Alignments for a candidate for lpd in Bacillus alkalinitrilicus DSM 22532

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Bacillus alkalinitrilicus DSM 22532

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_078428701.1 BK574_RS11495 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_002019605.1:WP_078428701.1
          Length = 473

 Score =  377 bits (967), Expect = e-109
 Identities = 201/476 (42%), Positives = 306/476 (64%), Gaps = 15/476 (3%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MA  +DL++LG G GGYVAAIRAAQL LK A+VE+  LGG CL+ GCIP+K+LLRSAEV+
Sbjct: 1   MAHEYDLVILGAGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVF 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
              + A  +G+ +     +  K+  R + +  +L +GV+ L++K K+++  G G++ G  
Sbjct: 61  VTTKRASDFGVETSDVSLNFIKVQERKQSIIDQLHNGVQHLMKKGKIDIYEGTGRILGPS 120

Query: 121 -------QMLVETTEGEE-KILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAM 172
                   + VE   GEE ++L  K++++ATG+R R LP + +DGK++ T   AL+   +
Sbjct: 121 IFSPTPGTISVEMNNGEENEMLIPKNVLVATGSRPRMLPGMQADGKYVLTSDEALQLEEL 180

Query: 173 PKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRIL 232
           P  ++++G G IGIE+AS  ADFG E++++E++ +ILP ED E+S    +  KK+GI+ +
Sbjct: 181 PTSMIIVGGGVIGIEWASMLADFGVEITVIEYSDRILPTEDHEISKEAQRLMKKKGIKFV 240

Query: 233 TQSALQNLTPD-DEGVTAEIAGADGKVTKERFS--HAIVAIGVVANVENIGLDKLGIKLD 289
           T + +   T +   GVT +   A+ K  ++ FS    +V++G  ANVE IGL+   I+++
Sbjct: 241 TGAKVLPETLEIASGVTIK---AEHKGEEKTFSADKLLVSVGRAANVEGIGLENTDIQVE 297

Query: 290 RGFIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPG 349
           +GF+  + F +T   H++AIGDV G   LAH ASH+G++A E IAG +    ++   +  
Sbjct: 298 KGFVLTNEFYQTKESHIYAIGDVIGGLQLAHVASHEGIVAVEHIAGLNP-DSIDYNTVSK 356

Query: 350 CTYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALL 409
           C Y+ P+VASVGL+E  A++QGY+VK G F F A GKA+  G +DGFVK V D  +  LL
Sbjct: 357 CIYSHPEVASVGLSETDAKEQGYSVKTGKFLFKAIGKALVFGESDGFVKFVVDEKTDDLL 416

Query: 410 GAHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           G HM+G  VT+MI    +A+ L+ +  E+  TI PHPTLSE + E+ LA  G+A+H
Sbjct: 417 GVHMIGPHVTDMISEAAIAKVLDASNWEVAHTIHPHPTLSEIIGEAALAVEGKAIH 472


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: 611
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: 473
Length adjustment: 33
Effective length of query: 433
Effective length of database: 440
Effective search space:   190520
Effective search space used:   190520
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_078428701.1 BK574_RS11495 (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.25168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-181  588.7   9.7   4.2e-181  588.5   9.7    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078428701.1  BK574_RS11495 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078428701.1  BK574_RS11495 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  588.5   9.7  4.2e-181  4.2e-181       1     460 [.       4     472 ..       4     473 .] 0.98

  Alignments for each domain:
  == domain 1  score: 588.5 bits;  conditional E-value: 4.2e-181
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgie 69 
                                               eyd+v++G+G+gGYvaAiraaqlglk+a+vekeklGGtCl++GCiP+KalL+saev+ + k a+++g+e
  lcl|NCBI__GCF_002019605.1:WP_078428701.1   4 EYDLVILGAGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVFVTTKRASDFGVE 72 
                                               69******************************************************************* PP

                                 TIGR01350  70 venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld.......kkevevkkekke..kk 129
                                               +++v+l++ k++erk++++++l +Gv++L+kk k++ ++G++++l+       +++++v+++++e  ++
  lcl|NCBI__GCF_002019605.1:WP_078428701.1  73 TSDVSLNFIKVQERKQSIIDQLHNGVQHLMKKGKIDIYEGTGRILGpsifsptPGTISVEMNNGEenEM 141
                                               *********************************************999999998999999998887799 PP

                                 TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198
                                               l  kn+++AtGs+pr+lp+ +++d+k+v+ts+eal+l+e+p+s++ivGgGviG+E+as++a++Gv++tv
  lcl|NCBI__GCF_002019605.1:WP_078428701.1 142 LIPKNVLVATGSRPRMLPG-MQADGKYVLTSDEALQLEELPTSMIIVGGGVIGIEWASMLADFGVEITV 209
                                               99*****************.************************************************* PP

                                 TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvt.evekeedevvveakkk.evetleaekvLvav 265
                                               ie++drilp++d+e+sk++++ +kkkg+k++t+akv  e+ + +  v+++a++k e++t +a+k+Lv+v
  lcl|NCBI__GCF_002019605.1:WP_078428701.1 210 IEYSDRILPTEDHEISKEAQRLMKKKGIKFVTGAKVLpETLEIASGVTIKAEHKgEEKTFSADKLLVSV 278
                                               ************************************988899999999999988899************ PP

                                 TIGR01350 266 GrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkek 334
                                               Gr +n+e++gle++++++++ g++ ++e ++t+ ++iyaiGDvig+l+LAhvAs+eg+va+e+iag ++
  lcl|NCBI__GCF_002019605.1:WP_078428701.1 279 GRAANVEGIGLENTDIQVEK-GFVLTNEFYQTKESHIYAIGDVIGGLQLAHVASHEGIVAVEHIAGLNP 346
                                               *****************999.************************************************ PP

                                 TIGR01350 335 seidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgei 403
                                                +idy++v ++iy++PevasvGl+e++ake+g++vk+gkf f+a+gkal+ +e+dGfvk +vd+kt+++
  lcl|NCBI__GCF_002019605.1:WP_078428701.1 347 DSIDYNTVSKCIYSHPEVASVGLSETDAKEQGYSVKTGKFLFKAIGKALVFGESDGFVKFVVDEKTDDL 415
                                               ********************************************************************* PP

                                 TIGR01350 404 lGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                               lG+h++g++++++ise+a+a  l+++ +e+a+tihpHPtlsE+i eaala+ gkaih
  lcl|NCBI__GCF_002019605.1:WP_078428701.1 416 LGVHMIGPHVTDMISEAAIAKVLDASNWEVAHTIHPHPTLSEIIGEAALAVEGKAIH 472
                                               ********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (473 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.18
//
[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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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