GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Limnohabitans curvus MWH-C5

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_108358556.1 B9Z44_RS13620 dihydrolipoyl dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_003063475.1:WP_108358556.1
          Length = 475

 Score =  490 bits (1262), Expect = e-143
 Identities = 265/474 (55%), Positives = 324/474 (68%), Gaps = 3/474 (0%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           MS++FDVVVIG GPGGY+AAIRAAQLG + ACI+++    G  A GGTC NVGCIPSKAL
Sbjct: 1   MSKQFDVVVIGGGPGGYIAAIRAAQLGFQVACIDEWKNAAGGPAPGGTCTNVGCIPSKAL 60

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

Query: 121 HGKLLANKQVEVT-GLDGKTQV-LEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQ 178
            G      +   T  + GKT+  + A+ VIIA+GS    +P  P  +  ++ + GAL   
Sbjct: 121 RGSFAGKAEGGYTVNVAGKTEESITAKQVIIATGSNARALPGTPFDEVNVLSNDGALRVG 180

Query: 179 AVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLN 238
           AVPKKL +IG+GVIGLE+GSVW RLGA+VT+LE L  FL A DEQIAKEA K   KQGL 
Sbjct: 181 AVPKKLALIGSGVIGLEMGSVWRRLGADVTILEGLPTFLGAVDEQIAKEAKKAFDKQGLK 240

Query: 239 IRLGARVTASEVKKKQVTVTFTDANGEQKET-FDKLIVAVGRRPVTTDLLAADSGVTLDE 297
           I LG +V      KK VTV +T+A GE      DKLIV++GR P T  L A   G+ +DE
Sbjct: 241 IELGVKVGEIVNGKKGVTVNYTNAKGEAIVLEADKLIVSIGRVPNTIGLNAEAIGLAVDE 300

Query: 298 RGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVI 357
           RG I VD  CKT+VPGV+A+GDVVRG MLAHKA EEGV VAERIAG    +N++ IP VI
Sbjct: 301 RGAIVVDGDCKTNVPGVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHGHVNFNTIPWVI 360

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

Query: 418 HVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471
           H++GP  +EL+ +  + MEF  SAED+  +  +HP+LSEA  EAALAV+   ++
Sbjct: 421 HMVGPQVSELISEAVVAMEFKASAEDIARICHAHPSLSEATKEAALAVDKRTLN 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: 684
Number of extensions: 31
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: 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 WP_108358556.1 B9Z44_RS13620 (dihydrolipoyl 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.2788997.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.9e-164  531.4   7.5     1e-163  531.3   7.5    1.0  1  NCBI__GCF_003063475.1:WP_108358556.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003063475.1:WP_108358556.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.3   7.5    1e-163    1e-163       1     459 [.       4     473 ..       4     475 .] 0.95

  Alignments for each domain:
  == domain 1  score: 531.3 bits;  conditional E-value: 1e-163
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.ek.l.....GGtClnvGCiPtKalLksaevveelke.ake 65 
                                           ++dvvviGgGpgGY+aAiraaqlg++va++++ ++       GGtC+nvGCiP+KalL+s+e ++++++ ++e
  NCBI__GCF_003063475.1:WP_108358556.1   4 QFDVVVIGGGPGGYIAAIRAAQLGFQVACIDEwKNaAggpapGGTCTNVGCIPSKALLQSSEHFDHANHhFAE 76 
                                           59****************************98643223333389************************99*** PP

                             TIGR01350  66 lgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld....kkevevkkekkekkleakn 134
                                           +gi++++vk+d++k+ +rk++vvk+ ++G+ +L+kknkv+ ++G++++ +      +v+v++++ e++++ak+
  NCBI__GCF_003063475.1:WP_108358556.1  77 HGISAKDVKMDVAKMIARKDNVVKQNNDGILYLFKKNKVTFFHGRGSFAGkaegGYTVNVAGKT-EESITAKQ 148
                                           **********************************************99883333458****998.57****** PP

                             TIGR01350 135 iiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207
                                           +iiAtGs+ r+lp+   +de  v+++++al++  vp++l+++G+GviG+E++s++++lG++vt++e l++ l 
  NCBI__GCF_003063475.1:WP_108358556.1 149 VIIATGSNARALPG-TPFDEVNVLSNDGALRVGAVPKKLALIGSGVIGLEMGSVWRRLGADVTILEGLPTFLG 220
                                           **************.6667667*************************************************** PP

                             TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelglek 278
                                           a+d++++k++kk++ k+g+ki  + kv e+ + ++ v+  +++ k+e+ +lea+k++v++Gr pn+ +l+ e+
  NCBI__GCF_003063475.1:WP_108358556.1 221 AVDEQIAKEAKKAFDKQGLKIELGVKVGEIVNGKKGVTvnYTNAKGEAIVLEADKLIVSIGRVPNTIGLNAEA 293
                                           ***********************************99965666666999************************ PP

                             TIGR01350 279 lgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePe 351
                                           +g+ +dergai+vd +++tnvpg++a+GDv++++mLAh+A++egv +ae+iag++  +++ +++P viyt+Pe
  NCBI__GCF_003063475.1:WP_108358556.1 294 IGLAVDERGAIVVDGDCKTNVPGVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHG-HVNFNTIPWVIYTSPE 365
                                           *****************************************************998.9*************** PP

                             TIGR01350 352 vasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalav 424
                                           +a vG te+q+k++g+++k+g fpf ang+a+al++t+G+vk ++d +t+eilG+h+vg+++selise+++a+
  NCBI__GCF_003063475.1:WP_108358556.1 366 IAWVGRTEQQLKADGVAYKAGTFPFLANGRARALGDTTGMVKFLADATTDEILGVHMVGPQVSELISEAVVAM 438
                                           ************************************************************************* PP

                             TIGR01350 425 eleltveelaktihpHPtlsEaikeaalaalgkai 459
                                           e+++++e++a+++h+HP+lsEa+keaala+ ++++
  NCBI__GCF_003063475.1:WP_108358556.1 439 EFKASAEDIARICHAHPSLSEATKEAALAVDKRTL 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.20
//
[ok]

This GapMind analysis is from Sep 24 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