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_19705 AO356_19705 dihydrolipoamide dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_19705
          Length = 478

 Score =  875 bits (2262), Expect = 0.0
 Identities = 450/478 (94%), Positives = 460/478 (96%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           MTQKFDVVVIGAGPGGYVAAIKAAQLGL TACIEKYTD EGK ALGGTCLNVGCIPSKAL
Sbjct: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLTTACIEKYTDGEGKQALGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLT GVATLFKANGVTSIQG
Sbjct: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTSGVATLFKANGVTSIQG 120

Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180
           HGKLL GKKVEVTK DG+ EVIEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEFQ+V
Sbjct: 121 HGKLLLGKKVEVTKPDGSVEVIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEFQSV 180

Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240
           PKRLGVIGAGVIGLELGSVW+RLGA+VTVLEALDTFLMAAD AVSKEA KTLTKQGLDIK
Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAQVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIK 240

Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300
           LGARVTGSKVNG EV V YT+A GEQ ITFDKLIVAVGRRPVTTDLLAADSGV +DERG+
Sbjct: 241 LGARVTGSKVNGEEVVVNYTDANGEQTITFDKLIVAVGRRPVTTDLLAADSGVDLDERGF 300

Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360
           I VDD+CAT+VPGV+AIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH
Sbjct: 301 IKVDDFCATTVPGVFAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360

Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420
           PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI
Sbjct: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420

Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478
           GPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR
Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478


Lambda     K      H
   0.316    0.133    0.374 

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: 915
Number of extensions: 17
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate AO356_19705 AO356_19705 (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.21198.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.1e-163  531.1  11.3   1.3e-163  530.9  11.3    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705  AO356_19705 dihydrolipoamide deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705  AO356_19705 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.9  11.3  1.3e-163  1.3e-163       1     461 []       4     472 ..       4     472 .. 0.97

  Alignments for each domain:
  == domain 1  score: 530.9 bits;  conditional E-value: 1.3e-163
                                       TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaev 56 
                                                     ++dvvviG+GpgGYvaAi+aaqlgl +a++e       k+ lGGtClnvGCiP+KalL s+  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705   4 KFDVVVIGAGPGGYVAAIKAAQLGLTTACIEkytdgegKQALGGTCLNVGCIPSKALLDSSWK 66 
                                                     59*****************************44444334579********************* PP

                                       TIGR01350  57 veelke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkke 118
                                                     ++e+ke ++ +gi++ +vk+d+++++ rk  +vk+l++Gv++L+k n+v++i+G++kll  k+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705  67 YKEAKEsFNVHGISTGEVKMDVAAMVGRKAGIVKNLTSGVATLFKANGVTSIQGHGKLLLGKK 129
                                                     ******9******************************************************** PP

                                       TIGR01350 119 vevkkekke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGv 180
                                                     vev+k +++ +++ea+n+i+A Gs+p+ +p    +d++v+++s++ale+++vp++l ++G+Gv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 130 VEVTKPDGSvEVIEAENVILAPGSRPIDIPP-APVDQNVIVDSTGALEFQSVPKRLGVIGAGV 191
                                                     *****998889*******************9.8999999************************ PP

                                       TIGR01350 181 iGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeede 243
                                                     iG+E++s++++lG++vtv+e+ld+ l a da vsk++ k+l+k+g++i+ +a+vt  + + +e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 192 IGLELGSVWSRLGAQVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIKLGARVTGSKVNGEE 254
                                                     *******************************************************98888888 PP

                                       TIGR01350 244 vvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyai 305
                                                     vvv+  +   ++t++ +k++vavGr+p +++l  +  gv+lderg+ikvd+ + t+vpg++ai
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 255 VVVNYTDAnGEQTITFDKLIVAVGRRPVTTDLLAADSGVDLDERGFIKVDDFCATTVPGVFAI 317
                                                     886666655679*************************************************** PP

                                       TIGR01350 306 GDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegie 368
                                                     GDv++++mLAh+As+eg++++e+i g+++ +++y+++Psviyt+Pe+a vG+te+ +k+eg+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 318 GDVVRGMMLAHKASEEGIMVVERIKGHKA-QMNYDLIPSVIYTHPEIAWVGKTEQALKAEGVE 379
                                                     **************************665.9******************************** PP

                                       TIGR01350 369 vkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431
                                                     v+vg fpfaa+g+a+a+++t Gfvkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 380 VNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAE 442
                                                     *************************************************************** PP

                                       TIGR01350 432 elaktihpHPtlsEaikeaalaalgkaihv 461
                                                     +l ++++ HPtlsEa++eaala++g aihv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 443 DLGMMVFSHPTLSEALHEAALAVNGGAIHV 472
                                                     ****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (478 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: 7.86
//
[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