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_078430612.1 BK574_RS25485 dihydrolipoyl dehydrogenase

Query= CharProtDB::CH_004665
         (470 letters)



>NCBI__GCF_002019605.1:WP_078430612.1
          Length = 469

 Score =  714 bits (1843), Expect = 0.0
 Identities = 353/470 (75%), Positives = 408/470 (86%), Gaps = 1/470 (0%)

Query: 1   MVVGDFPIETDTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALIN 60
           MVVGDF  E DTLVIG+GPGGYVAAIRAAQLGQKVT+VEK  LGGVCLNVGCIPSKALI 
Sbjct: 1   MVVGDFATEVDTLVIGSGPGGYVAAIRAAQLGQKVTIVEKDNLGGVCLNVGCIPSKALIE 60

Query: 61  AGHRYENAKHSDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAY 120
           AGHRY +A  SD+MGIT + V +DF+K+QEWK SVVNKLTGGV GLLKGNKV++VKGEAY
Sbjct: 61  AGHRYHDAHSSDNMGITVDKVNLDFSKMQEWKTSVVNKLTGGVEGLLKGNKVEIVKGEAY 120

Query: 121 FVDSNSVRVMDENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALKEIPKKLV 180
           F D +SVRVMD+  AQTY FKN IIATGSRPIE+P FK+S+RVL+STGAL L E+PKKL+
Sbjct: 121 FADKDSVRVMDDKQAQTYKFKNCIIATGSRPIEIPAFKFSKRVLSSTGALNLTELPKKLL 180

Query: 181 VIGGGYIGTELGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAM 240
           VIGGGYIG ELG AY+N G+E+V+LEGG +ILPGFEKQMS LVTRR+KK G VE +T A+
Sbjct: 181 VIGGGYIGIELGAAYSNLGSEVVVLEGGKQILPGFEKQMSQLVTRRMKKNG-VEFYTEAL 239

Query: 241 AKGVEERPDGVTVTFEVKGEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTD 300
           AKGVEE  +GVTVT EVKGE KT +ADYVL+TVGRRPNT+E+GLEQ+G+E+ +RG +K D
Sbjct: 240 AKGVEETENGVTVTAEVKGETKTFEADYVLVTVGRRPNTEEIGLEQIGVEIDERGFIKVD 299

Query: 301 KQCRTNVPNIYAIGDIIEGPPLAHKASYEGKIAAEAIAGEPAEIDYLGIPAVVFSEPELA 360
           KQC+T+V  IYAIGDI+ GP LAHKASYE K+AAEAI+G   E+DYL IPAVVFS PELA
Sbjct: 300 KQCKTSVDGIYAIGDIVAGPMLAHKASYEAKVAAEAISGHSVEVDYLAIPAVVFSGPELA 359

Query: 361 SVGYTEAQAKEEGLDIVAAKFPFAANGRALSLNETDGFMKLITRKEDGLVIGAQIAGASA 420
           +VG  E +AK EG D+V +KFPFAANGRALSL+ETDGFMK++TRKEDGLV+G QIAGA+A
Sbjct: 360 TVGLNEQEAKAEGYDVVVSKFPFAANGRALSLDETDGFMKMVTRKEDGLVLGVQIAGANA 419

Query: 421 SDMISELSLAIEGGMTAEDIAMTIHAHPTLGEITMEAAEVAIGSPIHIVK 470
           SDMISE  +AIE GMTAEDIA+TIHAHP+LGEITME AEVA+G PIHIVK
Sbjct: 420 SDMISEACVAIEAGMTAEDIALTIHAHPSLGEITMETAEVALGMPIHIVK 469


Lambda     K      H
   0.314    0.134    0.372 

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: 781
Number of extensions: 27
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: 470
Length of database: 469
Length adjustment: 33
Effective length of query: 437
Effective length of database: 436
Effective search space:   190532
Effective search space used:   190532
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_078430612.1 BK574_RS25485 (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.232491.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-183  596.7  12.8   1.6e-183  596.5  12.8    1.0  1  NCBI__GCF_002019605.1:WP_078430612.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430612.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.5  12.8  1.6e-183  1.6e-183       2     461 .]      10     467 ..       9     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 596.5 bits;  conditional E-value: 1.6e-183
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                           +d++viG+GpgGYvaAiraaqlg+kv++vek++lGG+ClnvGCiP+Kal+++++ +++++  +++gi+v++v+
  NCBI__GCF_002019605.1:WP_078430612.1  10 VDTLVIGSGPGGYVAAIRAAQLGQKVTIVEKDNLGGVCLNVGCIPSKALIEAGHRYHDAHSSDNMGITVDKVN 82 
                                           79*********************************************************************** PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           ld++k++e+k++vv+kl+gGv++Llk nkve +kGea + dk++v+v ++k+++++++kn+iiAtGs+p+e+p
  NCBI__GCF_002019605.1:WP_078430612.1  83 LDFSKMQEWKTSVVNKLTGGVEGLLKGNKVEIVKGEAYFADKDSVRVMDDKQAQTYKFKNCIIATGSRPIEIP 155
                                           ************************************************************************* PP

                             TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                             +++++ +v++s++al+l+e+p++l+++GgG+iG+E++ ++++lG++v v+e  ++ilp +++++s++++++
  NCBI__GCF_002019605.1:WP_078430612.1 156 A-FKFSK-RVLSSTGALNLTELPKKLLVIGGGYIGIELGAAYSNLGSEVVVLEGGKQILPGFEKQMSQLVTRR 226
                                           *.99997.8**************************************************************** PP

                             TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvd 292
                                           +kk+gv+++t+a  + ve++e+ v+v+a+ k e++t ea++vLv+vGr+pn+ee+gle++gve+derg+ikvd
  NCBI__GCF_002019605.1:WP_078430612.1 227 MKKNGVEFYTEALAKGVEETENGVTVTAEVKgETKTFEADYVLVTVGRRPNTEEIGLEQIGVEIDERGFIKVD 299
                                           *************************88877779**************************************** PP

                             TIGR01350 293 eelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakee 365
                                           ++++t+v+giyaiGD+++++mLAh+As+e+ vaae+i g++  e+dy a+P+v+++ Pe+a+vGl+e++ak+e
  NCBI__GCF_002019605.1:WP_078430612.1 300 KQCKTSVDGIYAIGDIVAGPMLAHKASYEAKVAAEAISGHS-VEVDYLAIPAVVFSGPELATVGLNEQEAKAE 371
                                           ***************************************55.59***************************** PP

                             TIGR01350 366 gievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktih 438
                                           g++v+v+kfpfaang+al+l+etdGf+k+++ k++g +lG++i ga+as++ise+ +a+e+++t+e++a tih
  NCBI__GCF_002019605.1:WP_078430612.1 372 GYDVVVSKFPFAANGRALSLDETDGFMKMVTRKEDGLVLGVQIAGANASDMISEACVAIEAGMTAEDIALTIH 444
                                           ************************************************************************* PP

                             TIGR01350 439 pHPtlsEaikeaalaalgkaihv 461
                                           +HP+l+E+++e+a+ alg++ih+
  NCBI__GCF_002019605.1:WP_078430612.1 445 AHPSLGEITMETAEVALGMPIHI 467
                                           *********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (469 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.45
//
[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