Alignments for a candidate for lpd in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas simiae WCS417

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF3432 PS417_17560 dihydrolipoamide dehydrogenase

Query= reanno::WCS417:GFF3432
         (459 letters)



>FitnessBrowser__WCS417:GFF3432
          Length = 459

 Score =  905 bits (2338), Expect = 0.0
 Identities = 459/459 (100%), Positives = 459/459 (100%)

Query: 1   MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60
           MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE
Sbjct: 1   MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60

Query: 61  QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120
           QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK
Sbjct: 61  QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120

Query: 121 VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG 180
           VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG
Sbjct: 121 VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG 180

Query: 181 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT 240
           GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT
Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT 240

Query: 241 DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN 300
           DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN
Sbjct: 241 DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN 300

Query: 301 VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA 360
           VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA
Sbjct: 301 VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA 360

Query: 361 KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL 420
           KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL
Sbjct: 361 KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL 420

Query: 421 SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL 459
           SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL 459


Lambda     K      H
   0.318    0.136    0.395 

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: 808
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: 459
Length of database: 459
Length adjustment: 33
Effective length of query: 426
Effective length of database: 426
Effective search space:   181476
Effective search space used:   181476
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 GFF3432 PS417_17560 (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.24840.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.7e-151  489.2   0.5   6.4e-151  489.0   0.5    1.0  1  lcl|FitnessBrowser__WCS417:GFF3432  PS417_17560 dihydrolipoamide deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3432  PS417_17560 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.0   0.5  6.4e-151  6.4e-151       3     460 ..       8     458 ..       6     459 .] 0.96

  Alignments for each domain:
  == domain 1  score: 489.0 bits;  conditional E-value: 6.4e-151
                           TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...akelgievenvk 74 
                                          +++iGgGpgGYvaAira+qlg  ++lve + lGGtCln GCiP+Kal++ ae +++  +    ++lgiev+  +
  lcl|FitnessBrowser__WCS417:GFF3432   8 TLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAEQFQQTIHhsqGSHLGIEVDVPT 82 
                                         578***************************************************9987653445789******** PP

                           TIGR01350  75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplk 149
                                         ld++k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak++d k+vev +++    ++ +++++AtGs+  +lp+ 
  lcl|FitnessBrowser__WCS417:GFF3432  83 LDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAKVVDGKTVEVGDQR----IQCEHLLLATGSKSVNLPM- 152
                                         ***********************************************9997....89*****************. PP

                           TIGR01350 150 leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkk 224
                                         l   +  +i+s+eal+ ++vp++l++vGgG+iG+E++ +++klG++v+v+e++drilpa dae+++ ++++lk+ 
  lcl|FitnessBrowser__WCS417:GFF3432 153 LPIGG-PIISSTEALAPTRVPKRLIVVGGGYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHL 226
                                         99998.69******************************************************************* PP

                           TIGR01350 225 gvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnv 299
                                         gvk++ +++vt  ++ + +v+    ++++ +l +++vLvavGrkpn+++ +le+l++e++   aik+d++++t++
  lcl|FitnessBrowser__WCS417:GFF3432 227 GVKLYLKHSVTGFTDGSLQVR--DPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNG-AAIKIDSRCQTSM 298
                                         ***********6666655555..5566689******************************9.78*********** PP

                           TIGR01350 300 pgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkf 374
                                          ++yaiGD+ g++mLAh+A+++g ++ae i gk++ e++  a+P+v +t+Pe+ +vG+t ++ak++g ++ v++f
  lcl|FitnessBrowser__WCS417:GFF3432 299 RNVYAIGDLSGEPMLAHRAMAQGEMVAELISGKHR-EFNPAAIPAVCFTDPELVVVGKTPDEAKAAGLDCIVSSF 372
                                         ********************************998.9************************************** PP

                           TIGR01350 375 pfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaike 449
                                         pfaang+a++le ++Gfv+v++ ++ + i+G + vg  +sel + + l +e++ ++e++a tih+HPtl+Ea++e
  lcl|FitnessBrowser__WCS417:GFF3432 373 PFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGLSLEMGSRLEDVAGTIHAHPTLGEAVQE 447
                                         *************************************************************************** PP

                           TIGR01350 450 aalaalgkaih 460
                                         aal alg+a+h
  lcl|FitnessBrowser__WCS417:GFF3432 448 AALRALGHALH 458
                                         ********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (459 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: 9.76
//
[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