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.19811.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 7.19
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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