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.3623169.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.98
//
[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