Alignments for a candidate for lpd in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens GW456-L13

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate PfGW456L13_3543 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543
          Length = 460

 Score =  906 bits (2342), Expect = 0.0
 Identities = 460/460 (100%), Positives = 460/460 (100%)

Query: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60
           MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ
Sbjct: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60

Query: 61  FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV 120
           FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV
Sbjct: 61  FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV 120

Query: 121 VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180
           VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG
Sbjct: 121 VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180

Query: 181 YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS 240
           YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS
Sbjct: 181 YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS 240

Query: 241 SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR 300
           SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR
Sbjct: 241 SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR 300

Query: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE 360
           NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE
Sbjct: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE 360

Query: 361 AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA 420
           AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA
Sbjct: 361 AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA 420

Query: 421 QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL 460
           QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL 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: 821
Number of extensions: 13
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 PfGW456L13_3543 (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.10215.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     9e-151  488.6   1.2     1e-150  488.4   1.2    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543  Dihydrolipoamide dehydrogenase o


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543  Dihydrolipoamide dehydrogenase of branched-chain alpha-keto a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.4   1.2    1e-150    1e-150       3     460 ..       7     459 ..       5     460 .] 0.97

  Alignments for each domain:
  == domain 1  score: 488.4 bits;  conditional E-value: 1e-150
                                               TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevv 57 
                                                              +++iGgGpgGYv+Aira+qlg  ++lve ++lGGtCln GCiP+Kal++ ae +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543   7 TLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQF 61 
                                                             578**************************************************** PP

                                               TIGR01350  58 eelke...akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikG 109
                                                             ++ ++    + lgi+v+  +ld+ k +e+k+ +v++l++Gv+aLlkknkv+v++G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543  62 HQTQHhsqHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQG 116
                                                             **9995434568******************************************* PP

                                               TIGR01350 110 eaklldkkevevkkekkekkleakniiiAtGseprelplkleedekvvitseeal 164
                                                              ak++d k+vev +++    ++ +++++AtGs+  +lp+ l   +  +i+s+eal
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543 117 WAKVVDGKTVEVGDTR----IQCEHLVLATGSKSVNLPM-LPIGG-PIISSTEAL 165
                                                             ************9998....89*****************.99998.69******* PP

                                               TIGR01350 165 elkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkk 219
                                                             + ++vp++l++vGgG+iG+E++ +++klG++v+v+e+++rilpa dae+++ +++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543 166 APTSVPKRLIVVGGGYIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHD 220
                                                             ******************************************************* PP

                                               TIGR01350 220 klkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleel 274
                                                             +lkk gvk++ +++v+   +++++++v a ++e+ +le+++vLvavGrkpn+++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543 221 ELKKLGVKLYLKHSVQGFDSSNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGW 275
                                                             **************************88888899********************* PP

                                               TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaeki 329
                                                             +le+l+++++   +ik+d++++t++ ++yaiGD+ g++mLAh+A+++g ++ae i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543 276 NLEALNLDMNG-SSIKIDNRCQTSMRNVYAIGDLSGEPMLAHRAMAQGEMVAELI 329
                                                             **********9.78***************************************** PP

                                               TIGR01350 330 agkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkala 384
                                                              gk++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfaang+a++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543 330 SGKTR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGWDCIVSSFPFAANGRAMT 383
                                                             **887.9************************************************ PP

                                               TIGR01350 385 leetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439
                                                             le ++Gfv+v++ ++ + i+G + vg  +sel + +a  +e+++++e++  tih+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543 384 LESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFAQSLEMGARLEDIGGTIHA 438
                                                             ******************************************************* PP

                                               TIGR01350 440 HPtlsEaikeaalaalgkaih 460
                                                             HPtl+Ea++eaal alg+a+h
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543 439 HPTLGEAVQEAALRALGHALH 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.86
//
[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