Aligments for a candidate for lpd in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for lpd in Paraburkholderia bryophila 376MFSha3.1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate H281DRAFT_00468 H281DRAFT_00468 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__Burk376:H281DRAFT_00468
          Length = 590

 Score =  887 bits (2291), Expect = 0.0
 Identities = 455/599 (75%), Positives = 509/599 (84%), Gaps = 14/599 (2%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           MS++EVKVPDIGDF  V+VIEV +K GD +E EQ+L+ LESDKAS++VPS  AG V EV+
Sbjct: 1   MSLVEVKVPDIGDFKDVDVIEVNIKPGDVIENEQALMTLESDKASIEVPSDTAGTVKEVR 60

Query: 61  VKVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAP--APAAAAP---APAPAAASHSG 115
           VK GDKV QG +I  +E   A AAPA     APA+ P  AP  A P   APAP A S SG
Sbjct: 61  VKAGDKVSQGTIIALVETS-ADAAPAKDAPKAPAKEPEKAPTEAKPQAAAPAPQAGSFSG 119

Query: 116 GADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAA 175
            ADI+C+MLVLG+GPGGYSAAFR+ADLGM TVLVERY+TLGGVCLNVGCIPSKALLH A 
Sbjct: 120 SADIECDMLVLGSGPGGYSAAFRSADLGMKTVLVERYATLGGVCLNVGCIPSKALLHTAL 179

Query: 176 VIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLD 235
           VIDEA+AL AHGI F + +IDLD LR +K+ VV KLTGGLAGMAK RKV+VV G G+F+D
Sbjct: 180 VIDEAEALGAHGITFAKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEVVTGTGSFVD 239

Query: 236 PHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEV 295
           P+HMEV+ TEG      GKK V++F++AIIAAGS+AVKLPFIPEDPR+VDSTGALEL ++
Sbjct: 240 PNHMEVQ-TEG------GKK-VVKFKQAIIAAGSEAVKLPFIPEDPRVVDSTGALELRQI 291

Query: 296 PNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVM 355
           P +MLVIGGGIIGLEMATVY+TLGA IDVVEMLDGLM GADRDLVKVWEK N  RF  VM
Sbjct: 292 PQRMLVIGGGIIGLEMATVYATLGAKIDVVEMLDGLMAGADRDLVKVWEKYNSKRFANVM 351

Query: 356 LKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERG 415
           LKTKT   EAK DGIYV FEGE AP E QRYDLVLV+VGRSPNGK+I A+KAGV V++RG
Sbjct: 352 LKTKTTAAEAKDDGIYVSFEGEKAPPEAQRYDLVLVAVGRSPNGKKIGADKAGVTVTDRG 411

Query: 416 FINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFT 475
           FI+VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHE HVAAEAAHGEKAYFDA QIPSVA+T
Sbjct: 412 FIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEGHVAAEAAHGEKAYFDALQIPSVAYT 471

Query: 476 DPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGI 535
           DPEVAWAG TED+ K +G+KY K VFPWAASGRAIANGRDEGFTKL+FDEETHRVIGGGI
Sbjct: 472 DPEVAWAGKTEDQLKAEGVKYGKAVFPWAASGRAIANGRDEGFTKLLFDEETHRVIGGGI 531

Query: 536 VGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           VG +AGDLISEVCLAIEMGADA DIGKTIHPHPTLGESIGMAAE+YEG CTD+PP +K+
Sbjct: 532 VGLNAGDLISEVCLAIEMGADATDIGKTIHPHPTLGESIGMAAELYEGVCTDLPPQKKK 590


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: 1101
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: 594
Length of database: 590
Length adjustment: 37
Effective length of query: 557
Effective length of database: 553
Effective search space:   308021
Effective search space used:   308021
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 H281DRAFT_00468 H281DRAFT_00468 (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.6046.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.9e-150  485.5   2.8   1.1e-149  485.0   2.8    1.1  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00468  H281DRAFT_00468 dihydrolipoamide


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00468  H281DRAFT_00468 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.0   2.8  1.1e-149  1.1e-149       2     453 ..     125     576 ..     124     582 .. 0.97

  Alignments for each domain:
  == domain 1  score: 485.0 bits;  conditional E-value: 1.1e-149
                                    TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakel 66 
                                                   d++v+G+GpgGY aA r+a lg+k++lve+  +lGG+ClnvGCiP+KalL++a v++e++ +  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00468 125 CDMLVLGSGPGGYSAAFRSADLGMKTVLVERyATLGGVCLNVGCIPSKALLHTALVIDEAEALGAH 190
                                                  699****************************99********************************* PP

                                    TIGR01350  67 gievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekklea 132
                                                  gi+ ++ ++dl+kl + k+ vvkkl+gG++++ k  kvev++G+++++d++++ev++e ++k++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00468 191 GITFAKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEVVTGTGSFVDPNHMEVQTEGGKKVVKF 256
                                                  ****************************************************************** PP

                                    TIGR01350 133 kniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198
                                                  k++iiA Gse  +lp+ + ed  +v++s++alel+++p++++++GgG+iG+E+a+++a+lG+k+ v
  lcl|FitnessBrowser__Burk376:H281DRAFT_00468 257 KQAIIAAGSEAVKLPF-IPEDP-RVVDSTGALELRQIPQRMLVIGGGIIGLEMATVYATLGAKIDV 320
                                                  ****************.77776.7****************************************** PP

                                    TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvL 262
                                                  +e+ld +++  d+++ kv +k  +k+  +++ ++k t+ e+++d + v+ +++    e  +++ vL
  lcl|FitnessBrowser__Burk376:H281DRAFT_00468 321 VEMLDGLMAGADRDLVKVWEKYNSKRFANVMLKTKTTAAEAKDDGIYVSFEGEkaPPEAQRYDLVL 386
                                                  ********************************************99988887733568999***** PP

                                    TIGR01350 263 vavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaek 328
                                                  vavGr+pn +++g +k gv++++rg+i vd+++rtnvp+i+aiGD++g++mLAh+A++eg vaae+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00468 387 VAVGRSPNGKKIGADKAGVTVTDRGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEGHVAAEA 452
                                                  ****************************************************************** PP

                                    TIGR01350 329 iagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkv 394
                                                  + g+++  +d+ ++Psv yt+Peva  G+te+q+k+eg+++  + fp aa+g+a+a + ++Gf k+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00468 453 AHGEKA-YFDALQIPSVAYTDPEVAWAGKTEDQLKAEGVKYGKAVFPWAASGRAIANGRDEGFTKL 517
                                                  ***776.9********************************************************** PP

                                    TIGR01350 395 ivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaala 453
                                                  ++d++t++++G  ivg +a +lise+ la+e+++ ++++ ktihpHPtl+E i  aa+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00468 518 LFDEETHRVIGGGIVGLNAGDLISEVCLAIEMGADATDIGKTIHPHPTLGESIGMAAEL 576
                                                  *****************************************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (590 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.99
//
[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, or view the source code.

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