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.22176.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.97
//
[ok]

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

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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