Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SMc03204 SMc03204 dihydrolipoamide dehydrogenase

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



>FitnessBrowser__Smeli:SMc03204
          Length = 464

 Score =  906 bits (2341), Expect = 0.0
 Identities = 464/464 (100%), Positives = 464/464 (100%)

Query: 1   MKEISCKLLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHAADE 60
           MKEISCKLLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHAADE
Sbjct: 1   MKEISCKLLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHAADE 60

Query: 61  YHRLRAAASGKGPLGLSLSAPAIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGR 120
           YHRLRAAASGKGPLGLSLSAPAIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGR
Sbjct: 61  YHRLRAAASGKGPLGLSLSAPAIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGR 120

Query: 121 FVDGKTVDVETETGLQRIRAEAIVIATGSAPVELPDLPFGGSVISSTQALALTDVPQTLA 180
           FVDGKTVDVETETGLQRIRAEAIVIATGSAPVELPDLPFGGSVISSTQALALTDVPQTLA
Sbjct: 121 FVDGKTVDVETETGLQRIRAEAIVIATGSAPVELPDLPFGGSVISSTQALALTDVPQTLA 180

Query: 181 VIGGGYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGELGVEVFTRTAA 240
           VIGGGYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGELGVEVFTRTAA
Sbjct: 181 VIGGGYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGELGVEVFTRTAA 240

Query: 241 KRLSADRRGLLAEENGRAFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSGRFIRIDDQCR 300
           KRLSADRRGLLAEENGRAFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSGRFIRIDDQCR
Sbjct: 241 KRLSADRRGLLAEENGRAFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSGRFIRIDDQCR 300

Query: 301 TSMRGVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHKRSWDKRCIPAVCFTDPEIVGAGL 360
           TSMRGVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHKRSWDKRCIPAVCFTDPEIVGAGL
Sbjct: 301 TSMRGVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHKRSWDKRCIPAVCFTDPEIVGAGL 360

Query: 361 SPEEARAAGIDVKIGQFPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSELS 420
           SPEEARAAGIDVKIGQFPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSELS
Sbjct: 361 SPEEARAAGIDVKIGQFPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSELS 420

Query: 421 ATFALAIEMGARLEDIAGTIHAHPTQSEAFQEAALKTLGHALHI 464
           ATFALAIEMGARLEDIAGTIHAHPTQSEAFQEAALKTLGHALHI
Sbjct: 421 ATFALAIEMGARLEDIAGTIHAHPTQSEAFQEAALKTLGHALHI 464


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: 908
Number of extensions: 19
Number of successful extensions: 1
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: 464
Length adjustment: 33
Effective length of query: 431
Effective length of database: 431
Effective search space:   185761
Effective search space used:   185761
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 SMc03204 SMc03204 (dihydrolipoamide 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.10819.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.6e-154  501.0   0.1   1.8e-154  500.8   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc03204  SMc03204 dihydrolipoamide dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03204  SMc03204 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.8   0.1  1.8e-154  1.8e-154       3     461 .]       7     464 .]       5     464 .] 0.97

  Alignments for each domain:
  == domain 1  score: 500.8 bits;  conditional E-value: 1.8e-154
                           TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeake....lgievenv 73 
                                          ++v+G+GpgGYvaAira+qlg ++++vek k GGtClnvGCiP+Kal+++a+ +++l+ a++    lg++++  
  lcl|FitnessBrowser__Smeli:SMc03204   7 KLLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHAADEYHRLRAAASgkgpLGLSLSAP 81 
                                         579******************************************************99954323448999*99* PP

                           TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelpl 148
                                         ++dl++  ++k+ +v +l+gGv++Llkk++v+ + Ge++++d k+v v++e++ + ++a++i+iAtGs p elp 
  lcl|FitnessBrowser__Smeli:SMc03204  82 AIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGRFVDGKTVDVETETGLQRIRAEAIVIATGSAPVELPD 156
                                         ****************************************************99********************* PP

                           TIGR01350 149 kleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkk 223
                                          l + +  vi+s++al+l+ vp++l+++GgG+iG+E++++faklG+kvtv+e+ldrilp+ da++sk ++k+l +
  lcl|FitnessBrowser__Smeli:SMc03204 157 -LPFGG-SVISSTQALALTDVPQTLAVIGGGYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGE 229
                                         .99998.7******************************************************************* PP

                           TIGR01350 224 kgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtn 298
                                          gv++ t +  ++++++++ + +e++++ + ++ aekvLv+vGr+p +++ gle+++++     +i +d+++rt+
  lcl|FitnessBrowser__Smeli:SMc03204 230 LGVEVFTRTAAKRLSADRRGLLAEENGR-AFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSG-RFIRIDDQCRTS 302
                                         **********************998888.6899**************************888.78********** PP

                           TIGR01350 299 vpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgk 373
                                         + g+yaiGDv+g++mLAh+A+++g ++ae +ag+++ + d++ +P+v +t+Pe+   Gl+ e+a+++gi+vk+g+
  lcl|FitnessBrowser__Smeli:SMc03204 303 MRGVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHKR-SWDKRCIPAVCFTDPEIVGAGLSPEEARAAGIDVKIGQ 376
                                         *********************************666.9************************************* PP

                           TIGR01350 374 fpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaik 448
                                         fpf+ang+a+++  +dGfv+vi+  + + +lG++ vg  +sel + +ala+e+++++e++a tih+HPt sEa++
  lcl|FitnessBrowser__Smeli:SMc03204 377 FPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSELSATFALAIEMGARLEDIAGTIHAHPTQSEAFQ 451
                                         *************************************************************************** PP

                           TIGR01350 449 eaalaalgkaihv 461
                                         eaal++lg+a+h+
  lcl|FitnessBrowser__Smeli:SMc03204 452 EAALKTLGHALHI 464
                                         **********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (464 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: 11.66
//
[ok]

This GapMind analysis is from Sep 17 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