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.17445.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: 9.12
//
[ok]

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

Links

Downloads

Related tools

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