Alignments for a candidate for lpd in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Dyella japonica UNC79MFTsu3.2

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate N515DRAFT_2778 N515DRAFT_2778 dihydrolipoamide dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2778
          Length = 474

 Score =  568 bits (1465), Expect = e-166
 Identities = 293/474 (61%), Positives = 348/474 (73%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           MS KFDV+VIGAGP GYVAAIRAAQLGLKTACI+ + GK+GK ALGGTCLNVGCIPSKAL
Sbjct: 1   MSDKFDVIVIGAGPAGYVAAIRAAQLGLKTACIDAFTGKDGKQALGGTCLNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           LDSS ++H     F VHGI A    IDV   + RK  IVK  TGGI  LFKAN VT+F G
Sbjct: 61  LDSSKQFHNLTHNFAVHGITADNAKIDVATFIGRKDKIVKQFTGGIGQLFKANKVTAFYG 120

Query: 121 HGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAV 180
            GKLL    VE+T  DG  Q + A NVI+ASGS P+E+P A   +  IVD+ GAL+F  V
Sbjct: 121 TGKLLKGNSVEITANDGSKQTISATNVILASGSVPIELPFAKFDNKFIVDNAGALDFPEV 180

Query: 181 PKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIR 240
           PK+LGVIGAGVIGLELGSVW RLGA+VT+LEAL  FL  AD  +AK A K   KQGL I+
Sbjct: 181 PKRLGVIGAGVIGLELGSVWGRLGADVTILEALPDFLSVADADVAKIAAKEFAKQGLKIK 240

Query: 241 LGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGF 300
           LGA++T +E+K  +V +T+ D +G  + T DKL+VAVGRR  T  LLA D+GV LDERG 
Sbjct: 241 LGAKLTKAEIKGNEVALTYEDKDGAHELTVDKLLVAVGRRAYTAGLLADDTGVKLDERGR 300

Query: 301 IYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTH 360
           I VD+H  T V GV+AIGD VRG MLAHK SEEGV VAE IAG    +N+D IP VIYT 
Sbjct: 301 IVVDEHNHTGVDGVWAIGDAVRGPMLAHKGSEEGVAVAEWIAGKAGHVNFDTIPWVIYTE 360

Query: 361 PEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVI 420
           PEIAW GKTE+ LK  G+   VGTFPFAA GRA+A N+  G VK++A A+TDR+LGVH++
Sbjct: 361 PEIAWAGKTEKELKDAGIPYKVGTFPFAAIGRAVAMNEAVGQVKMLAHAETDRLLGVHMV 420

Query: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIAN 474
           GP  +EL+ +  + MEF  SAEDL  +V +HPTLSEA+HEAAL+V+  AIH  N
Sbjct: 421 GPGVSELIAEAVVTMEFKGSAEDLARIVHAHPTLSEAVHEAALSVDKRAIHKGN 474


Lambda     K      H
   0.316    0.134    0.375 

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: 667
Number of extensions: 25
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: 478
Length of database: 474
Length adjustment: 33
Effective length of query: 445
Effective length of database: 441
Effective search space:   196245
Effective search space used:   196245
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 N515DRAFT_2778 N515DRAFT_2778 (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.11056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     2e-162  527.0   5.7   2.3e-162  526.8   5.7    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778  N515DRAFT_2778 dihydrolipoamide 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2778  N515DRAFT_2778 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.8   5.7  2.3e-162  2.3e-162       1     460 [.       4     471 ..       4     472 .. 0.97

  Alignments for each domain:
  == domain 1  score: 526.8 bits;  conditional E-value: 2.3e-162
                                    TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaevvee 59 
                                                  ++dv+viG+Gp+GYvaAiraaqlglk+a+++       k+ lGGtClnvGCiP+KalL s++ +++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778   4 KFDVIVIGAGPAGYVAAIRAAQLGLKTACIDaftgkdgKQALGGTCLNVGCIPSKALLDSSKQFHN 69 
                                                  59****************************86666665789************************* PP

                                    TIGR01350  60 lke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkke 124
                                                  l++ ++ +gi+++n k+d++++  rk+k+vk+ +gG+ +L+k nkv+ + G++kll+ ++ve++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778  70 LTHnFAVHGITADNAKIDVATFIGRKDKIVKQFTGGIGQLFKANKVTAFYGTGKLLKGNSVEITAN 135
                                                  ****************************************************************99 PP

                                    TIGR01350 125 kke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasif 189
                                                  +++ ++++a n+i+A+Gs p+elp+  ++d+k+++++ +al ++evp++l ++G+GviG+E++s++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778 136 DGSkQTISATNVILASGSVPIELPF-AKFDNKFIVDNAGALDFPEVPKRLGVIGAGVIGLELGSVW 200
                                                  987799*******************.999************************************* PP

                                    TIGR01350 190 aklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.eve 254
                                                   +lG++vt++e+l+  l + da+v+k+++k++ k+g+ki+ +ak+t+ e + +ev ++ ++k  ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778 201 GRLGADVTILEALPDFLSVADADVAKIAAKEFAKQGLKIKLGAKLTKAEIKGNEVALTYEDKdGAH 266
                                                  **********************************************88888888885555555689 PP

                                    TIGR01350 255 tleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAsk 320
                                                  +l+++k+LvavGr++ + +l  + +gv+lderg+i+vde+ +t v+g++aiGD+++++mLAh+ s+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778 267 ELTVDKLLVAVGRRAYTAGLLADDTGVKLDERGRIVVDEHNHTGVDGVWAIGDAVRGPMLAHKGSE 332
                                                  ****************************************************************** PP

                                    TIGR01350 321 egvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalale 386
                                                  egv +ae iagk+  +++ +++P viytePe+a  G+te+++k++gi +kvg fpfaa+g+a+a++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778 333 EGVAVAEWIAGKAG-HVNFDTIPWVIYTEPEIAWAGKTEKELKDAGIPYKVGTFPFAAIGRAVAMN 397
                                                  ***********998.9************************************************** PP

                                    TIGR01350 387 etdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaal 452
                                                  e+ G vk++++ +t+++lG+h+vg+ +seli+e+++ +e+++++e+la+++h+HPtlsEa++eaal
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778 398 EAVGQVKMLAHAETDRLLGVHMVGPGVSELIAEAVVTMEFKGSAEDLARIVHAHPTLSEAVHEAAL 463
                                                  ****************************************************************** PP

                                    TIGR01350 453 aalgkaih 460
                                                  ++ ++aih
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2778 464 SVDKRAIH 471
                                                  ******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (474 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.99
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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