Alignments for a candidate for lpd in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Dechlorosoma suillum PS

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Dsui_1576 Dsui_1576 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__PS:Dsui_1576
          Length = 581

 Score =  815 bits (2105), Expect = 0.0
 Identities = 417/593 (70%), Positives = 484/593 (81%), Gaps = 16/593 (2%)

Query: 3   VIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVK 62
           ++EVKVPDIGDF  V VIEV VK GDTV+VE  L+ LESDKA+MDVPSSAAG V E+KVK
Sbjct: 4   LVEVKVPDIGDFKDVPVIEVFVKVGDTVKVEDPLVSLESDKATMDVPSSAAGVVKEIKVK 63

Query: 63  VGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCE 122
           +GDKV +G VI  +EA  AAAAPAP Q  APA APAPAAA P   P A SH GGAD++C+
Sbjct: 64  LGDKVAEGTVIVVVEAGAAAAAPAP-QPAAPAAAPAPAAAPP---PVAGSHGGGADVECD 119

Query: 123 MLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKA 182
           MLVLGAGPGGYSAAFR+ADLG+ TVLVERY TLGGVCLNVGCIPSKALLH AAV++EA+ 
Sbjct: 120 MLVLGAGPGGYSAAFRSADLGLKTVLVERYPTLGGVCLNVGCIPSKALLHVAAVLEEAQH 179

Query: 183 LAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVE 242
           LA  G+ F   ++D+D LR +K +VVGKLTGGLAGMAK RKVQ V+G+G F+DPHH+EV 
Sbjct: 180 LADCGVTFAAPQVDVDKLRAHKEKVVGKLTGGLAGMAKGRKVQHVQGVGQFIDPHHIEVT 239

Query: 243 LTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIP-EDPRIVDSTGALELPEVPNKMLV 301
             +G       KK V++F+ AIIAAGSQ V LPF+P +DPR++DSTGALEL  VP KMLV
Sbjct: 240 AADG-------KKQVVKFKNAIIAAGSQPVALPFMPKDDPRVIDSTGALELRSVPKKMLV 292

Query: 302 IGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTV 361
           IGGGIIGLEMATVYS LG  I VVE+  GLM GADRDLVKVWEKKN  RF +++L T   
Sbjct: 293 IGGGIIGLEMATVYSALGTRITVVELGPGLMPGADRDLVKVWEKKNTQRFDRILLATGVT 352

Query: 362 GVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDK 421
             EAK +GI V +    +  E + +DLVLV+VGR+PNGK+I+A+KAGVAV++RGFINVD 
Sbjct: 353 AAEAKAEGIEVTY----STGEKEAFDLVLVAVGRTPNGKKIAADKAGVAVTDRGFINVDA 408

Query: 422 QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAW 481
           QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAE A GEKA FDA QIPSVA+T PE+AW
Sbjct: 409 QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVAAGEKAAFDALQIPSVAYTHPEIAW 468

Query: 482 AGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAG 541
           AG TED+ K  GIK+ K VFPWAASGRAIANG +EGFTKL+FD E+HR++GGGIVG +AG
Sbjct: 469 AGKTEDQLKNDGIKFEKAVFPWAASGRAIANGAEEGFTKLLFDAESHRLLGGGIVGMNAG 528

Query: 542 DLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           DLI EVCLA+EMG DAVDIGKTIHPHPTL ESIGMAAE+  G+CTD+PP +K+
Sbjct: 529 DLIGEVCLAVEMGCDAVDIGKTIHPHPTLCESIGMAAEVAHGSCTDLPPMKKK 581


Lambda     K      H
   0.316    0.134    0.387 

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: 1053
Number of extensions: 41
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: 594
Length of database: 581
Length adjustment: 37
Effective length of query: 557
Effective length of database: 544
Effective search space:   303008
Effective search space used:   303008
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: 53 (25.0 bits)

Align candidate Dsui_1576 Dsui_1576 (dihydrolipoamide dehydrogenase)
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.20486.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.4e-150  486.7   4.5   4.4e-150  486.3   4.5    1.1  1  lcl|FitnessBrowser__PS:Dsui_1576  Dsui_1576 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1576  Dsui_1576 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.3   4.5  4.4e-150  4.4e-150       2     456 ..     118     570 ..     117     574 .. 0.98

  Alignments for each domain:
  == domain 1  score: 486.3 bits;  conditional E-value: 4.4e-150
                         TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldl 77 
                                        d++v+G+GpgGY aA r+a lglk++lve+  +lGG+ClnvGCiP+KalL+ a v+ee+++++++g++ +  ++d+
  lcl|FitnessBrowser__PS:Dsui_1576 118 CDMLVLGAGPGGYSAAFRSADLGLKTVLVERyPTLGGVCLNVGCIPSKALLHVAAVLEEAQHLADCGVTFAAPQVDV 194
                                       699****************************99******************************************** PP

                         TIGR01350  78 ekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelplkleed 153
                                       +kl ++kekvv kl+gG++++ k  kv++++G +++ d++++ev++ +++ +++++kn+iiA Gs+p +lp+ + +d
  lcl|FitnessBrowser__PS:Dsui_1576 195 DKLRAHKEKVVGKLTGGLAGMAKGRKVQHVQGVGQFIDPHHIEVTAADGKkQVVKFKNAIIAAGSQPVALPF-MPKD 270
                                       *********************************************998877999******************.9999 PP

                         TIGR01350 154 ekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkilt 230
                                         +vi+s++alel++vp++++++GgG+iG+E+a++++ lG+ +tv+el + ++p  d+++ kv +kk +++  +il 
  lcl|FitnessBrowser__PS:Dsui_1576 271 DPRVIDSTGALELRSVPKKMLVIGGGIIGLEMATVYSALGTRITVVELGPGLMPGADRDLVKVWEKKNTQRFDRILL 347
                                       99*************************************************************************** PP

                         TIGR01350 231 nakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGD 307
                                        + vt+ e++++ ++v+ + +  e+   + vLvavGr+pn +++  +k gv +++rg+i+vd+++rtnvp+i+aiGD
  lcl|FitnessBrowser__PS:Dsui_1576 348 ATGVTAAEAKAEGIEVTYSTG--EKEAFDLVLVAVGRTPNGKKIAADKAGVAVTDRGFINVDAQMRTNVPHIFAIGD 422
                                       ***************998777..68899************************************************* PP

                         TIGR01350 308 vigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkala 384
                                       ++g++mLAh+A++e+ vaae +ag+++ ++d+ ++Psv yt+Pe+a  G+te+q+k++gi+++ + fp aa+g+a+a
  lcl|FitnessBrowser__PS:Dsui_1576 423 IVGQPMLAHKAVHEAHVAAEVAAGEKA-AFDALQIPSVAYTHPEIAWAGKTEDQLKNDGIKFEKAVFPWAASGRAIA 498
                                       ************************776.9************************************************ PP

                         TIGR01350 385 leetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                        + ++Gf k+++d +++++lG  ivg +a +li e+ lave++  + ++ ktihpHPtl E i  aa+ a g
  lcl|FitnessBrowser__PS:Dsui_1576 499 NGAEEGFTKLLFDAESHRLLGGGIVGMNAGDLIGEVCLAVEMGCDAVDIGKTIHPHPTLCESIGMAAEVAHG 570
                                       ****************************************************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (581 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: 10.33
//
[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