Alignments for a candidate for lpd in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Dechlorosoma suillum PS

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate Dsui_2219 Dsui_2219 dihydrolipoamide dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>FitnessBrowser__PS:Dsui_2219
          Length = 474

 Score =  508 bits (1308), Expect = e-148
 Identities = 267/478 (55%), Positives = 340/478 (71%), Gaps = 12/478 (2%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEK--YIGKEGKVALGGTCLNVGCIPSK 58
           MS++FDV+VIG GPGGYVAAIRAAQLG   AC E   Y   +G+  LGGTCLNVGCIPSK
Sbjct: 1   MSKQFDVLVIGGGPGGYVAAIRAAQLGFSVACCESNPYADPKGEPRLGGTCLNVGCIPSK 60

Query: 59  ALLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSF 118
           ALL +S+ + EA  AF   GI+     IDVP M+ RK  +V  LT GI  LFK N VT  
Sbjct: 61  ALLHTSHLFEEAGHAFAAQGIQVSAPKIDVPTMIGRKTAVVTQLTSGIKGLFKKNKVTQL 120

Query: 119 EGHGKLL----ANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGA 174
            GHG  +    A  QV+V       +V+EA+ VI+A+GS+   +P   +   I++D+ GA
Sbjct: 121 NGHGSFVGQGGAGWQVKVGD-----EVVEAKQVIVATGSKARHLPGIAVDQKIVLDNEGA 175

Query: 175 LEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTK 234
           LE Q+VPKKL +IGAGVIGLE+GSVW RLG+EVT+LEA   FL AAD+ +AKEALK+ TK
Sbjct: 176 LEQQSVPKKLAIIGAGVIGLEMGSVWRRLGSEVTILEASPDFLAAADQDVAKEALKLFTK 235

Query: 235 QGLNIRLGARVTASEVKKKQVTVTFTDANG-EQKETFDKLIVAVGRRPVTTDLLAADSGV 293
           QGLNI++G ++  ++V KK V++ +TD +G EQK   ++LIV+VGR P T  L A   G+
Sbjct: 236 QGLNIQMGVKLGETKVSKKGVSIAYTDKDGKEQKLDAERLIVSVGRVPNTDGLNAEKIGL 295

Query: 294 TLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLI 353
            L+ERG I VD HC+T++PGV+A+GDVV G MLAHKA EE VMVAE +AG     N+D I
Sbjct: 296 KLNERGQIEVDGHCRTNLPGVWAVGDVVSGPMLAHKAMEEAVMVAELMAGQAGHCNFDTI 355

Query: 354 PSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDR 413
           P VIYT PEIAWVGKTEQ LKA+GV    G  PF A+GRA+   D TG VK++A AKTDR
Sbjct: 356 PWVIYTSPEIAWVGKTEQQLKADGVAYKAGKIPFLANGRALGMGDPTGFVKMLACAKTDR 415

Query: 414 VLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471
           +LGVH+IGP+A+EL+ +  + MEFG ++EDL  +  +HPTLSEA+HEAALA +   +H
Sbjct: 416 ILGVHIIGPNASELIAEAVVTMEFGGASEDLARICHAHPTLSEAVHEAALACDKRPLH 473


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: 638
Number of extensions: 23
Number of successful extensions: 5
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 Dsui_2219 Dsui_2219 (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.6834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.5e-165  535.0   3.4   8.6e-165  534.8   3.4    1.0  1  lcl|FitnessBrowser__PS:Dsui_2219  Dsui_2219 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2219  Dsui_2219 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.8   3.4  8.6e-165  8.6e-165       1     461 []       4     474 .]       4     474 .] 0.96

  Alignments for each domain:
  == domain 1  score: 534.8 bits;  conditional E-value: 8.6e-165
                         TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalveke.........klGGtClnvGCiPtKalLksaevveelke.akelg 67 
                                       ++dv+viGgGpgGYvaAiraaqlg++va+ e +         +lGGtClnvGCiP+KalL++++++ee+ + ++  g
  lcl|FitnessBrowser__PS:Dsui_2219   4 QFDVLVIGGGPGGYVAAIRAAQLGFSVACCESNpyadpkgepRLGGTCLNVGCIPSKALLHTSHLFEEAGHaFAAQG 80 
                                       59*****************************6533333333369***************************99**** PP

                         TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGsepr 144
                                       i+v+  k+d+ ++  rk++vv++l++G+k+L+kknkv++++G++++++++    + + + +++eak++i+AtGs+ r
  lcl|FitnessBrowser__PS:Dsui_2219  81 IQVSAPKIDVPTMIGRKTAVVTQLTSGIKGLFKKNKVTQLNGHGSFVGQGGAGWQVKVGDEVVEAKQVIVATGSKAR 157
                                       ************************************************99988888888899*************** PP

                         TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkkl 221
                                       +lp+ +++d+k+v+++e+ale ++vp++l+i+G+GviG+E++s++++lG++vt++e+++  l+a d++v+k++ k +
  lcl|FitnessBrowser__PS:Dsui_2219 158 HLPG-IAVDQKIVLDNEGALEQQSVPKKLAIIGAGVIGLEMGSVWRRLGSEVTILEASPDFLAAADQDVAKEALKLF 233
                                       ****.************************************************************************ PP

                         TIGR01350 222 kkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelr 296
                                       +k+g++i ++ k+ e++ +++ v+  ++ k++++++l+ae+++v+vGr pn+++l+ ek+g++l+erg+i+vd ++r
  lcl|FitnessBrowser__PS:Dsui_2219 234 TKQGLNIQMGVKLGETKVSKKGVSiaYTDKDGKEQKLDAERLIVSVGRVPNTDGLNAEKIGLKLNERGQIEVDGHCR 310
                                       *************966666555554377777789******************************************* PP

                         TIGR01350 297 tnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgk 373
                                       tn+pg++a+GDv++++mLAh+A++e+v++ae +ag++  +++ +++P viyt+Pe+a vG+te+q+k++g+++k+gk
  lcl|FitnessBrowser__PS:Dsui_2219 311 TNLPGVWAVGDVVSGPMLAHKAMEEAVMVAELMAGQAG-HCNFDTIPWVIYTSPEIAWVGKTEQQLKADGVAYKAGK 386
                                       ***********************************998.9************************************* PP

                         TIGR01350 374 fpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikea 450
                                       +pf ang+al +++ +Gfvk+++  kt++ilG+hi+g++aseli+e+++ +e+++ +e+la+++h+HPtlsEa++ea
  lcl|FitnessBrowser__PS:Dsui_2219 387 IPFLANGRALGMGDPTGFVKMLACAKTDRILGVHIIGPNASELIAEAVVTMEFGGASEDLARICHAHPTLSEAVHEA 463
                                       ***************************************************************************** PP

                         TIGR01350 451 alaalgkaihv 461
                                       ala  ++++h+
  lcl|FitnessBrowser__PS:Dsui_2219 464 ALACDKRPLHF 474
                                       *****999995 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 6.91
//
[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