Alignments for a candidate for lpd in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Burkholderia phytofirmans PsJN

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate BPHYT_RS12830 BPHYT_RS12830 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__BFirm:BPHYT_RS12830
          Length = 600

 Score =  897 bits (2317), Expect = 0.0
 Identities = 460/608 (75%), Positives = 515/608 (84%), Gaps = 22/608 (3%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           MS++EVKVPDIGDF  V+VIEV +KAGD +E EQ+L+ LESDKAS++VPS  AG V EV+
Sbjct: 1   MSLVEVKVPDIGDFKDVDVIEVNIKAGDVIENEQALMTLESDKASIEVPSDTAGTVKEVR 60

Query: 61  VKVGDKVGQGAVICTIE-------AQQAAAAPA--PAQAPAPAQA-PAPAAAAPA----P 106
           VK GDKV QG VI  +E       A+ A  APA  P +APA A+A P  A AAPA    P
Sbjct: 61  VKAGDKVSQGTVIALVETSADAAPAKDAPKAPAKEPEKAPAQAEAKPQAAQAAPAKAATP 120

Query: 107 APAAASHSGGADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIP 166
           AP A S SG ADI+C+MLVLG+GPGGYSAAFR+ADLGM TVLVERY+TLGGVCLNVGCIP
Sbjct: 121 APQAGSFSGNADIECDMLVLGSGPGGYSAAFRSADLGMKTVLVERYATLGGVCLNVGCIP 180

Query: 167 SKALLHNAAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQV 226
           SKALLH A VIDEA+AL +HGI FG+ +IDLD LR +K+ VV KLTGGLAGMAK RKV+V
Sbjct: 181 SKALLHTALVIDEAEALRSHGITFGKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEV 240

Query: 227 VRGIGNFLDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDS 286
           V G G+F+DPHHMEV++  G        K V++F++AIIAAGS+AVKLPFIPEDPR+VDS
Sbjct: 241 VTGTGSFVDPHHMEVQVEGG--------KKVVKFKQAIIAAGSEAVKLPFIPEDPRVVDS 292

Query: 287 TGALELPEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKK 346
           TGALEL ++P +MLVIGGGIIGLEMATVY+TLGA IDVVEMLDGLM GADRDLVKVWEK 
Sbjct: 293 TGALELRQIPQRMLVIGGGIIGLEMATVYATLGAQIDVVEMLDGLMAGADRDLVKVWEKY 352

Query: 347 NKDRFGKVMLKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEK 406
           N  RF  VMLKTKT   EAK DGIYV FEGE APAE QRYDLVLV+VGRSPNGK+I A+K
Sbjct: 353 NSKRFANVMLKTKTTAAEAKDDGIYVSFEGEKAPAEAQRYDLVLVAVGRSPNGKKIGADK 412

Query: 407 AGVAVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDA 466
           AGVAV+ERGFI+VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAE AHGEKAYFDA
Sbjct: 413 AGVAVTERGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVAHGEKAYFDA 472

Query: 467 KQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEE 526
            QIPSVA+TDPEVAWAG TED+ K +GIKY K VFPWAASGRAIANGRDEGFTKL+FDEE
Sbjct: 473 LQIPSVAYTDPEVAWAGKTEDQLKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLLFDEE 532

Query: 527 THRVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCT 586
           THRVIGGGIVG +AGDLISEVCLA+EMGADA DIGKTIHPHPTLGESIGMAAE+YEG CT
Sbjct: 533 THRVIGGGIVGLNAGDLISEVCLAVEMGADATDIGKTIHPHPTLGESIGMAAELYEGVCT 592

Query: 587 DVPPPRKR 594
           D+PP +K+
Sbjct: 593 DLPPQKKK 600


Lambda     K      H
   0.316    0.134    0.387 

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: 1111
Number of extensions: 33
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: 594
Length of database: 600
Length adjustment: 37
Effective length of query: 557
Effective length of database: 563
Effective search space:   313591
Effective search space used:   313591
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: 53 (25.0 bits)

Align candidate BPHYT_RS12830 BPHYT_RS12830 (dihydrolipoamide 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.25541.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   5.6e-149  482.7   3.6   8.3e-149  482.1   3.6    1.2  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12830  BPHYT_RS12830 dihydrolipoamide d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12830  BPHYT_RS12830 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.1   3.6  8.3e-149  8.3e-149       2     453 ..     135     586 ..     134     592 .. 0.97

  Alignments for each domain:
  == domain 1  score: 482.1 bits;  conditional E-value: 8.3e-149
                                TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                               d++v+G+GpgGY aA r+a lg+k++lve+  +lGG+ClnvGCiP+KalL++a v++e++ + ++gi+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12830 135 CDMLVLGSGPGGYSAAFRSADLGMKTVLVERyATLGGVCLNVGCIPSKALLHTALVIDEAEALRSHGITF 204
                                              699****************************99************************************* PP

                                TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtG 140
                                               + ++dl+kl + k+ vvkkl+gG++++ k  kvev++G+++++d++++ev+ e ++k++++k++iiA G
  lcl|FitnessBrowser__BFirm:BPHYT_RS12830 205 GKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEVVTGTGSFVDPHHMEVQVEGGKKVVKFKQAIIAAG 274
                                              *******************************************************9************** PP

                                TIGR01350 141 seprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpald 210
                                              se  +lp+ + ed  +v++s++alel+++p++++++GgG+iG+E+a+++a+lG+++ v+e+ld +++  d
  lcl|FitnessBrowser__BFirm:BPHYT_RS12830 275 SEAVKLPF-IPEDP-RVVDSTGALELRQIPQRMLVIGGGIIGLEMATVYATLGAQIDVVEMLDGLMAGAD 342
                                              ********.77776.7****************************************************** PP

                                TIGR01350 211 aevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelglek 278
                                              +++ kv +k  +k+  +++ ++k t+ e+++d + v+ +++   +e  +++ vLvavGr+pn +++g +k
  lcl|FitnessBrowser__BFirm:BPHYT_RS12830 343 RDLVKVWEKYNSKRFANVMLKTKTTAAEAKDDGIYVSFEGEkaPAEAQRYDLVLVAVGRSPNGKKIGADK 412
                                              ********************************99987777644679999********************* PP

                                TIGR01350 279 lgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviyt 348
                                               gv ++erg+i vd+++rtnvp+i+aiGD++g++mLAh+A++e+ vaae + g+++  +d+ ++Psv yt
  lcl|FitnessBrowser__BFirm:BPHYT_RS12830 413 AGVAVTERGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVAHGEKA-YFDALQIPSVAYT 481
                                              *****************************************************776.9************ PP

                                TIGR01350 349 ePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaselis 418
                                              +Peva  G+te+q+k+egi++  + fp aa+g+a+a + ++Gf k+++d++t++++G  ivg +a +lis
  lcl|FitnessBrowser__BFirm:BPHYT_RS12830 482 DPEVAWAGKTEDQLKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLLFDEETHRVIGGGIVGLNAGDLIS 551
                                              ********************************************************************** PP

                                TIGR01350 419 elalaveleltveelaktihpHPtlsEaikeaala 453
                                              e+ lave+++ ++++ ktihpHPtl+E i  aa+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12830 552 EVCLAVEMGADATDIGKTIHPHPTLGESIGMAAEL 586
                                              *****************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (600 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.88
//
[ok]

This GapMind analysis is from Sep 17 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 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