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.13640.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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.04
//
[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:

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:

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:

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:

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