Alignments for a candidate for lpd in Novosphingobium fuchskuhlense FNE08-7

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Novosphingobium fuchskuhlense FNE08-7

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_067913115.1 AQZ52_RS15715 dihydrolipoyl dehydrogenase

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>NCBI__GCF_001519075.1:WP_067913115.1
          Length = 466

 Score =  508 bits (1307), Expect = e-148
 Identities = 264/463 (57%), Positives = 331/463 (71%), Gaps = 10/463 (2%)

Query: 5   YDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELYAAA 64
           YDV+VIGAGPGGY AAIRA QLGLKVAC EGRETLGGTCLNVGC+PSKALLH SE +A A
Sbjct: 6   YDVLVIGAGPGGYVAAIRAAQLGLKVACAEGRETLGGTCLNVGCIPSKALLHGSEKFAEA 65

Query: 65  SGGEFARLGIRVSP-ELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGEGR 123
             G FA  GI+  P  LDLA M +QK +SV  LT G+EFLF+K+KV W+KG+A  +    
Sbjct: 66  VDGTFASYGIKTGPVTLDLAAMQQQKLDSVKQLTGGIEFLFKKNKVTWLKGYAAFEDAHT 125

Query: 124 VGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQR--ILDSTGALELAEVPRHLVVI 181
           V V     G A++ A+D+VIATGS   PLPGV VDN    ++DSTGAL L  VP H+VVI
Sbjct: 126 VSV-----GGAKVTAKDVVIATGSSVTPLPGVTVDNDAGVVVDSTGALALDRVPEHMVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           G GVIGLELGSVWRRLGA+VTV+E+L+++ PG+DG+  +   +   +QGM  RL T+V  
Sbjct: 181 GGGVIGLELGSVWRRLGAKVTVVEFLDQLLPGMDGDVRKEAAKIFKKQGMELRLSTKVTG 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLE-NQ 300
                +   L L+P+AGGA E+L AD VLVAIGRRP  +GLGLE +GL  ++RG +E   
Sbjct: 241 VAVKGKTATLTLEPSAGGAAETLSADCVLVAIGRRPNVDGLGLEKIGLELNKRGQIETGH 300

Query: 301 GQRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVAS 360
             R++ PGVW IGDV  GPMLAHKAE+E +   E IAGH   +N  VIP V+YT PE A 
Sbjct: 301 DFRTSVPGVWAIGDVIPGPMLAHKAEDEGVAVAEFIAGHTGIVNHAVIPGVVYTFPEFAG 360

Query: 361 VGLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVS 420
           VGL EE  +  + E KV +FP  ANSRAK NHE +GF+K+++DA++++VLGV  I     
Sbjct: 361 VGLTEEAAR-EKGEVKVSKFPMLANSRAKTNHEPDGFVKVIADAKTERVLGVWCIASVAG 419

Query: 421 EMIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGR 463
            MI EA +A+EF A+AED+A TCH HPT +EAL++AAM + G+
Sbjct: 420 SMIAEAALALEFGATAEDIAYTCHAHPTHAEALKEAAMGIGGK 462


Lambda     K      H
   0.318    0.135    0.390 

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: 716
Number of extensions: 29
Number of successful extensions: 6
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: 467
Length of database: 466
Length adjustment: 33
Effective length of query: 434
Effective length of database: 433
Effective search space:   187922
Effective search space used:   187922
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_067913115.1 AQZ52_RS15715 (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.962888.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-165  537.4   6.4   1.6e-165  537.2   6.4    1.0  1  NCBI__GCF_001519075.1:WP_067913115.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001519075.1:WP_067913115.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.2   6.4  1.6e-165  1.6e-165       1     461 []       5     466 .]       5     466 .] 0.97

  Alignments for each domain:
  == domain 1  score: 537.2 bits;  conditional E-value: 1.6e-165
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke..akelgiev 70 
                                           +ydv+viG+GpgGYvaAiraaqlglkva+ e  e+lGGtClnvGCiP+KalL+ +e ++e+ +  ++++gi++
  NCBI__GCF_001519075.1:WP_067913115.1   5 HYDVLVIGAGPGGYVAAIRAAQLGLKVACAEGrETLGGTCLNVGCIPSKALLHGSEKFAEAVDgtFASYGIKT 77 
                                           69*****************************879**************************998889******* PP

                             TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGsep 143
                                             v+ldl++++++k   vk+l+gG+++L+kknkv+ +kG+a ++d+++v+v + k    ++ak+++iAtGs++
  NCBI__GCF_001519075.1:WP_067913115.1  78 GPVTLDLAAMQQQKLDSVKQLTGGIEFLFKKNKVTWLKGYAAFEDAHTVSVGGAK----VTAKDVVIATGSSV 146
                                           99*************************************************9997....88************ PP

                             TIGR01350 144 relplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevsk 215
                                           + lp+  +++d  vv++s++al+l++vpe++v++GgGviG+E++s++++lG+kvtv+e+ld++lp +d +v k
  NCBI__GCF_001519075.1:WP_067913115.1 147 TPLPGVtVDNDAGVVVDSTGALALDRVPEHMVVIGGGVIGLELGSVWRRLGAKVTVVEFLDQLLPGMDGDVRK 219
                                           *****98999999************************************************************ PP

                             TIGR01350 216 vlkkklkkkgvkiltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgvelde 285
                                           +++k +kk+g+++  ++kvt  +v+ + +++++e + +  +etl+a+ vLva+Gr+pn+++lglek+g+el++
  NCBI__GCF_001519075.1:WP_067913115.1 220 EAAKIFKKQGMELRLSTKVTgvAVKGKTATLTLEPSAGgAAETLSADCVLVAIGRRPNVDGLGLEKIGLELNK 292
                                           ********************666666666777777666689******************************** PP

                             TIGR01350 286 rgaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlt 358
                                           rg+i++ +++rt+vpg++aiGDvi ++mLAh+A++egv +ae iag++   +++ ++P v+yt Pe a vGlt
  NCBI__GCF_001519075.1:WP_067913115.1 293 RGQIETGHDFRTSVPGVWAIGDVIPGPMLAHKAEDEGVAVAEFIAGHTG-IVNHAVIPGVVYTFPEFAGVGLT 364
                                           **********************************************877.9********************** PP

                             TIGR01350 359 eeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431
                                           ee a+e+  evkv+kfp+ an++a + +e dGfvkvi+d kt+++lG+  ++  a  +i+e+ala+e+++t+e
  NCBI__GCF_001519075.1:WP_067913115.1 365 EEAAREK-GEVKVSKFPMLANSRAKTNHEPDGFVKVIADAKTERVLGVWCIASVAGSMIAEAALALEFGATAE 436
                                           ******9.79*************************************************************** PP

                             TIGR01350 432 elaktihpHPtlsEaikeaalaalgkaihv 461
                                           ++a t+h+HPt +Ea+keaa  + gk+ih+
  NCBI__GCF_001519075.1:WP_067913115.1 437 DIAYTCHAHPTHAEALKEAAMGIGGKPIHI 466
                                           ****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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: 16.90
//
[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