Aligments for a candidate for lpd in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for lpd in Cupriavidus basilensis 4G11

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate RR42_RS26115 RR42_RS26115 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS26115 RR42_RS26115
           dihydrolipoamide dehydrogenase
          Length = 589

 Score =  857 bits (2215), Expect = 0.0
 Identities = 438/593 (73%), Positives = 495/593 (83%), Gaps = 10/593 (1%)

Query: 4   IEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVKV 63
           +EVKVPDIGDF  V VIEV+VK G+ + V+ SLI +ESDKASM++PS+ AG V E+ VKV
Sbjct: 5   VEVKVPDIGDFKDVTVIEVMVKPGEIIAVDTSLIAVESDKASMEIPSTHAGVVKEITVKV 64

Query: 64  GDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPA--PAPAAASHSGGADIQC 121
            DKV +G+VI  +EA  AAA  A   APAPA   AP   APA  P P AAS++G AD +C
Sbjct: 65  NDKVSEGSVILVVEAAAAAATVAAPAAPAPAAPSAPPGPAPAAAPVPNAASYTGKADQEC 124

Query: 122 EMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAK 181
           EMLVLGAGPGGYSAAFR+ADLGM TVLVERY TLGGVCLNVGCIPSKALLH A+V+DE  
Sbjct: 125 EMLVLGAGPGGYSAAFRSADLGMKTVLVERYDTLGGVCLNVGCIPSKALLHTASVMDEVA 184

Query: 182 ALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEV 241
            L  HGI +G  +IDLD LR +K+ V+ KLTGGLAGMAKARKV+VV G+G+FLDP+H+EV
Sbjct: 185 TLPDHGIRYGAPEIDLDKLRGFKDSVIKKLTGGLAGMAKARKVEVVTGVGSFLDPYHLEV 244

Query: 242 ELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPNKMLV 301
              +G GKR      VI+F KAIIAAGSQAVKLPF+P+D R+VDSTGAL L  +P +MLV
Sbjct: 245 VAADG-GKR------VIKFAKAIIAAGSQAVKLPFMPDDERVVDSTGALLLKSIPKRMLV 297

Query: 302 IGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTV 361
           +GGGIIGLEMATVYSTLG  IDVVEMLDGLM GADRDLVKVWEKKN  RF  VMLKT+T+
Sbjct: 298 VGGGIIGLEMATVYSTLGTRIDVVEMLDGLMQGADRDLVKVWEKKNTHRFDHVMLKTRTI 357

Query: 362 GVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDK 421
           G +A P GI V FEGE APA PQ YDLVLV+VGRSPNG+ I AEKAGVAV+ERGFI+VD+
Sbjct: 358 GAKATPAGIEVSFEGEKAPA-PQVYDLVLVAVGRSPNGRAIGAEKAGVAVTERGFIDVDR 416

Query: 422 QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAW 481
           QMRTNV HI AIGDIVGQPMLAHKAVHEAHVAAEAAHGE AYFDA+QIPSVA+TDPEVAW
Sbjct: 417 QMRTNVAHIHAIGDIVGQPMLAHKAVHEAHVAAEAAHGEAAYFDARQIPSVAYTDPEVAW 476

Query: 482 AGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAG 541
           AG TE++CK +GIK  K VFPWAASGRAIANGRDEGFTKL+FDE THRVIGGGIVGTHAG
Sbjct: 477 AGKTEEQCKAEGIKIGKAVFPWAASGRAIANGRDEGFTKLLFDEATHRVIGGGIVGTHAG 536

Query: 542 DLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           DLISEVCLAIEMG +  DIGKTIHPHPTLGESIGMAAE++EG CTD+PP +K+
Sbjct: 537 DLISEVCLAIEMGCEPADIGKTIHPHPTLGESIGMAAEVFEGHCTDLPPVKKK 589


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: 1126
Number of extensions: 41
Number of successful extensions: 7
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: 589
Length adjustment: 37
Effective length of query: 557
Effective length of database: 552
Effective search space:   307464
Effective search space used:   307464
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 RR42_RS26115 RR42_RS26115 (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.1101.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-142  461.3   2.0   2.8e-142  460.6   2.0    1.2  1  lcl|FitnessBrowser__Cup4G11:RR42_RS26115  RR42_RS26115 dihydrolipoamide de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS26115  RR42_RS26115 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.6   2.0  2.8e-142  2.8e-142       3     456 ..     125     578 ..     123     582 .. 0.96

  Alignments for each domain:
  == domain 1  score: 460.6 bits;  conditional E-value: 2.8e-142
                                 TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                               +++v+G+GpgGY aA r+a lg+k++lve+ ++lGG+ClnvGCiP+KalL++a v++e+ ++ ++gi+ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS26115 125 EMLVLGAGPGGYSAAFRSADLGMKTVLVERyDTLGGVCLNVGCIPSKALLHTASVMDEVATLPDHGIRY 193
                                               789***************************9************************************** PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiA 138
                                                  ++dl+kl   k++v+kkl+gG++++ k  kvev++G +++ld+ ++ev + ++  +++++ ++iiA
  lcl|FitnessBrowser__Cup4G11:RR42_RS26115 194 GAPEIDLDKLRGFKDSVIKKLTGGLAGMAKARKVEVVTGVGSFLDPYHLEVVAADGGkRVIKFAKAIIA 262
                                               ************************************************9987776554899******** PP

                                 TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207
                                                Gs+  +lp+ +  de +v++s++al lk++p+++++vGgG+iG+E+a+++++lG+ + v+e+ld +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS26115 263 AGSQAVKLPF-MPDDE-RVVDSTGALLLKSIPKRMLVVGGGIIGLEMATVYSTLGTRIDVVEMLDGLMQ 329
                                               **********.66665.7*************************************************** PP

                                 TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelg 275
                                                 d+++ kv +kk +++  +++ +++    +++ + ++v+ +++       ++ vLvavGr+pn + +g
  lcl|FitnessBrowser__Cup4G11:RR42_RS26115 330 GADRDLVKVWEKKNTHRFDHVMLKTRTIGAKATPAGIEVSFEGEkAPAPQVYDLVLVAVGRSPNGRAIG 398
                                               ****************************9*********99999945566789***************** PP

                                 TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPs 344
                                                ek gv ++erg+i vd+++rtnv++i+aiGD++g++mLAh+A++e+ vaae++ g+++  +d++++Ps
  lcl|FitnessBrowser__Cup4G11:RR42_RS26115 399 AEKAGVAVTERGFIDVDRQMRTNVAHIHAIGDIVGQPMLAHKAVHEAHVAAEAAHGEAA-YFDARQIPS 466
                                               ********************************************************877.9******** PP

                                 TIGR01350 345 viytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaea 413
                                               v yt+Peva  G+teeq+k+egi++  + fp aa+g+a+a + ++Gf k+++d+ t++++G  ivg++a
  lcl|FitnessBrowser__Cup4G11:RR42_RS26115 467 VAYTDPEVAWAGKTEEQCKAEGIKIGKAVFPWAASGRAIANGRDEGFTKLLFDEATHRVIGGGIVGTHA 535
                                               ********************************************************************* PP

                                 TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                                +lise+ la+e++ +  ++ ktihpHPtl+E i  aa+   g
  lcl|FitnessBrowser__Cup4G11:RR42_RS26115 536 GDLISEVCLAIEMGCEPADIGKTIHPHPTLGESIGMAAEVFEG 578
                                               **********************************999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (589 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.21
//
[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, or view the source code.

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