Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2C3

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate AO356_22975 AO356_22975 dihydrolipoamide dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_22975
          Length = 461

 Score =  908 bits (2346), Expect = 0.0
 Identities = 461/461 (100%), Positives = 461/461 (100%)

Query: 1   MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE 60
           MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE
Sbjct: 1   MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE 60

Query: 61  QFHQTRHHSQGSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120
           QFHQTRHHSQGSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK
Sbjct: 61  QFHQTRHHSQGSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120

Query: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPLGGPIISSTEALAPTSVPKHLVVVGG 180
           VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPLGGPIISSTEALAPTSVPKHLVVVGG
Sbjct: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPLGGPIISSTEALAPTSVPKHLVVVGG 180

Query: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240
           GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD
Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240

Query: 241 AQASTLQVRDPNGDTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNGSAVKIDSRCQTSM 300
           AQASTLQVRDPNGDTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNGSAVKIDSRCQTSM
Sbjct: 241 AQASTLQVRDPNGDTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNGSAVKIDSRCQTSM 300

Query: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360
           RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD
Sbjct: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360

Query: 361 EAKAAGLDCLVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420
           EAKAAGLDCLVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF
Sbjct: 361 EAKAAGLDCLVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 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: 833
Number of extensions: 14
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 AO356_22975 AO356_22975 (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.13545.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.3e-148  481.5   0.7   1.4e-148  481.3   0.7    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975  AO356_22975 dihydrolipoamide deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975  AO356_22975 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.3   0.7  1.4e-148  1.4e-148       3     460 ..       8     460 ..       6     461 .] 0.98

  Alignments for each domain:
  == domain 1  score: 481.3 bits;  conditional E-value: 1.4e-148
                                       TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke... 62 
                                                      +++iGgGpgGYvaAira+qlg +++lve + lGGtCln GCiP+Kal++ ae +++ ++   
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975   8 TLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAEQFHQTRHhsq 70 
                                                     578*******************************************************99533 PP

                                       TIGR01350  63 akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkek 125
                                                      + lgi+v+  +ld+ k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak+ d k+vev +++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975  71 GSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAKVIDGKTVEVGDTR 133
                                                     3579*******************************************************9998 PP

                                       TIGR01350 126 kekkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasi 188
                                                         ++ +++++AtGs+  +lp+ l   +  +i+s+eal+ ++vp++lv+vGgG+iG+E++ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 134 ----IQCEHLLLATGSKSVNLPM-LPLGG-PIISSTEALAPTSVPKHLVVVGGGYIGLELGIA 190
                                                     ....89*****************.89888.69******************************* PP

                                       TIGR01350 189 faklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk 251
                                                     ++klG++v+v+e+++rilpa d e+++ ++++lk+ gvk++ +++v+   +++ +++v+  ++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 191 YRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFDAQASTLQVRDPNG 253
                                                     *********************************************************999999 PP

                                       TIGR01350 252 evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmL 314
                                                     ++ +le+++vLvavGrkpn+++ +l++l++ ++   a+k+d++++t++ +++aiGD+ g++mL
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 254 DTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNG-SAVKIDSRCQTSMRNVWAIGDLSGEPML 315
                                                     9********************************9.78************************** PP

                                       TIGR01350 315 AhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfa 377
                                                     Ah+A+++g ++ae iag+++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 316 AHRAMAQGEMVAELIAGQHR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGLDCLVSSFPFA 377
                                                     *****************998.9***************************************** PP

                                       TIGR01350 378 angkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpH 440
                                                     ang+a++le ++Gfv+v++ ++ + i+G + vg  +sel + +   +e+++++e++a tih+H
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 378 ANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGQSLEMGARLEDIAGTIHAH 440
                                                     *************************************************************** PP

                                       TIGR01350 441 PtlsEaikeaalaalgkaih 460
                                                     Ptl+Ea++eaal alg+a+h
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 441 PTLGEAVQEAALRALGHALH 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.41
//
[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