Alignments for a candidate for lpd in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Flavobacterium beibuense F44-8

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_035130862.1 Q763_RS02450 dihydrolipoyl dehydrogenase

Query= CharProtDB::CH_123536
         (491 letters)



>NCBI__GCF_000769915.1:WP_035130862.1
          Length = 468

 Score =  475 bits (1222), Expect = e-138
 Identities = 247/458 (53%), Positives = 325/458 (70%), Gaps = 2/458 (0%)

Query: 26  YDVVVIGGGPGGYVAAIKAAQLGLNTACIEKRGALGGTCLNVGCIPSKSLLNNSHLLHQI 85
           +DVVVIG GPGGYVAAI+ AQLG NTA IEK   LGGTCLNVGCIPSK+LL++SH  H  
Sbjct: 4   FDVVVIGSGPGGYVAAIRCAQLGFNTAIIEKYPTLGGTCLNVGCIPSKALLDSSHHYHDA 63

Query: 86  QHEAKERGISIQGEVGVDFPKLMAAKEKAVKQLTGGIEMLFKKNKVDYLKGAGSFVNEKT 145
               KE GI I GE+ V+F +++A K+  V Q   GI+ L  KNK+   +G GSF +   
Sbjct: 64  ISHFKEHGIDIPGEIKVNFEQMIARKQGVVDQNVSGIKYLMDKNKITVFEGVGSFEDATH 123

Query: 146 VKVTPIDGSEAQEVEADHIIVATGSEPTPFPGIEIDEERIVTSTGILSLKEVPERLAIIG 205
           +KVT  DGSE + +EA + I+ATGS+P+  P I+ID+E+I+TST  L LKEVP+ L +IG
Sbjct: 124 IKVTKNDGSE-ETIEAKNTILATGSKPSSLPFIKIDKEKIITSTEALKLKEVPKHLIVIG 182

Query: 206 GGIIGLEMASVYARLGSKVTVIEFQNAIGAGMDAEVAKQSQKLLAKQGLDFKLGTKVVKG 265
           GG+IGLE+  VY RLG++V+V+E+ + I  GMDA ++K+  K+L KQG+ F    KV   
Sbjct: 183 GGVIGLELGQVYLRLGAQVSVVEYLDRIIPGMDAGLSKELTKVLKKQGMKFYTSHKVKSV 242

Query: 266 ERDGEVVKIEVEDVKSGKKSDLEADVLLVAIGRRPFTEGLNFEAIGLEKDNKGRLIIDDQ 325
           ER+GE V+++ E+ K G+   L+ D  LV++GRRPFT+GLN E  G++  ++G++ ++D 
Sbjct: 243 ERNGEGVQVQAENAK-GETITLDGDYSLVSVGRRPFTDGLNLEKAGIKVSDRGQIEVNDH 301

Query: 326 FKTKHDHIRVIGDVTFGPMLAHKAEEEGIAAAEYIKKGHGHVNYANIPSVMYTHPEVAWV 385
            +T   +I  IGDV  G MLAHKAEEEG+  AE +     H++Y  IP V+YT PEVA V
Sbjct: 302 LQTNVSNIYAIGDVVRGAMLAHKAEEEGVFVAETLAGQKPHIDYNLIPGVVYTWPEVAAV 361

Query: 386 GLNEEQLKEQGIKYKVGKFPFIANSRAKTNMDTDGFVKFIADAETQRVLGVHIIGPNAGE 445
           G  EEQLKE+G+KYK G FPF A  R++ +MDTDGFVK +ADAET  VLGVH+IG    +
Sbjct: 362 GKTEEQLKEEGVKYKSGSFPFKALGRSRASMDTDGFVKILADAETDEVLGVHMIGARVAD 421

Query: 446 MIAEAGLALEYGASTEDISRTCHAHPTLSEAFKEAALA 483
           +IAEA  A+E+ AS EDISR  HAHPT +EA KEAALA
Sbjct: 422 LIAEAVTAMEFRASAEDISRMSHAHPTYAEAVKEAALA 459


Lambda     K      H
   0.316    0.135    0.381 

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: 600
Number of extensions: 31
Number of successful extensions: 3
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: 491
Length of database: 468
Length adjustment: 34
Effective length of query: 457
Effective length of database: 434
Effective search space:   198338
Effective search space used:   198338
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_035130862.1 Q763_RS02450 (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.682423.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-182  592.8   8.9   2.5e-182  592.6   8.9    1.0  1  NCBI__GCF_000769915.1:WP_035130862.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000769915.1:WP_035130862.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.6   8.9  2.5e-182  2.5e-182       2     457 ..       4     463 ..       3     468 .] 0.97

  Alignments for each domain:
  == domain 1  score: 592.6 bits;  conditional E-value: 2.5e-182
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevvee.lkeakelgieven 72 
                                           +dvvviG+GpgGYvaAir+aqlg+++a++ek  +lGGtClnvGCiP+KalL s++ +++ ++++ke+gi++ +
  NCBI__GCF_000769915.1:WP_035130862.1   4 FDVVVIGSGPGGYVAAIRCAQLGFNTAIIEKyPTLGGTCLNVGCIPSKALLDSSHHYHDaISHFKEHGIDIPG 76 
                                           9******************************99***********************9872567*******999 PP

                             TIGR01350  73 .vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsep 143
                                            +k+++e++ +rk+ vv++ v+G+k+L++knk++v++G ++++d+++++v+k++++ +++eakn i+AtGs+p
  NCBI__GCF_000769915.1:WP_035130862.1  77 eIKVNFEQMIARKQGVVDQNVSGIKYLMDKNKITVFEGVGSFEDATHIKVTKNDGSeETIEAKNTILATGSKP 149
                                           9**************************************************9998779*************** PP

                             TIGR01350 144 relplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                           ++lp+ ++ d++ +its+eal+lkevp++l+++GgGviG+E+++++ +lG++v+v+e+ldri+p +da +sk+
  NCBI__GCF_000769915.1:WP_035130862.1 150 SSLPF-IKIDKEKIITSTEALKLKEVPKHLIVIGGGVIGLELGQVYLRLGAQVSVVEYLDRIIPGMDAGLSKE 221
                                           *****.9999999************************************************************ PP

                             TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgvelderg 287
                                           l+k lkk+g+k++t++kv++ve++ + v+v+a++   e+ tl++++ Lv+vGr+p +++l+lek g+++ +rg
  NCBI__GCF_000769915.1:WP_035130862.1 222 LTKVLKKQGMKFYTSHKVKSVERNGEGVQVQAENAkgETITLDGDYSLVSVGRRPFTDGLNLEKAGIKVSDRG 294
                                           **************************99977666545888999****************************** PP

                             TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGltee 360
                                           +i+v+++l+tnv++iyaiGDv++++mLAh+A++egv +ae++ag+++ +idy+++P v+yt Peva+vG+tee
  NCBI__GCF_000769915.1:WP_035130862.1 295 QIEVNDHLQTNVSNIYAIGDVVRGAMLAHKAEEEGVFVAETLAGQKP-HIDYNLIPGVVYTWPEVAAVGKTEE 366
                                           ********************************************998.9************************ PP

                             TIGR01350 361 qakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveel 433
                                           q+keeg+++k+g+fpf+a g+++a+ +tdGfvk+++d +t+e+lG+h++ga++++li+e++ a+e+++++e++
  NCBI__GCF_000769915.1:WP_035130862.1 367 QLKEEGVKYKSGSFPFKALGRSRASMDTDGFVKILADAETDEVLGVHMIGARVADLIAEAVTAMEFRASAEDI 439
                                           ************************************************************************* PP

                             TIGR01350 434 aktihpHPtlsEaikeaalaalgk 457
                                           +++ h+HPt++Ea+keaalaa+ +
  NCBI__GCF_000769915.1:WP_035130862.1 440 SRMSHAHPTYAEAVKEAALAATAN 463
                                           ******************998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (468 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.72
//
[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:

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 2024 update 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