Alignments for a candidate for lpd in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Rhizobium leguminosarum 3841

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011654335.1 RL_RS28930 dihydrolipoyl dehydrogenase

Query= reanno::Smeli:SMc03204
         (464 letters)



>NCBI__GCF_000009265.1:WP_011654335.1
          Length = 465

 Score =  648 bits (1671), Expect = 0.0
 Identities = 326/465 (70%), Positives = 386/465 (83%), Gaps = 1/465 (0%)

Query: 1   MKEISCKLLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHAADE 60
           MKEI CKLLV+GAGPGGYV AIRAGQLGV+TVIVE  K GGTCL VGCIPSKALIHAA+E
Sbjct: 1   MKEIVCKLLVIGAGPGGYVCAIRAGQLGVDTVIVEAGKPGGTCLTVGCIPSKALIHAAEE 60

Query: 61  YHRLRAAASGKGPLGLSLSAPAIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGR 120
           +   +   +GK P+G+ +   +IDL RTIAWKDGIVGRL  GV+GLL+KA VK V G   
Sbjct: 61  FDATQKMLAGKNPMGIRVEGASIDLGRTIAWKDGIVGRLTSGVSGLLQKARVKIVHGRAH 120

Query: 121 FVDGKTVDVETETGLQRIRAEAIVIATGSAPVELPDLPFGGSVISSTQALALTDVPQTLA 180
           F DGKTV+VETETG Q IRAE +VIATGS PVEL +LPFGG VISST+AL+LT++P+ L 
Sbjct: 121 FRDGKTVEVETETGQQIIRAETVVIATGSDPVELSNLPFGGRVISSTEALSLTELPKKLV 180

Query: 181 VIGGGYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGELGVEVFTRTAA 240
           V+GGGYIGLELGTAF+K+GS VTV+EA  ++LPQYDA+L +PVM++L E  + + T   A
Sbjct: 181 VVGGGYIGLELGTAFSKMGSDVTVVEATPQVLPQYDAELVRPVMRKLTEGSIRLLTGAKA 240

Query: 241 KRLSADRRGLLAEE-NGRAFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSGRFIRIDDQC 299
             L+ +   L+ E  +GR   +PA+++LVTVGRRP T G GLEE+DLD +G ++RIDD+C
Sbjct: 241 IGLADNGEALIVEAADGRRESLPADRILVTVGRRPRTAGSGLEELDLDRAGPYLRIDDRC 300

Query: 300 RTSMRGVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHKRSWDKRCIPAVCFTDPEIVGAG 359
           RTSMRG+YAIGDVTGEPMLAHRAMAQGEMVAEI+AG KR+WDKRCIPA+CFTDPEIV AG
Sbjct: 301 RTSMRGIYAIGDVTGEPMLAHRAMAQGEMVAEIIAGKKRAWDKRCIPAICFTDPEIVSAG 360

Query: 360 LSPEEARAAGIDVKIGQFPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSEL 419
           LSP +A+A G +++ GQFPF ANGRAMT LSE+GFVR++ARAD +LVLG+QAVG GVSEL
Sbjct: 361 LSPADAKAQGYEIRTGQFPFSANGRAMTMLSEEGFVRIVARADTNLVLGLQAVGAGVSEL 420

Query: 420 SATFALAIEMGARLEDIAGTIHAHPTQSEAFQEAALKTLGHALHI 464
           SA FALAIEMGARLEDIAGTIHAHPT+SEA  EAALK LG ALHI
Sbjct: 421 SAAFALAIEMGARLEDIAGTIHAHPTRSEAVMEAALKALGSALHI 465


Lambda     K      H
   0.319    0.137    0.396 

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: 728
Number of extensions: 24
Number of successful extensions: 3
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: 464
Length of database: 465
Length adjustment: 33
Effective length of query: 431
Effective length of database: 432
Effective search space:   186192
Effective search space used:   186192
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_011654335.1 RL_RS28930 (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.20641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-155  503.1   0.4   3.9e-155  502.9   0.4    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011654335.1  RL_RS28930 dihydrolipoyl dehydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011654335.1  RL_RS28930 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.9   0.4  3.9e-155  3.9e-155       4     461 .]       8     465 .]       5     465 .] 0.98

  Alignments for each domain:
  == domain 1  score: 502.9 bits;  conditional E-value: 3.9e-155
                                 TIGR01350   4 vvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke....akelgi 68 
                                               ++viG+GpgGYv+Aira+qlg  +++ve  k GGtCl vGCiP+Kal+++ae ++  ++    ++ +gi
  lcl|NCBI__GCF_000009265.1:WP_011654335.1   8 LLVIGAGPGGYVCAIRAGQLGVDTVIVEAGKPGGTCLTVGCIPSKALIHAAEEFDATQKmlagKNPMGI 76 
                                               78**************************************************99987765323467*** PP

                                 TIGR01350  69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniii 137
                                               +ve+ ++dl +  ++k+ +v +l++Gv++Ll+k++v+ ++G+a+++d k+vev++e++++ ++a++++i
  lcl|NCBI__GCF_000009265.1:WP_011654335.1  77 RVEGASIDLGRTIAWKDGIVGRLTSGVSGLLQKARVKIVHGRAHFRDGKTVEVETETGQQIIRAETVVI 145
                                               ********************************************************************* PP

                                 TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206
                                               AtGs+p el+  l + + +vi+s+eal+l+e+p++lv+vGgG+iG+E++++f+k+G++vtv+e+++++l
  lcl|NCBI__GCF_000009265.1:WP_011654335.1 146 ATGSDPVELSN-LPFGG-RVISSTEALSLTELPKKLVVVGGGYIGLELGTAFSKMGSDVTVVEATPQVL 212
                                               ***********.99998.7************************************************** PP

                                 TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelg 275
                                               p+ dae+ + +++kl++  +++lt+ak   + ++ +++ vea ++  e+l a+++Lv+vGr+p++ + g
  lcl|NCBI__GCF_000009265.1:WP_011654335.1 213 PQYDAELVRPVMRKLTEGSIRLLTGAKAIGLADNGEALIVEAADGRRESLPADRILVTVGRRPRTAGSG 281
                                               ******************************************99999********************** PP

                                 TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPs 344
                                               le+l+++     ++ +d+++rt++ giyaiGDv+g++mLAh+A+++g ++ae iagk++ + d++ +P+
  lcl|NCBI__GCF_000009265.1:WP_011654335.1 282 LEELDLDRAG-PYLRIDDRCRTSMRGIYAIGDVTGEPMLAHRAMAQGEMVAEIIAGKKR-AWDKRCIPA 348
                                               *******888.99*******************************************887.9******** PP

                                 TIGR01350 345 viytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaea 413
                                               + +t+Pe+ s Gl+ ++ak++g+e+++g+fpf+ang+a+++  ++Gfv++++  +t+ +lG++ vga +
  lcl|NCBI__GCF_000009265.1:WP_011654335.1 349 ICFTDPEIVSAGLSPADAKAQGYEIRTGQFPFSANGRAMTMLSEEGFVRIVARADTNLVLGLQAVGAGV 417
                                               ********************************************************************* PP

                                 TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               sel + +ala+e+++++e++a tih+HPt sEa++eaal+alg+a+h+
  lcl|NCBI__GCF_000009265.1:WP_011654335.1 418 SELSAAFALAIEMGARLEDIAGTIHAHPTRSEAVMEAALKALGSALHI 465
                                               ********************************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 00:00:00.02
# Mc/sec: 9.32
//
[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