Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N1B4

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf1N1B4_4477 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3543
         (460 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477
          Length = 460

 Score =  861 bits (2224), Expect = 0.0
 Identities = 435/460 (94%), Positives = 450/460 (97%)

Query: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60
           MQTLNTTLLIIGGGPGGYVTAIRAGQLGI TILVEGQSLGGTCLNIGCIPSKALIHVAEQ
Sbjct: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGISTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60

Query: 61  FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV 120
           FHQTQHHSQHSALGISVSAPTL+IGKSVEWKDGIVDRLTTGV+ALLKK+KVQV+QGWAKV
Sbjct: 61  FHQTQHHSQHSALGISVSAPTLNIGKSVEWKDGIVDRLTTGVSALLKKHKVQVIQGWAKV 120

Query: 121 VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180
           +DGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG
Sbjct: 121 IDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180

Query: 181 YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS 240
           YIGLELGIAYRKLGAEVSVVEAQ+RILPAYDAELT PVH+ LK+L VKLYLKHSVQGFDS
Sbjct: 181 YIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTHPVHEALKQLDVKLYLKHSVQGFDS 240

Query: 241 SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR 300
            NNTLQV+ P+G++LNL+TDQVLVAVGRKPNTQGWNLEALNLDMNGS+IKIDNRCQTSMR
Sbjct: 241 VNNTLQVIDPSGDSLNLKTDQVLVAVGRKPNTQGWNLEALNLDMNGSAIKIDNRCQTSMR 300

Query: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE 360
           NVYAIGDLSGEPMLAHRAMAQGEMVAELISGK REFNPTAIAAVCFTDPELVVVGKTPDE
Sbjct: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPTAIAAVCFTDPELVVVGKTPDE 360

Query: 361 AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA 420
           AKAAG DCIVSSFPFAANGRAMTLES+SGFVRVVARRDNHVIVGWQAVGVGVSELSTAF 
Sbjct: 361 AKAAGLDCIVSSFPFAANGRAMTLESRSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFG 420

Query: 421 QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL 460
           QSLEMGARLEDI GTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 QSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 460


Lambda     K      H
   0.317    0.134    0.388 

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: 765
Number of extensions: 16
Number of successful extensions: 2
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: 460
Length of database: 460
Length adjustment: 33
Effective length of query: 427
Effective length of database: 427
Effective search space:   182329
Effective search space used:   182329
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: 51 (24.3 bits)

Align candidate Pf1N1B4_4477 (Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid 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.9792.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.1e-149  483.5   1.6   3.5e-149  483.3   1.6    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477  Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehyd
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.3   1.6  3.5e-149  3.5e-149       3     460 ..       7     459 ..       5     460 .] 0.97

  Alignments for each domain:
  == domain 1  score: 483.3 bits;  conditional E-value: 3.5e-149
                                      TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...a 63 
                                                     +++iGgGpgGYv+Aira+qlg +++lve ++lGGtCln GCiP+Kal++ ae +++ ++    
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477   7 TLLIIGGGPGGYVTAIRAGQLGISTILVEGQSLGGTCLNIGCIPSKALIHVAEQFHQTQHhsqH 70 
                                                    578******************************************************9995434 PP

                                      TIGR01350  64 kelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke 127
                                                    + lgi+v+  +l++ k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak+ d k+vev +++  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477  71 SALGISVSAPTLNIGKSVEWKDGIVDRLTTGVSALLKKHKVQVIQGWAKVIDGKTVEVGDTR-- 132
                                                    568*******************************************************9998.. PP

                                      TIGR01350 128 kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifak 191
                                                      ++ +++++AtGs+  +lp+ l   +  +i+s+eal+ ++vp++l++vGgG+iG+E++ +++k
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 133 --IQCEHLVLATGSKSVNLPM-LPIGG-PIISSTEALAPTSVPKRLIVVGGGYIGLELGIAYRK 192
                                                    ..89*****************.99998.69********************************** PP

                                      TIGR01350 192 lGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevet 255
                                                    lG++v+v+e++drilpa dae+++ ++++lk+  vk++ +++v+   + +++++v   +++  +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 193 LGAEVSVVEAQDRILPAYDAELTHPVHEALKQLDVKLYLKHSVQGFDSVNNTLQVIDPSGDSLN 256
                                                    *****************************************************987777789** PP

                                      TIGR01350 256 leaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAs 319
                                                    l++++vLvavGrkpn+++ +le+l+++++   aik+d++++t++ ++yaiGD+ g++mLAh+A+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 257 LKTDQVLVAVGRKPNTQGWNLEALNLDMNG-SAIKIDNRCQTSMRNVYAIGDLSGEPMLAHRAM 319
                                                    *****************************9.78******************************* PP

                                      TIGR01350 320 kegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkal 383
                                                    ++g ++ae i gk++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfaang+a+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 320 AQGEMVAELISGKHR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGLDCIVSSFPFAANGRAM 382
                                                    ************998.9*********************************************** PP

                                      TIGR01350 384 aleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEai 447
                                                    +le ++Gfv+v++ ++ + i+G + vg  +sel + +   +e+++++e++a tih+HPtl+Ea+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 383 TLESRSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFGQSLEMGARLEDIAGTIHAHPTLGEAV 446
                                                    **************************************************************** PP

                                      TIGR01350 448 keaalaalgkaih 460
                                                    +eaal alg+a+h
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 447 QEAALRALGHALH 459
                                                    **********999 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.60
//
[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