Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E2

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf6N2E2_4251 Dihydrolipoamide dehydrogenase (EC 1.8.1.4)

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251
          Length = 466

 Score =  719 bits (1857), Expect = 0.0
 Identities = 351/465 (75%), Positives = 402/465 (86%)

Query: 2   MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61
           M +YDVI++G GPGGYNAAIRAGQLGLK ACVEGR TLGGTCLNVGCMPSKALLHASELY
Sbjct: 1   MSNYDVIILGGGPGGYNAAIRAGQLGLKAACVEGRATLGGTCLNVGCMPSKALLHASELY 60

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
            AA+G EFA LGI VSP L+LAQMMKQKDESVA LT+G+EFLFRK+KV WIKGW  + G 
Sbjct: 61  EAATGAEFANLGIEVSPTLNLAQMMKQKDESVAGLTKGIEFLFRKNKVDWIKGWGHIDGP 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G+V V   DG   +L A+DIVIATGSEP PLPGVP+DNQRILDSTGAL L EVPRHLVVI
Sbjct: 121 GKVIVTGDDGAKTELSAKDIVIATGSEPMPLPGVPIDNQRILDSTGALSLGEVPRHLVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVWRRLGAQVTV+EYL+RICPG+DGE  +TLQRAL +QG++F+L ++V  
Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEYLDRICPGVDGEAGKTLQRALAKQGIQFKLSSKVTG 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301
           A +   GV+L ++PAAGG  + L ADYVLVAIGRRPYT+GLGLE VGL+ D+RGML NQ 
Sbjct: 241 ATTSASGVQLQIEPAAGGEAQPLDADYVLVAIGRRPYTQGLGLENVGLSPDQRGMLANQN 300

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            R+ APGVWVIGDVTSGPMLAHKAE+EA+ CIE+IAG AAE+N  +IPSVIYT+PE+ASV
Sbjct: 301 HRTEAPGVWVIGDVTSGPMLAHKAEDEAMACIEQIAGKAAEVNYALIPSVIYTRPELASV 360

Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421
           G  EEQL+A  R YKVG+FPF+ANSRAKINHE+EGF K+L+D R+D++LGVH++GP VSE
Sbjct: 361 GKTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVLADERTDEILGVHLVGPSVSE 420

Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466
           MIGE CVAMEFSASAED+ALTCHPHPTRSEALRQAAMDV G A Q
Sbjct: 421 MIGEYCVAMEFSASAEDIALTCHPHPTRSEALRQAAMDVEGMATQ 465


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: 809
Number of extensions: 25
Number of successful extensions: 1
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 Pf6N2E2_4251 (Dihydrolipoamide dehydrogenase (EC 1.8.1.4))
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.10972.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.3e-165  536.7   0.2   2.6e-165  536.5   0.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251  Dihydrolipoamide dehydrogenase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251  Dihydrolipoamide dehydrogenase (EC 1.8.1.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.5   0.2  2.6e-165  2.6e-165       1     460 [.       3     465 ..       3     466 .] 0.96

  Alignments for each domain:
  == domain 1  score: 536.5 bits;  conditional E-value: 2.6e-165
                                      TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke. 62 
                                                    +ydv+++GgGpgGY aAira+qlglk a+ve   +lGGtClnvGC+P+KalL+++e++e ++  
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251   3 NYDVIILGGGPGGYNAAIRAGQLGLKAACVEGrATLGGTCLNVGCMPSKALLHASELYEAATGa 66 
                                                    69*****************************8799************************99865 PP

                                      TIGR01350  63 .akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkek 125
                                                     +++lgiev + +l+l++++++k++ v  l++G+++L++knkv+ ikG +++ ++++v v++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251  67 eFANLGIEV-SPTLNLAQMMKQKDESVAGLTKGIEFLFRKNKVDWIKGWGHIDGPGKVIVTGDD 129
                                                    588999988.689*************************************************99 PP

                                      TIGR01350 126 ke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasi 188
                                                    ++ ++l+ak+i+iAtGsep  lp+ +  d++++++s++al+l evp++lv++G+GviG+E++s+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251 130 GAkTELSAKDIVIATGSEPMPLPG-VPIDNQRILDSTGALSLGEVPRHLVVIGAGVIGLELGSV 192
                                                    8867899*****************.9999999******************************** PP

                                      TIGR01350 189 faklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakk 250
                                                    +++lG++vtv+e+ldri+p +d e  k+l+++l k+g++++ ++kvt  ++++  v+  +e   
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251 193 WRRLGAQVTVVEYLDRICPGVDGEAGKTLQRALAKQGIQFKLSSKVTGATTSASGVQlqIEPAA 256
                                                    ***********************************************77777777773355555 PP

                                      TIGR01350 251 k.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklm 313
                                                    + e++ l+a++vLva+Gr+p +++lgle++g++ d+rg+   +++ rt++pg+++iGDv++++m
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251 257 GgEAQPLDADYVLVAIGRRPYTQGLGLENVGLSPDQRGM-LANQNHRTEAPGVWVIGDVTSGPM 319
                                                    5699********************************995.5799******************** PP

                                      TIGR01350 314 LAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfa 377
                                                    LAh+A++e++ ++e+iagk++ e++y ++Psviyt+Pe+asvG+teeq+k+eg ++kvgkfpf+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251 320 LAHKAEDEAMACIEQIAGKAA-EVNYALIPSVIYTRPELASVGKTEEQLKAEGRAYKVGKFPFT 382
                                                    ******************887.9***************************************** PP

                                      TIGR01350 378 angkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHP 441
                                                    an++a + +et+Gf+kv++d+ t+eilG+h+vg+++se+i e  +a+e+ +++e++a t+hpHP
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251 383 ANSRAKINHETEGFAKVLADERTDEILGVHLVGPSVSEMIGEYCVAMEFSASAEDIALTCHPHP 446
                                                    **************************************************************** PP

                                      TIGR01350 442 tlsEaikeaalaalgkaih 460
                                                    t sEa+ +aa ++ g+a +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251 447 TRSEALRQAAMDVEGMATQ 465
                                                    ***********99988765 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.54
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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