GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Phaeobacter inhibens BS107

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF2287 PGA1_c23190 dihydrolipoyl dehydrogenase LpdA

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__Phaeo:GFF2287
          Length = 459

 Score =  464 bits (1194), Expect = e-135
 Identities = 238/459 (51%), Positives = 314/459 (68%), Gaps = 8/459 (1%)

Query: 9   VVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEEAKA 68
           ++VLGAGP GY+ AFR ADLG   +IV+   TLGGVCLNVGCIPSKALLH A++I E + 
Sbjct: 8   LIVLGAGPGGYACAFRAADLGRSVIIVDPRATLGGVCLNVGCIPSKALLHAAEMIRETRH 67

Query: 69  LAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVE 128
               GI+ G    D++K+R  K+ ++ QLT GL G+AK RKV+ + G  +FT   +LE++
Sbjct: 68  GGGWGILTGNVSVDLNKLRAKKDSIVEQLTTGLVGLAKRRKVQTIRGSAQFTSDKSLEID 127

Query: 129 GENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGL 188
           GE+      FD A+IA GS P++LP  P ED RIWDSTDALEL+E+P+RL ++GGGIIGL
Sbjct: 128 GESW----TFDQAVIAVGSAPVRLPGWP-EDDRIWDSTDALELREIPKRLSIVGGGIIGL 182

Query: 189 EMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRI-SKKFNLMLETKVTAVEAKEDG 247
           EM TVY ALGS++ V+E  DQ+ P AD D V +    + ++   +   TKVT V+A +  
Sbjct: 183 EMATVYAALGSKVTVIEFMDQIAPGADADAVTILRAALETEDVTIHTGTKVTEVKASKTA 242

Query: 248 IYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPH 307
           + +T EG        + DA + A+GR  NG  +D   AGVE DDRG I VD   RTNV  
Sbjct: 243 LTLTCEGGFEGTI--KADAAIQAVGRRSNGSLVDPAAAGVEADDRGIIPVDASCRTNVAT 300

Query: 308 IFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWVGLTEKEA 367
           +FAIGD+ G PMLAH+  H+GHVAAEV +G     D  +IPS+AYT PE+AW GLT+ +A
Sbjct: 301 VFAIGDVTGNPMLAHRATHQGHVAAEVASGHATALDTDLIPSVAYTAPELAWAGLTQAKA 360

Query: 368 KEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGL 427
            E+GI +  A FPWAASGR ++S   +G+TKL++  +SHR++G  IVG N GELL E  L
Sbjct: 361 TERGIPHRVANFPWAASGRNLSSGGGEGLTKLVYCPDSHRLLGATIVGRNAGELLAECVL 420

Query: 428 AIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDL 466
           A+EMG   ED++L +HAHPTL E+VG AAE   G++TDL
Sbjct: 421 AMEMGATLEDMSLAVHAHPTLSETVGFAAERALGTLTDL 459


Lambda     K      H
   0.317    0.137    0.396 

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: 562
Number of extensions: 18
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 474
Length of database: 459
Length adjustment: 33
Effective length of query: 441
Effective length of database: 426
Effective search space:   187866
Effective search space used:   187866
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 GFF2287 PGA1_c23190 (dihydrolipoyl dehydrogenase LpdA)
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.919109.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     4e-149  483.1   0.1   4.9e-149  482.8   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2287  PGA1_c23190 dihydrolipoyl dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2287  PGA1_c23190 dihydrolipoyl dehydrogenase LpdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.8   0.1  4.9e-149  4.9e-149       2     457 ..       6     455 ..       5     458 .. 0.98

  Alignments for each domain:
  == domain 1  score: 482.8 bits;  conditional E-value: 4.9e-149
                          TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkld 76 
                                         d++v+G+GpgGY +A raa lg +v++v+   +lGG+ClnvGCiP+KalL++ae+++e ++   +gi + nv++d
  lcl|FitnessBrowser__Phaeo:GFF2287   6 ADLIVLGAGPGGYACAFRAADLGRSVIIVDPrATLGGVCLNVGCIPSKALLHAAEMIRETRHGGGWGILTGNVSVD 81 
                                        69****************************8799****************************************** PP

                          TIGR01350  77 lekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplklee 152
                                        l+kl ++k+++v++l++G+ +L k+ kv++i G+a+++++k++e+++e+     ++++++iA Gs p +lp+   e
  lcl|FitnessBrowser__Phaeo:GFF2287  82 LNKLRAKKDSIVEQLTTGLVGLAKRRKVQTIRGSAQFTSDKSLEIDGES----WTFDQAVIAVGSAPVRLPG-WPE 152
                                        ***********************************************98....68*****************.555 PP

                          TIGR01350 153 dekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvki 228
                                        d  ++++s++alel+e+p++l+ivGgG+iG+E+a+++a lG+kvtvie++d+i p  da+   +l+ +l+++ v+i
  lcl|FitnessBrowser__Phaeo:GFF2287 153 DD-RIWDSTDALELREIPKRLSIVGGGIIGLEMATVYAALGSKVTVIEFMDQIAPGADADAVTILRAALETEDVTI 227
                                        54.6************************************************************************ PP

                          TIGR01350 229 ltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiya 304
                                        +t++kvtev++++ +++++ +++ + t++a++ + avGr++n + ++ ++ gve d+rg+i+vd+++rtnv+ ++a
  lcl|FitnessBrowser__Phaeo:GFF2287 228 HTGTKVTEVKASKTALTLTCEGGFEGTIKADAAIQAVGRRSNGSLVDPAAAGVEADDRGIIPVDASCRTNVATVFA 303
                                        *****************99999966*************************************************** PP

                          TIGR01350 305 iGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaang 380
                                        iGDv+g++mLAh+A+++g vaae + g+++ ++d++++Psv yt Pe+a  Glt+++a e+gi  +v++fp aa+g
  lcl|FitnessBrowser__Phaeo:GFF2287 304 IGDVTGNPMLAHRATHQGHVAAEVASGHAT-ALDTDLIPSVAYTAPELAWAGLTQAKATERGIPHRVANFPWAASG 378
                                        ***************************776.9******************************************** PP

                          TIGR01350 381 kalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                        + l+++  +G+ k+++ ++++++lGa+ivg +a el++e +la+e+++t+e+++ ++h+HPtlsE++  aa+ alg
  lcl|FitnessBrowser__Phaeo:GFF2287 379 RNLSSGGGEGLTKLVYCPDSHRLLGATIVGRNAGELLAECVLAMEMGATLEDMSLAVHAHPTLSETVGFAAERALG 454
                                        ***********************************************************************99987 PP

                          TIGR01350 457 k 457
                                        +
  lcl|FitnessBrowser__Phaeo:GFF2287 455 T 455
                                        5 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 19.48
//
[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