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.1370921.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: 00:00:00.00
# Mc/sec: 24.63
//
[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