Alignments for a candidate for lpd in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Acidovorax sp. GW101-3H11

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate Ac3H11_2465 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)

Query= SwissProt::P14218
         (478 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2465
          Length = 475

 Score =  496 bits (1277), Expect = e-145
 Identities = 257/474 (54%), Positives = 329/474 (69%), Gaps = 3/474 (0%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           MS++FDV+VIG GPGGY+AAIRAAQLG   ACI+++   +G  A GGTC NVGCIPSKAL
Sbjct: 1   MSKQFDVIVIGGGPGGYIAAIRAAQLGFNVACIDEWKNGKGGPAPGGTCTNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           L SS  +  A + F  HGI A GV +DV  M+ARK  +VK    GI  LFK N V+ F G
Sbjct: 61  LQSSEHFEHANKHFAEHGITATGVKMDVAKMIARKDTVVKQNNDGILYLFKKNKVSFFHG 120

Query: 121 HGKLL--ANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQ 178
            G  +  A    E+       + +  + +IIA+GS    +P  P  +++++ + GAL   
Sbjct: 121 RGSFVKAAEGGYEIKVAGAAEESIVGKQIIIATGSNARALPGTPFDEELVLSNDGALRVG 180

Query: 179 AVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLN 238
           AVPKKLG+IG+GVIGLE+GSVW RLGAEVT+LE L  FL A DEQIAKEA K   KQGL 
Sbjct: 181 AVPKKLGLIGSGVIGLEMGSVWRRLGAEVTILEGLPTFLGAVDEQIAKEAKKAFDKQGLK 240

Query: 239 IRLGARVTASEVKKKQVTVTFTDANGE-QKETFDKLIVAVGRRPVTTDLLAADSGVTLDE 297
           I LG +V   +  KK V++ +T+A GE Q    DKLIV++GR P T  L     G+ LDE
Sbjct: 241 IELGVKVGEIKTGKKGVSIAYTNAKGEAQSLDVDKLIVSIGRVPNTIGLNVEAVGLALDE 300

Query: 298 RGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVI 357
           RG I VD  CKT++PGV+A+GDVVRG MLAHKA EEGV VAERIAG    +N++ +P VI
Sbjct: 301 RGAIVVDGDCKTNLPGVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHGHVNFNTVPWVI 360

Query: 358 YTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGV 417
           YT PEIAWVG+TEQ LKA+GV+   GTFPF A+GRA A  DTTG+VK++ADA+TD +LGV
Sbjct: 361 YTSPEIAWVGRTEQQLKADGVKYKAGTFPFLANGRARALGDTTGMVKMLADAETDEILGV 420

Query: 418 HVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471
           H++GP A+EL+ +  + MEF  S+ED+  +  +HP+LSEA  EAALAV+   ++
Sbjct: 421 HIVGPQASELISEAVVAMEFKASSEDIARICHAHPSLSEATKEAALAVDKRTLN 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: 698
Number of extensions: 29
Number of successful extensions: 4
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: 475
Length adjustment: 33
Effective length of query: 445
Effective length of database: 442
Effective search space:   196690
Effective search space used:   196690
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 Ac3H11_2465 (Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4))
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.31246.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.4e-164  534.1   6.7   1.5e-164  534.0   6.7    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465  Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.0   6.7  1.5e-164  1.5e-164       1     459 [.       4     473 ..       4     475 .] 0.95

  Alignments for each domain:
  == domain 1  score: 534.0 bits;  conditional E-value: 1.5e-164
                                        TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.ek......lGGtClnvGCiPtKalLksae 55 
                                                      ++dv+viGgGpgGY+aAiraaqlg++va++++ ++       GGtC+nvGCiP+KalL+s+e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465   4 QFDVIVIGGGPGGYIAAIRAAQLGFNVACIDEwKNgkggpaPGGTCTNVGCIPSKALLQSSE 65 
                                                      59****************************9843222333368******************* PP

                                        TIGR01350  56 vveelke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld. 115
                                                       +e++++ ++e+gi++++vk+d++k+ +rk++vvk+ ++G+ +L+kknkv+ ++G++++++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465  66 HFEHANKhFAEHGITATGVKMDVAKMIARKDTVVKQNNDGILYLFKKNKVSFFHGRGSFVKa 127
                                                      **998777***************************************************994 PP

                                        TIGR01350 116 ...kkevevkkekkekkleakniiiAtGseprelplkleedekvvitseealelkevpeslv 174
                                                           e++v++ + e+++  k+iiiAtGs+ r+lp+   +de++v+++++al++  vp++l 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465 128 aegGYEIKVAGAA-EESIVGKQIIIATGSNARALPG-TPFDEELVLSNDGALRVGAVPKKLG 187
                                                      4444589999998.579*******************.8888899****************** PP

                                        TIGR01350 175 ivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvte 236
                                                      ++G+GviG+E++s++++lG++vt++e l++ l a+d++++k++kk++ k+g+ki  + kv e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465 188 LIGSGVIGLEMGSVWRRLGAEVTILEGLPTFLGAVDEQIAKEAKKAFDKQGLKIELGVKVGE 249
                                                      ************************************************************** PP

                                        TIGR01350 237 vekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelr 296
                                                      +++ ++ v+  +++ k+e+++l+++k++v++Gr pn+ +l++e++g+ ldergai+vd +++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465 250 IKTGKKGVSiaYTNAKGEAQSLDVDKLIVSIGRVPNTIGLNVEAVGLALDERGAIVVDGDCK 311
                                                      ***999999766667779******************************************** PP

                                        TIGR01350 297 tnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlt 358
                                                      tn+pg++a+GDv++++mLAh+A++egv +ae+iag++  +++ ++vP viyt+Pe+a vG t
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465 312 TNLPGVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHG-HVNFNTVPWVIYTSPEIAWVGRT 372
                                                      ***********************************998.9********************** PP

                                        TIGR01350 359 eeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaselisel 420
                                                      e+q+k++g+++k+g fpf ang+a+al++t+G+vk+++d +t+eilG+hivg++aselise+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465 373 EQQLKADGVKYKAGTFPFLANGRARALGDTTGMVKMLADAETDEILGVHIVGPQASELISEA 434
                                                      ************************************************************** PP

                                        TIGR01350 421 alaveleltveelaktihpHPtlsEaikeaalaalgkai 459
                                                      ++a+e+++++e++a+++h+HP+lsEa+keaala+ ++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2465 435 VVAMEFKASSEDIARICHAHPSLSEATKEAALAVDKRTL 473
                                                      ********************************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (475 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: 11.69
//
[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