Alignments for a candidate for lpd in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Bacteroides thetaiotaomicron VPI-5482

Align TPP-dependent acetoin dehydrogenase complex, E3 component, dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 352713 BT3186 dihydrolipoamide dehydrogenase (NCBI ptt file)

Query= CharProtDB::CH_006552
         (578 letters)



>FitnessBrowser__Btheta:352713
          Length = 447

 Score =  333 bits (853), Expect = 1e-95
 Identities = 188/449 (41%), Positives = 270/449 (60%), Gaps = 9/449 (2%)

Query: 118 LVVIGGGPGGYVAAIRAAQLGAKVTLIEKESLGGTCLNVGCIPTKVLLHSSQLLTEMKEG 177
           +++IGGGP GY AA  A + G  V LIEK +LGG CLN GCIPTK LL+S++     +  
Sbjct: 5   VIIIGGGPAGYTAAEAAGKAGLSVLLIEKNNLGGVCLNEGCIPTKTLLYSAKTYDSARHS 64

Query: 178 DKLGIDIEGSIVVNWKHIQKRKKIVIKKLVSGVSGLLTCNKVKVIKGTAKFESKDTILVT 237
            K  +++   +  +   I  RK  V++KLV GV   LT N V ++ G A+   K+T+   
Sbjct: 65  SKYAVNVS-EVSFDLPKIIARKSKVVRKLVLGVKAKLTSNNVAMVTGEAQIIDKNTVRCG 123

Query: 238 KEDGVAEKVNFDNAIIATGSMPFIPEIEGNKLSGVIDSTGALSLESNPESIAIIGGGVIG 297
           +E       N +N I+ TGS  FIP I G +         AL  +  P S+AI+GGGVIG
Sbjct: 124 EET-----YNAENLILCTGSETFIPPITGVETVNYWTHRDALDSKELPASLAIVGGGVIG 178

Query: 298 VEFASIFNSLGCKVSIIEMLPHILPPMDREISEIAKAKLIRDGININNNCKVTRIEQGED 357
           +EFAS FNSLG +V++IEM+  IL  MD+E+S + +A+  + GI    + KV  + Q E+
Sbjct: 179 MEFASFFNSLGVQVTVIEMMDEILGGMDKELSALLRAEYAKRGIKFLLSTKVVALSQTEE 238

Query: 358 GLKVSFIGDKGEESIDVEKVLIAVGRRSNIEGLDVEKIGV-KTEGGSIIVNDKMETNVEG 416
           G  VS+   +G+ S+  EK+L++VGRR   +G  +E + + KT  G+I VN+KM+T++ G
Sbjct: 239 GAVVSYENAEGKGSVIAEKLLMSVGRRPVTKGFGLENLNLDKTGRGAIKVNEKMQTSLSG 298

Query: 417 IYAIGDCTGKIMLAHVASDQGVVAAENIMGQNKKMDYKTVPACVYTKPELASVGLTEEQA 476
           +Y  GD TG  +LAH A  +  VA  +I+G+   M Y+ +P  VYT PE+A VG TEE A
Sbjct: 299 VYVCGDLTGFSLLAHTAVREAEVAVHSILGKEDAMSYRAIPGVVYTNPEIAGVGETEESA 358

Query: 477 KEKGIDYKVGKFQLAANGKSLIMNE-TGGVIKIITDKKYEEILGVHILGPRATDLITEAA 535
             KGI YKV K  +A +G+ +  NE   GV K++ D++ E I+G H+LG  A+++IT A 
Sbjct: 359 SAKGITYKVVKLPMAYSGRFVAENEGVNGVCKVLLDEQ-ERIIGAHVLGNPASEIITLAG 417

Query: 536 LALRLEATLEEIITTVHAHPTVGEAMKEA 564
            A+ L  T       V  HPTVGE  +EA
Sbjct: 418 TAIELGLTAAAWKKVVFPHPTVGEIFREA 446


Lambda     K      H
   0.313    0.134    0.365 

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: 610
Number of extensions: 29
Number of successful extensions: 4
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: 578
Length of database: 447
Length adjustment: 34
Effective length of query: 544
Effective length of database: 413
Effective search space:   224672
Effective search space used:   224672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 352713 BT3186 (dihydrolipoamide dehydrogenase (NCBI ptt file))
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.32389.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     6e-145  469.4   8.1   6.7e-145  469.2   8.1    1.0  1  lcl|FitnessBrowser__Btheta:352713  BT3186 dihydrolipoamide dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:352713  BT3186 dihydrolipoamide dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.2   8.1  6.7e-145  6.7e-145       1     450 [.       2     446 ..       2     447 .] 0.96

  Alignments for each domain:
  == domain 1  score: 469.2 bits;  conditional E-value: 6.7e-145
                          TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvkld 76 
                                        +y+v++iGgGp+GY+aA  a+++gl+v+l+ek++lGG+Cln+GCiPtK+lL sa++++++++ +++ ++v++v++d
  lcl|FitnessBrowser__Btheta:352713   2 KYQVIIIGGGPAGYTAAEAAGKAGLSVLLIEKNNLGGVCLNEGCIPTKTLLYSAKTYDSARHSSKYAVNVSEVSFD 77 
                                        599************************************************************************* PP

                          TIGR01350  77 lekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplklee 152
                                        l k+ +rk+kvv+klv Gvka l++n+v +++Gea++ dk++v+  +e+    ++a+n+i+ tGse   +p++  +
  lcl|FitnessBrowser__Btheta:352713  78 LPKIIARKSKVVRKLVLGVKAKLTSNNVAMVTGEAQIIDKNTVRCGEET----YNAENLILCTGSETFIPPIT-GV 148
                                        *******************************************998887....67*****************5.44 PP

                          TIGR01350 153 dekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvki 228
                                        ++   +t ++al  ke+p sl+ivGgGviG+Efas+f++lGv+vtvie++d+il  +d+e+s +l+ ++ k+g+k+
  lcl|FitnessBrowser__Btheta:352713 149 ETVNYWTHRDALDSKELPASLAIVGGGVIGMEFASFFNSLGVQVTVIEMMDEILGGMDKELSALLRAEYAKRGIKF 224
                                        44458*********************************************************************** PP

                          TIGR01350 229 ltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiy 303
                                        l ++kv +++++e+  vv+ ++   + ++ aek+L++vGr+p ++++gle+l+++ + rgaikv+e+++t+++g+y
  lcl|FitnessBrowser__Btheta:352713 225 LLSTKVVALSQTEEGAVVSYENAeGKGSVIAEKLLMSVGRRPVTKGFGLENLNLDKTGRGAIKVNEKMQTSLSGVY 300
                                        *******999999888876666646799************************************************ PP

                          TIGR01350 304 aiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaan 379
                                        ++GD++g   LAh+A++e+ va++ i+gke+ ++ y+a+P v+yt+Pe+a vG tee a ++gi +kv+k+p+a +
  lcl|FitnessBrowser__Btheta:352713 301 VCGDLTGFSLLAHTAVREAEVAVHSILGKED-AMSYRAIPGVVYTNPEIAGVGETEESASAKGITYKVVKLPMAYS 375
                                        ****************************887.9******************************************* PP

                          TIGR01350 380 gkalalee.tdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikea 450
                                        g+ +a +e  +G+ kv++d++ ++i+Gah++g+ ase+i+ +  a+el+lt+   +k+++pHPt++E++ ea
  lcl|FitnessBrowser__Btheta:352713 376 GRFVAENEgVNGVCKVLLDEQ-ERIIGAHVLGNPASEIITLAGTAIELGLTAAAWKKVVFPHPTVGEIFREA 446
                                        *****99978********975.79*********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (447 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 10.07
//
[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