Alignments for a candidate for lpd in Hyphomicrobium sulfonivorans WDL6

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Hyphomicrobium sulfonivorans WDL6

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_083509555.1 APY04_RS06755 dihydrolipoyl dehydrogenase

Query= BRENDA::P0A9P0
         (474 letters)



>NCBI__GCF_001541235.1:WP_083509555.1
          Length = 476

 Score =  550 bits (1417), Expect = e-161
 Identities = 279/474 (58%), Positives = 350/474 (73%), Gaps = 2/474 (0%)

Query: 2   STEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAK 61
           + +I+  +VVLGAGP GY+AAFR ADLG + V+VER   LGGVCLNVGCIPSKALLH AK
Sbjct: 4   AVDIEADIVVLGAGPGGYTAAFRAADLGKKVVVVERGPALGGVCLNVGCIPSKALLHAAK 63

Query: 62  VIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTG 121
           V+E+A  + E G+ F  P+ D+DK+R WK  ++++LTGGLA +A+ RKV VV G G+F  
Sbjct: 64  VLEDADEMTEAGLGFTRPQLDLDKLRRWKSGIVSKLTGGLAALARQRKVIVVTGFGRFVS 123

Query: 122 ANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVM 181
            N +EV  E     + F  AIIAAGS P +LP  P  D RI DST AL+L++VP RLLV+
Sbjct: 124 PNEIEVTHEGATKRVAFTQAIIAAGSEPARLPIAPKHDSRILDSTGALDLQDVPPRLLVV 183

Query: 182 GGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLM-LETKVTA 240
           GGGIIGLEM TVYHALGS++ VVE  DQ+I  AD+DIV    KRIS +++ + L TKV  
Sbjct: 184 GGGIIGLEMATVYHALGSRVTVVEAMDQLISGADRDIVAPLMKRISTRYDAVHLGTKVRN 243

Query: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300
           + +    + VT EG  AP E Q +D +LVA+GRVPN   L    AGV VD RGFIRVDKQ
Sbjct: 244 IASAAAELTVTFEGANAPEE-QSFDKILVAVGRVPNSGTLGLAAAGVAVDQRGFIRVDKQ 302

Query: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360
           +RTNVPHIFAIGD+VGQPMLAHK VHEG VAAEV AG K  FD +VIPS+AYT+PEVAWV
Sbjct: 303 MRTNVPHIFAIGDVVGQPMLAHKAVHEGKVAAEVAAGLKAAFDARVIPSVAYTDPEVAWV 362

Query: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420
           GLTE EA   G++Y   +FPW ASGRA++   ++G+TK++FD E+HR +G  IVG + GE
Sbjct: 363 GLTEAEANANGVAYGKGSFPWEASGRALSQGRSEGLTKVLFDPETHRTLGCGIVGAHAGE 422

Query: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           L+GE+ LAIEMG DA DIA TIH HPTL E++  +AE+FEG+ITDL   +A+++
Sbjct: 423 LIGEMVLAIEMGADAADIAGTIHPHPTLSETIAQSAEMFEGTITDLIARQARQR 476


Lambda     K      H
   0.317    0.137    0.396 

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: 689
Number of extensions: 35
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: 474
Length of database: 476
Length adjustment: 33
Effective length of query: 441
Effective length of database: 443
Effective search space:   195363
Effective search space used:   195363
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_083509555.1 APY04_RS06755 (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.359535.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-156  505.2   0.6   9.8e-156  504.9   0.6    1.0  1  NCBI__GCF_001541235.1:WP_083509555.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001541235.1:WP_083509555.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.9   0.6  9.8e-156  9.8e-156       2     455 ..       9     462 ..       8     467 .. 0.98

  Alignments for each domain:
  == domain 1  score: 504.9 bits;  conditional E-value: 9.8e-156
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                            d+vv+G+GpgGY+aA raa lg+kv++ve+   lGG+ClnvGCiP+KalL++a+v+e++ e+ e g+  +  
  NCBI__GCF_001541235.1:WP_083509555.1   9 ADIVVLGAGPGGYTAAFRAADLGKKVVVVERgPALGGVCLNVGCIPSKALLHAAKVLEDADEMTEAGLGFTRP 81 
                                           69*****************************99**************************************** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprel 146
                                           +ldl+kl  +k+ +v+kl+gG++aL ++ kv v++G +++++++e+ev++e ++k + + ++iiA Gsep++l
  NCBI__GCF_001541235.1:WP_083509555.1  82 QLDLDKLRRWKSGIVSKLTGGLAALARQRKVIVVTGFGRFVSPNEIEVTHEGATKRVAFTQAIIAAGSEPARL 154
                                           ************************************************************************* PP

                             TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219
                                           p++ ++d +++++s++al l+ vp +l++vGgG+iG+E+a++++ lG+ vtv+e++d+++   d+++   l+k
  NCBI__GCF_001541235.1:WP_083509555.1 155 PIAPKHD-SRILDSTGALDLQDVPPRLLVVGGGIIGLEMATVYHALGSRVTVVEAMDQLISGADRDIVAPLMK 226
                                           **55555.58*************************************************************** PP

                             TIGR01350 220 klkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikv 291
                                           +++++   ++ ++kv ++ + ++e++v+ ++    e+ + +k+LvavGr pn   lgl++ gv +d+rg+i v
  NCBI__GCF_001541235.1:WP_083509555.1 227 RISTRYDAVHLGTKVRNIASAAAELTVTFEGAnAPEEQSFDKILVAVGRVPNSGTLGLAAAGVAVDQRGFIRV 299
                                           **************************99999977899999********************************* PP

                             TIGR01350 292 deelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqake 364
                                           d+++rtnvp+i+aiGDv+g++mLAh+A++eg vaae +ag ++ ++d++++Psv yt+Peva vGlte++a++
  NCBI__GCF_001541235.1:WP_083509555.1 300 DKQMRTNVPHIFAIGDVVGQPMLAHKAVHEGKVAAEVAAGLKA-AFDARVIPSVAYTDPEVAWVGLTEAEANA 371
                                           ****************************************666.9**************************** PP

                             TIGR01350 365 egievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelakti 437
                                           +g+++  g+fp +a+g+al+++ ++G+ kv++d++t++ lG+ ivga+a eli e++la+e+++ + ++a ti
  NCBI__GCF_001541235.1:WP_083509555.1 372 NGVAYGKGSFPWEASGRALSQGRSEGLTKVLFDPETHRTLGCGIVGAHAGELIGEMVLAIEMGADAADIAGTI 444
                                           ************************************************************************* PP

                             TIGR01350 438 hpHPtlsEaikeaalaal 455
                                           hpHPtlsE+i+++a+   
  NCBI__GCF_001541235.1:WP_083509555.1 445 HPHPTLSETIAQSAEMFE 462
                                           ************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (476 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: 16.10
//
[ok]

This GapMind analysis is from Apr 09 2024. 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