Alignments for a candidate for lpd in Frankia alni ACN14a

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Frankia alni ACN14a

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of branched-chain alpha-keto acid dehydrogenase complex; LPD-Val (uncharacterized)
to candidate WP_011606255.1 FRAAL_RS22460 dihydrolipoyl dehydrogenase

Query= curated2:P54533
         (474 letters)



>NCBI__GCF_000058485.1:WP_011606255.1
          Length = 460

 Score =  332 bits (852), Expect = 1e-95
 Identities = 191/468 (40%), Positives = 279/468 (59%), Gaps = 20/468 (4%)

Query: 6   DVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRTARE 65
           D+VILGGG+GGY AA+RAA+L L   ++EK+KLGGTCLH+GCIP+KALL SAE+     E
Sbjct: 10  DLVILGGGSGGYAAALRAAELDLSVVLIEKDKLGGTCLHRGCIPTKALLHSAEIVDNINE 69

Query: 66  ADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGKIDVYTGYGRILGPSIFSPL 125
           ++ FG+ +    ++  KV   K +V+  L  G+  L+K   I+V  G+GR++ P+     
Sbjct: 70  SESFGIRSTFDGIDMAKVNSYKDSVIAGLFKGLTGLIKSRGIEVVEGFGRLVSPT----- 124

Query: 126 PGTISVERGNGEENDMLIPKQVIIATGSRPRMLPGLEVDGKSVLTSDEALQMEELPQSII 185
               SV  G    + ++  + V++ATGS  + LPGL++D   V+TSD+AL ++ +P S +
Sbjct: 125 ----SVAVG----DRVISGRHVLLATGSYSKSLPGLDIDHDRVITSDDALTLDHVPASAV 176

Query: 186 IVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFITGAKV 245
           ++G G IG E+AS+   +G +VT++E    ++P ED   SK +E   +K+GI    GA+ 
Sbjct: 177 VLGAGAIGCEFASVWRSYGAEVTIVEALPHLVPLEDESSSKLLERAFRKRGIAQHLGARF 236

Query: 246 LPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDIVTENGMISVN 305
                 KT+D     + + G T+   AE +LV++GR     G+G E   I T+ G + V+
Sbjct: 237 ---AGVKTTDHGVTVSLESGTTI--DAELLLVAVGRGPVSAGLGYEEVGIATDRGYVLVD 291

Query: 306 ESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYSSPEA 365
              +T    + A+GD+  GLQLAHV   EGI   E  AGLNP P+D   VP+  YS PE 
Sbjct: 292 RFLRTNVPTVSALGDLRPGLQLAHVGFAEGIFVAEQLAGLNPVPVDYDNVPRVTYSHPEV 351

Query: 366 ASVGLTEDEAKANGHNVKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVHMIGPH 425
           ASVGLT   A+     +    +     GK+ +  ++ G V +VA  D   ++GVHM+G  
Sbjct: 352 ASVGLTAAAARERFGEISTVTYNLAGNGKSQIL-KTAGAVTLVAVPD-GPVVGVHMVGDR 409

Query: 426 VTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIGEAALAADGKAIH 473
           V ++I+EA L    +A P EV Q IHPHPTLSEA+GEA LA  GK +H
Sbjct: 410 VGELIAEAQLITNWEAFPAEVAQLIHPHPTLSEALGEAHLALAGKPLH 457


Lambda     K      H
   0.315    0.135    0.382 

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: 581
Number of extensions: 21
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: 460
Length adjustment: 33
Effective length of query: 441
Effective length of database: 427
Effective search space:   188307
Effective search space used:   188307
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_011606255.1 FRAAL_RS22460 (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.1422540.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-137  444.2   0.0     3e-137  444.0   0.0    1.0  1  NCBI__GCF_000058485.1:WP_011606255.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000058485.1:WP_011606255.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.0   0.0    3e-137    3e-137       2     461 .]       9     458 ..       8     458 .. 0.98

  Alignments for each domain:
  == domain 1  score: 444.0 bits;  conditional E-value: 3e-137
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvk 74 
                                           +d+v++GgG gGY aA raa+l l+v+l+ek+klGGtCl++GCiPtKalL+sae+v++++e +++gi+++   
  NCBI__GCF_000058485.1:WP_011606255.1   9 VDLVILGGGSGGYAAALRAAELDLSVVLIEKDKLGGTCLHRGCIPTKALLHSAEIVDNINESESFGIRSTFDG 81 
                                           69*****************************************************************999899 PP

                             TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelp 147
                                           +d++k+   k++v+  l +G+++L+k+ ++ev++G ++l+++++v v ++     ++  ++++AtGs  ++lp
  NCBI__GCF_000058485.1:WP_011606255.1  82 IDMAKVNSYKDSVIAGLFKGLTGLIKSRGIEVVEGFGRLVSPTSVAVGDRV----ISGRHVLLATGSYSKSLP 150
                                           ***********************************************9875....89**************** PP

                             TIGR01350 148 lkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                           + l+ d+++vits++al+l++vp s v++G+G+iG+Efas+++++G++vt++e+l++++p +d+  sk+l+++
  NCBI__GCF_000058485.1:WP_011606255.1 151 G-LDIDHDRVITSDDALTLDHVPASAVVLGAGAIGCEFASVWRSYGAEVTIVEALPHLVPLEDESSSKLLERA 222
                                           *.9********************************************************************** PP

                             TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvde 293
                                           ++k+g+  + +a+   v+++++ v+v+ +++  +t++ae +LvavGr p   +lg e++g+ +d+ g++ vd+
  NCBI__GCF_000058485.1:WP_011606255.1 223 FRKRGIAQHLGARFAGVKTTDHGVTVSLESG--TTIDAELLLVAVGRGPVSAGLGYEEVGIATDR-GYVLVDR 292
                                           ***************************9999..8****************************766.******* PP

                             TIGR01350 294 elrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366
                                            lrtnvp + a GD+  +l+LAhv ++eg+ +ae++ag ++  +dy+ vP+v+y++PevasvGlt + a+e+ 
  NCBI__GCF_000058485.1:WP_011606255.1 293 FLRTNVPTVSALGDLRPGLQLAHVGFAEGIFVAEQLAGLNPVPVDYDNVPRVTYSHPEVASVGLTAAAARERF 365
                                           ************************************************************************* PP

                             TIGR01350 367 ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439
                                            e+ ++ +++a ngk+ +l +t G v +++ + +g ++G+h+vg ++ eli+e+ l+ ++e+   e+a++ihp
  NCBI__GCF_000058485.1:WP_011606255.1 366 GEISTVTYNLAGNGKSQIL-KTAGAVTLVAVP-DGPVVGVHMVGDRVGELIAEAQLITNWEAFPAEVAQLIHP 436
                                           ****************876.688999999887.589************************************* PP

                             TIGR01350 440 HPtlsEaikeaalaalgkaihv 461
                                           HPtlsEa+ ea la+ gk++hv
  NCBI__GCF_000058485.1:WP_011606255.1 437 HPTLSEALGEAHLALAGKPLHV 458
                                           *******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (460 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 16.53
//
[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