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; Dihydrolipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes (uncharacterized)
to candidate GFF344 PGA1_c03550 dihydrolipoyl dehydrogenase 2

Query= curated2:P95596
         (454 letters)



>FitnessBrowser__Phaeo:GFF344
          Length = 465

 Score =  654 bits (1688), Expect = 0.0
 Identities = 329/465 (70%), Positives = 375/465 (80%), Gaps = 11/465 (2%)

Query: 1   MAEFDVIIIGGGPGGYVCAIRCAQLGLKTACVEGRGALGGTCLNVGCIPSKALLHATHEL 60
           MA +DVI+IG GPGGYVCAIRCAQLGLKTA VEGR  LGGTCLNVGCIPSKALLH+TH L
Sbjct: 1   MASYDVIVIGAGPGGYVCAIRCAQLGLKTAVVEGRETLGGTCLNVGCIPSKALLHSTHLL 60

Query: 61  HEVHENFEKMGLMGAKVKVDWAK--------IDGNTKGIEFLFKKNKVTYLRGWGSIPAP 112
           HE   NF  MGL G    VDW++        I  NT GIEFLFKKNK+ +++GW S+   
Sbjct: 61  HEAEHNFAHMGLKGKSPSVDWSQMKSYKEEVIGQNTGGIEFLFKKNKIDWIKGWASLSEA 120

Query: 113 GQVKVGDEVHTAKNIVIATGSESSGLPGIEIDEQT--VVTSTGALSLAKVPKSMVVIGAG 170
           G+VKVGD+ H AKNIVIA+GS  S LPG+E+D     VV STGAL L K+PK MVVIGAG
Sbjct: 121 GKVKVGDDTHEAKNIVIASGSVPSSLPGVEVDNDKGIVVDSTGALDLPKIPKKMVVIGAG 180

Query: 171 VIGLELGSVYARLGAEVTVVEYLDAITPGMDAEVAKGLQRILTRQGLKFVLGAAVQGVDK 230
           VIGLELGSVYARLG++VTVVEY+DA+ PGMD +V +  +RIL +QGL F++GAAVQ V+ 
Sbjct: 181 VIGLELGSVYARLGSDVTVVEYMDAVCPGMDKDVQRSFKRILEKQGLNFIMGAAVQEVET 240

Query: 231 AKGKNTVRYTLRKDESAHAIEAEVVLVATGRKPFTKGLGLEALGVEMLPRGQVKADSHWA 290
           +K K  V+Y  +K      I+A+VVLVATGRKP+ +GLGL+ALGV+M  RGQ+  D+HWA
Sbjct: 241 SKTKAKVKYQPKKGGDEEVIDADVVLVATGRKPYAEGLGLDALGVKMTERGQIATDAHWA 300

Query: 291 TNVPGLYAIGDAIVGPMLAHKAEDEGMAVAEVIAGKHGHVNYDVIPGVIYTTPEVAAVGK 350
           TNV G+YAIGD I GPMLAHKAEDEGMAVAEVIA KHGHVNY VIPGV+YTTPEVA VG+
Sbjct: 301 TNVNGVYAIGDVIEGPMLAHKAEDEGMAVAEVIADKHGHVNYGVIPGVVYTTPEVATVGQ 360

Query: 351 TEDALKQEGRAYKVGKFSFMGNGRAKAVFQAE-GFVKILADAATDRILGAHIIGPSAGDM 409
           TEDALK EGR  K GKF FMGN RAKAV QAE GFVK++AD  TDRILGA IIGP AGD+
Sbjct: 361 TEDALKAEGRKIKTGKFMFMGNARAKAVHQAEGGFVKLIADKETDRILGAAIIGPGAGDL 420

Query: 410 IHEICVAMEFGASAQDLALTCHAHPTYSEAVREAALACGDGAIHA 454
           IHEICVAMEFGASA+DLALTCHAHPTYSEAVREAALACGDG IH+
Sbjct: 421 IHEICVAMEFGASAEDLALTCHAHPTYSEAVREAALACGDGPIHS 465


Lambda     K      H
   0.318    0.136    0.397 

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: 848
Number of extensions: 42
Number of successful extensions: 5
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: 454
Length of database: 465
Length adjustment: 33
Effective length of query: 421
Effective length of database: 432
Effective search space:   181872
Effective search space used:   181872
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 GFF344 PGA1_c03550 (dihydrolipoyl dehydrogenase 2)
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.8018.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.1e-174  564.9   9.7   6.9e-174  564.8   9.7    1.0  1  lcl|FitnessBrowser__Phaeo:GFF344  PGA1_c03550 dihydrolipoyl dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF344  PGA1_c03550 dihydrolipoyl dehydrogenase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.8   9.7  6.9e-174  6.9e-174       1     460 [.       3     464 ..       3     465 .] 0.97

  Alignments for each domain:
  == domain 1  score: 564.8 bits;  conditional E-value: 6.9e-174
                         TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgievenvkl 75 
                                       +ydv+viG+GpgGYv+Air+aqlglk+a+ve  e+lGGtClnvGCiP+KalL+s+++++e+++ ++++g++ ++ ++
  lcl|FitnessBrowser__Phaeo:GFF344   3 SYDVIVIGAGPGGYVCAIRCAQLGLKTAVVEGrETLGGTCLNVGCIPSKALLHSTHLLHEAEHnFAHMGLKGKSPSV 79 
                                       59*****************************879******************************************* PP

                         TIGR01350  76 dlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplk.le 151
                                       d+++++  ke+v+ + +gG+++L+kknk++ ikG a+l+++++v+v ++++    eakni+iA+Gs p++lp+  ++
  lcl|FitnessBrowser__Phaeo:GFF344  80 DWSQMKSYKEEVIGQNTGGIEFLFKKNKIDWIKGWASLSEAGKVKVGDDTH----EAKNIVIASGSVPSSLPGVeVD 152
                                       **********************************************99974....6*****************8888 PP

                         TIGR01350 152 edekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvki 228
                                       +d+ +v++s++al l+++p+++v++G+GviG+E++s++a+lG++vtv+e++d ++p +d++v +  k+ l+k+g+++
  lcl|FitnessBrowser__Phaeo:GFF344 153 NDKGIVVDSTGALDLPKIPKKMVVIGAGVIGLELGSVYARLGSDVTVVEYMDAVCPGMDKDVQRSFKRILEKQGLNF 229
                                       8888************************************************************************* PP

                         TIGR01350 229 ltnakvteve..keedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgi 302
                                       +++a v+eve  k++++v+++ kk+ ++e+++a+ vLva Grkp  e+lgl++lgv+++erg+i +d++  tnv+g+
  lcl|FitnessBrowser__Phaeo:GFF344 230 IMGAAVQEVEtsKTKAKVKYQPKKGgDEEVIDADVVLVATGRKPYAEGLGLDALGVKMTERGQIATDAHWATNVNGV 306
                                       *******666115566777998888899************************************************* PP

                         TIGR01350 303 yaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaan 379
                                       yaiGDvi+++mLAh+A++eg+ +ae ia+k+  +++y ++P v+yt+Peva+vG te+ +k+eg ++k+gkf f+ n
  lcl|FitnessBrowser__Phaeo:GFF344 307 YAIGDVIEGPMLAHKAEDEGMAVAEVIADKHG-HVNYGVIPGVVYTTPEVATVGQTEDALKAEGRKIKTGKFMFMGN 382
                                       *****************************998.9******************************************* PP

                         TIGR01350 380 gkalalee.tdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455
                                       ++a a+++ + Gfvk+i+dk+t++ilGa i+g+ a +li+e+ +a+e+++++e+la t+h+HPt+sEa+ eaala  
  lcl|FitnessBrowser__Phaeo:GFF344 383 ARAKAVHQaEGGFVKLIADKETDRILGAAIIGPGAGDLIHEICVAMEFGASAEDLALTCHAHPTYSEAVREAALACG 459
                                       *****9984568***************************************************************99 PP

                         TIGR01350 456 gkaih 460
                                       + +ih
  lcl|FitnessBrowser__Phaeo:GFF344 460 DGPIH 464
                                       99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 10.51
//
[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