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.22331.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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.53
//
[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:

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