Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E3

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate AO353_26650 AO353_26650 dihydrolipoamide dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_22975
         (461 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_26650
          Length = 461

 Score =  860 bits (2221), Expect = 0.0
 Identities = 433/461 (93%), Positives = 450/461 (97%)

Query: 1   MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE 60
           MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE
Sbjct: 1   MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE 60

Query: 61  QFHQTRHHSQGSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120
           QFHQT+HHSQ SALGI V+APTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVI GWAK
Sbjct: 61  QFHQTQHHSQHSALGINVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIQGWAK 120

Query: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPLGGPIISSTEALAPTSVPKHLVVVGG 180
           VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLP+GGPIISSTEALAP SVPK L+VVGG
Sbjct: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPKSVPKRLIVVGG 180

Query: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240
           GYIGLELGIAYRKLGAEVSVVEAQ+RILPAYD ELTQPV+EALKQLGVKLYLKHSVEGFD
Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNEALKQLGVKLYLKHSVEGFD 240

Query: 241 AQASTLQVRDPNGDTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNGSAVKIDSRCQTSM 300
           +QA+TLQVRDPNG+ LNL TD+VLVAVGRKPNTQGWNL AL+L MNGSA+KID+RC TSM
Sbjct: 241 SQANTLQVRDPNGEILNLATDQVLVAVGRKPNTQGWNLEALNLDMNGSAIKIDNRCATSM 300

Query: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360
           RNVWAIGDLSGEPMLAHRAMAQGEMVAELI+G+HREFNPTAIAAVCFTDPELVVVGKTPD
Sbjct: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPTAIAAVCFTDPELVVVGKTPD 360

Query: 361 EAKAAGLDCLVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420
           EAKAAGLDC+VS+FPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF
Sbjct: 361 EAKAAGLDCIVSNFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420

Query: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461
           GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461


Lambda     K      H
   0.318    0.134    0.392 

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: 805
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: 461
Length of database: 461
Length adjustment: 33
Effective length of query: 428
Effective length of database: 428
Effective search space:   183184
Effective search space used:   183184
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 AO353_26650 AO353_26650 (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.11160.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     1e-149  485.1   1.3   1.2e-149  484.9   1.3    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650  AO353_26650 dihydrolipoamide deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650  AO353_26650 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.9   1.3  1.2e-149  1.2e-149       3     460 ..       8     460 ..       6     461 .] 0.98

  Alignments for each domain:
  == domain 1  score: 484.9 bits;  conditional E-value: 1.2e-149
                                     TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...ak 64 
                                                    +++iGgGpgGYvaAira+qlg +++lve + lGGtCln GCiP+Kal++ ae +++ ++    +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650   8 TLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAEQFHQTQHhsqHS 72 
                                                   578******************************************************99954345 PP

                                     TIGR01350  65 elgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekk 129
                                                    lgi+v+  +ld+ k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak+ d k+vev +++    
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650  73 ALGINVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIQGWAKVIDGKTVEVGDTR---- 133
                                                   68*******************************************************9998.... PP

                                     TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGv 194
                                                   ++ +++++AtGs+  +lp+ l   +  +i+s+eal+ k+vp++l++vGgG+iG+E++ +++klG+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650 134 IQCEHLLLATGSKSVNLPM-LPIGG-PIISSTEALAPKSVPKRLIVVGGGYIGLELGIAYRKLGA 196
                                                   89*****************.99998.69************************************* PP

                                     TIGR01350 195 kvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevetleae 259
                                                   +v+v+e++drilpa dae+++ ++++lk+ gvk++ +++v+   +++++++v+  ++e+ +l ++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650 197 EVSVVEAQDRILPAYDAELTQPVNEALKQLGVKLYLKHSVEGFDSQANTLQVRDPNGEILNLATD 261
                                                   *****************************************************9999******** PP

                                     TIGR01350 260 kvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvv 324
                                                   +vLvavGrkpn+++ +le+l+++++   aik+d+++ t++ +++aiGD+ g++mLAh+A+++g +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650 262 QVLVAVGRKPNTQGWNLEALNLDMNG-SAIKIDNRCATSMRNVWAIGDLSGEPMLAHRAMAQGEM 325
                                                   *************************9.78************************************ PP

                                     TIGR01350 325 aaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetd 389
                                                   +ae i gk++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfaang+a++le ++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650 326 VAELISGKHR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGLDCIVSNFPFAANGRAMTLESKS 389
                                                   *******998.9***************************************************** PP

                                     TIGR01350 390 GfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaa 454
                                                   Gfv+v++ ++ + i+G + vg  +sel + +   +e+++++e++a tih+HPtl+Ea++eaal a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650 390 GFVRVVARRDNHLIVGWQAVGVGVSELSTAFGQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRA 454
                                                   ***************************************************************** PP

                                     TIGR01350 455 lgkaih 460
                                                   lg+a+h
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_26650 455 LGHALH 460
                                                   ***999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (461 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: 7.68
//
[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