Alignments for a candidate for lpd in Bacillus altitudinis 41KF2b

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Bacillus altitudinis 41KF2b

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_035700441.1 BA79_RS01115 dihydrolipoyl dehydrogenase

Query= SwissProt::P85207
         (461 letters)



>NCBI__GCF_000691145.1:WP_035700441.1
          Length = 460

 Score =  295 bits (756), Expect = 2e-84
 Identities = 184/455 (40%), Positives = 261/455 (57%), Gaps = 14/455 (3%)

Query: 2   KTYDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHH 61
           KTYDL VIG GPGGY AA++ A+ G KV  +E   +GG CLN GCIP+K LL  AE +  
Sbjct: 3   KTYDLTVIGGGPGGYTAALQAAERGHKVALIEEDFLGGTCLNRGCIPSKTLLKHAEVIES 62

Query: 62  LKGAEGFGLKA-KPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELL--RGFARFKGPR 118
           ++ A+ +G++  +  L   K+   +D V++KL GG+A LLK  K+++   RG A  K   
Sbjct: 63  IEKAKSWGIETGEMVLSFDKMRKRKDDVIEKLRGGIAFLLKQGKIDVYNGRGTAVTKNRI 122

Query: 119 EIEVN--GETYGAQSFIIATGSEPM--PLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGG 174
           +IE     ET   +  IIATGS P   P+ G    E  +D++  +     IP  +++IGG
Sbjct: 123 DIEKQDGSETIETKELIIATGSSPAIPPIPGLK--EIQFDTSDTIFDIPDIPASVVIIGG 180

Query: 175 GAVGLELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYE 234
           G +GLEL  I+  L S+VT+IE  P I+P  D E + LL K L+K+G+ +   T  V   
Sbjct: 181 GVIGLELACIFQSLQSKVTIIEAAPSIIPQEDEEASKLLEKELKKKGIHIAKKT-TVTEV 239

Query: 235 KKQDGLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARM 294
            + +G+  +      G       +++LV VGRRP    +   +  +++D   FI+VN  M
Sbjct: 240 TESEGVKAIHATDDKGETHIFTAERLLVCVGRRPNVSAVS--QLDLQLDGP-FIKVNDEM 296

Query: 295 ETSAPGVYAIGDVARPPLLAHKAMKEGLVAAENAAGKNALFDFQ-VPSVVYTGPEWAGVG 353
           +TS  GVYAIGDVA    LAH AM E  VA  N  G+    +   VP  +YT PE A VG
Sbjct: 297 KTSVEGVYAIGDVAGGYQLAHAAMAEAAVAVSNICGEPERMNHDIVPRCIYTLPEVASVG 356

Query: 354 LTEEEARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGEL 413
           LTE+EA+  G NV+  +F  +ASG+AL  G   G IK+V D     ++G  +VGP   E+
Sbjct: 357 LTEKEAKAKGLNVRAERFDLAASGKALAAGVQTGFIKLVYDTVYGEVIGATMVGPHVTEM 416

Query: 414 IAEATLALEMGATVSDLGLTIHPHPTLSEGLMEAA 448
           I+EA+  + +  T  ++   IHPHPT+SEG  EAA
Sbjct: 417 ISEASSFMYLEGTAEEMAKMIHPHPTISEGFYEAA 451


Lambda     K      H
   0.316    0.138    0.395 

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: 574
Number of extensions: 39
Number of successful extensions: 7
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: 461
Length of database: 460
Length adjustment: 33
Effective length of query: 428
Effective length of database: 427
Effective search space:   182756
Effective search space used:   182756
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_035700441.1 BA79_RS01115 (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.3267784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-168  545.7   7.7   4.7e-168  545.5   7.7    1.0  1  NCBI__GCF_000691145.1:WP_035700441.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000691145.1:WP_035700441.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.5   7.7  4.7e-168  4.7e-168       2     457 ..       5     457 ..       4     460 .] 0.96

  Alignments for each domain:
  == domain 1  score: 545.5 bits;  conditional E-value: 4.7e-168
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                           yd+ viGgGpgGY+aA +aa+ g kval+e++ lGGtCln+GCiP+K+lLk+aev+e++++ak++gie+ ++ 
  NCBI__GCF_000691145.1:WP_035700441.1   5 YDLTVIGGGPGGYTAALQAAERGHKVALIEEDFLGGTCLNRGCIPSKTLLKHAEVIESIEKAKSWGIETGEMV 77 
                                           9************************************************************************ PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           l+++k+ +rk+ v++kl+gG+++Llk+ k++v++G+++ + k+++ ++k+++++++e+k++iiAtGs+p+ +p
  NCBI__GCF_000691145.1:WP_035700441.1  78 LSFDKMRKRKDDVIEKLRGGIAFLLKQGKIDVYNGRGTAVTKNRIDIEKQDGSETIETKELIIATGSSPAIPP 150
                                           ************************************************************************* PP

                             TIGR01350 148 lk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219
                                           ++ l+e +    ts++++ ++ +p s+vi+GgGviG+E+a+if++l++kvt+ie+++ i+p++d+e sk+l+k
  NCBI__GCF_000691145.1:WP_035700441.1 151 IPgLKEIQ--FDTSDTIFDIPDIPASVVIIGGGVIGLELACIFQSLQSKVTIIEAAPSIIPQEDEEASKLLEK 221
                                           *8654444..899************************************************************ PP

                             TIGR01350 220 klkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergaik 290
                                           +lkkkg++i ++++vtev+++e      ++ +k+e++  +ae++Lv+vGr+pn++   + +l+++ld   +ik
  NCBI__GCF_000691145.1:WP_035700441.1 222 ELKKKGIHIAKKTTVTEVTESEGVKAihATDDKGETHIFTAERLLVCVGRRPNVS--AVSQLDLQLDG-PFIK 291
                                           ****************9988876555325555559********************..9**********.99** PP

                             TIGR01350 291 vdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqak 363
                                           v++e++t+v+g+yaiGDv+g+ +LAh A++e+ va+ +i+g+ +  ++++ vP++iyt PevasvGlte++ak
  NCBI__GCF_000691145.1:WP_035700441.1 292 VNDEMKTSVEGVYAIGDVAGGYQLAHAAMAEAAVAVSNICGEPE-RMNHDIVPRCIYTLPEVASVGLTEKEAK 363
                                           *****************************************777.9*************************** PP

                             TIGR01350 364 eegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelakt 436
                                           ++g +v++ +f++aa+gkala++ ++Gf+k+++d  +ge++Ga++vg++++e+ise++ ++ le+t+ee+ak+
  NCBI__GCF_000691145.1:WP_035700441.1 364 AKGLNVRAERFDLAASGKALAAGVQTGFIKLVYDTVYGEVIGATMVGPHVTEMISEASSFMYLEGTAEEMAKM 436
                                           ************************************************************************* PP

                             TIGR01350 437 ihpHPtlsEaikeaalaalgk 457
                                           ihpHPt+sE ++eaal+++ k
  NCBI__GCF_000691145.1:WP_035700441.1 437 IHPHPTISEGFYEAALDIVSK 457
                                           ****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (460 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.11
//
[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 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