHKIIGGGIVGTHAGDFIGEVALAIEMGADVVDIAKTIHPHPTLGESIGMAAEVAEGVCT 603

Query: 587 DVPPPRKR 594
           D+PP RK+
Sbjct: 604 DLPPARKK 611


Lambda     K      H
   0.316    0.134    0.387 

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: 1131
Number of extensions: 38
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: 594
Length of database: 611
Length adjustment: 37
Effective length of query: 557
Effective length of database: 574
Effective search space:   319718
Effective search space used:   319718
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: 53 (25.0 bits)

Align candidate WP_028312512.1 H566_RS0117905 (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.20147.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.5e-148  478.6   6.0   1.2e-147  478.2   6.0    1.1  1  lcl|NCBI__GCF_000482785.1:WP_028312512.1  H566_RS0117905 dihydrolipoyl deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028312512.1  H566_RS0117905 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.2   6.0  1.2e-147  1.2e-147       4     455 ..     140     599 ..     137     604 .. 0.96

  Alignments for each domain:
  == domain 1  score: 478.2 bits;  conditional E-value: 1.2e-147
                                 TIGR01350   4 vvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgieve 71 
                                               ++v+G+GpgGY aA r+a lg+ +++ve+  +lGG+ClnvGCiP+KalL+ a v++e++++++lg+e +
  lcl|NCBI__GCF_000482785.1:WP_028312512.1 140 MLVLGAGPGGYSAAFRSADLGMDTIIVERyATLGGVCLNVGCIPSKALLHVAAVMDEASHFADLGVEFA 208
                                               78***************************99************************************** PP

                                 TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke........kklea 132
                                                 k+d++kl ++kekvv kl+gG++++ k  kv ++ G +++ d++++ev+  +++        +++++
  lcl|NCBI__GCF_000482785.1:WP_028312512.1 209 APKIDIDKLRAHKEKVVGKLTGGLAGMAKARKVRTVRGVGRFIDSHHLEVSVASGTgqeltgekQVIKF 277
                                               ********************************************9988877666556689999999*** PP

                                 TIGR01350 133 kniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtviel 201
                                               +++iiA Gs+p +lp+ + ed  ++++s++alel++vp++++++GgG+iG+E+a+++++lG+ + v+e+
  lcl|NCBI__GCF_000482785.1:WP_028312512.1 278 EQAIIAAGSQPVKLPF-VPEDP-RIVDSTGALELRQVPKKMLVIGGGIIGLEMATVYSTLGARIDVVEM 344
                                               ****************.77776.7********************************************* PP

                                 TIGR01350 202 ldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrk 268
                                               +d ++   d+++ +v +k   k+  k++ ++k   ve++ + + v+ +++   +e   ++ vLvavGr+
  lcl|NCBI__GCF_000482785.1:WP_028312512.1 345 MDGLMVGPDRDLVNVWQKYNAKRFDKVMLKTKTVGVEAKPEGIAVTFEGEqaPAEPQLYDLVLVAVGRS 413
                                               *******************999999*******999999999999777776436788899********** PP

                                 TIGR01350 269 pnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeksei 337
                                               pn +++g e+ gv +++rg+i+vd+++rtnvp+i+aiGD++g++mLAh+A++e+ vaae++ag+++  +
  lcl|NCBI__GCF_000482785.1:WP_028312512.1 414 PNGKKIGAEAAGVAVTDRGFIPVDRQMRTNVPHIFAIGDLVGQPMLAHKAVHEAHVAAEAAAGEKA-FF 481
                                               ***************************************************************776.9* PP

                                 TIGR01350 338 dykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGa 406
                                               d++++P v yt+Peva vG te++ak++gi+vkvgkfp aa+g+a+a   ++Gf k+i+d+ +++i+G 
  lcl|NCBI__GCF_000482785.1:WP_028312512.1 482 DARVIPGVAYTDPEVAWVGTTEDEAKKAGIKVKVGKFPWAASGRAIANTRDEGFTKLIFDEASHKIIGG 550
                                               ********************************************************************* PP

                                 TIGR01350 407 hivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455
                                                ivg++a ++i e+ala+e+++ v ++aktihpHPtl+E i  aa+ a 
  lcl|NCBI__GCF_000482785.1:WP_028312512.1 551 GIVGTHAGDFIGEVALAIEMGADVVDIAKTIHPHPTLGESIGMAAEVAE 599
                                               *****************************************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (611 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: 12.85
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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