Alignments for a candidate for lpd in Phaeobacter inhibens BS107

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.16155.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.73
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources