GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Herbaspirillum seropedicae SmR1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate HSERO_RS07315 HSERO_RS07315 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__HerbieS:HSERO_RS07315
          Length = 596

 Score =  864 bits (2233), Expect = 0.0
 Identities = 440/603 (72%), Positives = 504/603 (83%), Gaps = 16/603 (2%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           MS+ EVKVPDIGDF  VEVIEV+VK GDT++V+QSLI +ESDKASM++PSS AG V EVK
Sbjct: 1   MSLSEVKVPDIGDFKEVEVIEVMVKVGDTIKVDQSLITVESDKASMEIPSSQAGVVKEVK 60

Query: 61  VKVGDKVGQGAVICTIEAQ-QAAAAPAPAQAPAPAQAPAPA-----AAAPAPAPAAASHS 114
           VKVGDKV +G+++  +EA  QAAAAPAPA  PAPA A APA     AAAP  AP AAS  
Sbjct: 61  VKVGDKVAEGSLLLLVEAAGQAAAAPAPAAPPAPAAAAAPAPAAAPAAAPTAAPTAASFG 120

Query: 115 GGADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNA 174
           G AD+QC+++VLG GPGGYSAAFRAADLG+NTV+VER +TLGGVCLNVGCIPSKALLH A
Sbjct: 121 GSADVQCDVMVLGGGPGGYSAAFRAADLGLNTVIVEREATLGGVCLNVGCIPSKALLHVA 180

Query: 175 AVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFL 234
           AVIDE  A+A+HG+ FG+ +ID+D LR YK++V+G +TGGLAGMAKARKVQVV G G F 
Sbjct: 181 AVIDETAAMASHGVTFGKPQIDIDKLRAYKDKVIGTMTGGLAGMAKARKVQVVNGDGQFA 240

Query: 235 DPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPE 294
            P+H+EV   +G        K V++F+ AIIAAGS  V LPF+P+DPRIVDSTGALEL +
Sbjct: 241 GPNHIEVTAADGS-------KKVVQFKHAIIAAGSSVVNLPFVPQDPRIVDSTGALELRQ 293

Query: 295 VPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKV 354
           VP +MLVIGGGIIGLEMATVYSTLGA IDVVEM+DGLM GADRD+VKVW+K N+ RF  V
Sbjct: 294 VPKRMLVIGGGIIGLEMATVYSTLGARIDVVEMMDGLMQGADRDMVKVWQKFNEKRFDNV 353

Query: 355 MLKTKTVGVEAKPDGIYVKFEGEAAPA---EPQRYDLVLVSVGRSPNGKRISAEKAGVAV 411
           M+KTKTV VEA P+GI V FE   A A   EPQ YDLVLV+VGRSPNGK++SA+KAGV V
Sbjct: 354 MVKTKTVAVEALPEGIKVTFEAAEAGATAPEPQLYDLVLVAVGRSPNGKKLSADKAGVIV 413

Query: 412 SERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPS 471
           S+RGFI VDKQMRTNVPHIFAIGD+VGQPMLAHKAVHE HVAAEA  GEK++FDA  IPS
Sbjct: 414 SDRGFIAVDKQMRTNVPHIFAIGDLVGQPMLAHKAVHEGHVAAEAIAGEKSFFDASVIPS 473

Query: 472 VAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVI 531
           VA+TDPEVAW G+TEDE K KGIK  KG FPWAASGRA+ANGR EGFTKL+FD ETHR+I
Sbjct: 474 VAYTDPEVAWVGVTEDEAKAKGIKIEKGHFPWAASGRAVANGRSEGFTKLLFDAETHRII 533

Query: 532 GGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPP 591
           GGGIVGTHAGD+I EV LAIEMGADAVDIGKTIHPHPTLGES+GMAAE+ EG CTD+PP 
Sbjct: 534 GGGIVGTHAGDMIGEVALAIEMGADAVDIGKTIHPHPTLGESLGMAAEVAEGHCTDLPPQ 593

Query: 592 RKR 594
           RK+
Sbjct: 594 RKK 596


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: 1067
Number of extensions: 43
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: 596
Length adjustment: 37
Effective length of query: 557
Effective length of database: 559
Effective search space:   311363
Effective search space used:   311363
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 HSERO_RS07315 HSERO_RS07315 (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.3552.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-146  474.4   8.8   2.6e-146  473.9   8.8    1.2  1  lcl|FitnessBrowser__HerbieS:HSERO_RS07315  HSERO_RS07315 dihydrolipoamide d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS07315  HSERO_RS07315 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.9   8.8  2.6e-146  2.6e-146       2     457 ..     127     586 ..     126     590 .. 0.94

  Alignments for each domain:
  == domain 1  score: 473.9 bits;  conditional E-value: 2.6e-146
                                  TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgi 68 
                                                 dv+v+GgGpgGY aA raa lgl++++ve+  +lGG+ClnvGCiP+KalL+ a v++e   ++++g+
  lcl|FitnessBrowser__HerbieS:HSERO_RS07315 127 CDVMVLGGGPGGYSAAFRAADLGLNTVIVEReATLGGVCLNVGCIPSKALLHVAAVIDETAAMASHGV 194
                                                69*****************************789********************************** PP

                                  TIGR01350  69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakni 135
                                                +  + ++d++kl + k+kv+ +++gG++++ k  kv+v++G +++ +++++ev++ +++ k++++k++
  lcl|FitnessBrowser__HerbieS:HSERO_RS07315 195 TFGKPQIDIDKLRAYKDKVIGTMTGGLAGMAKARKVQVVNGDGQFAGPNHIEVTAADGSkKVVQFKHA 262
                                                ******************************************************999877899***** PP

                                  TIGR01350 136 iiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielld 203
                                                iiA Gs++ +lp+ + +d  ++++s++alel++vp++++++GgG+iG+E+a+++++lG+ + v+e++d
  lcl|FitnessBrowser__HerbieS:HSERO_RS07315 263 IIAAGSSVVNLPF-VPQDP-RIVDSTGALELRQVPKRMLVIGGGIIGLEMATVYSTLGARIDVVEMMD 328
                                                *************.88886.7*********************************************** PP

                                  TIGR01350 204 rilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.....evetleaekvLvavG 266
                                                 +++  d+++ kv +k  +k+  +++ ++k  +ve+  + ++v+ +         e   ++ vLvavG
  lcl|FitnessBrowser__HerbieS:HSERO_RS07315 329 GLMQGADRDMVKVWQKFNEKRFDNVMVKTKTVAVEALPEGIKVTFEAAeagatAPEPQLYDLVLVAVG 396
                                                ****************999998888888888888887777775544441011233555689******* PP

                                  TIGR01350 267 rkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkek 334
                                                r+pn ++l  +k gv + +rg+i vd+++rtnvp+i+aiGD++g++mLAh+A++eg vaae+iag+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS07315 397 RSPNGKKLSADKAGVIVSDRGFIAVDKQMRTNVPHIFAIGDLVGQPMLAHKAVHEGHVAAEAIAGEKS 464
                                                *****************************************************************665 PP

                                  TIGR01350 335 seidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktge 402
                                                  +d++++Psv yt+Peva vG+te++ak++gi+++ g+fp aa+g+a+a + ++Gf k+++d +t++
  lcl|FitnessBrowser__HerbieS:HSERO_RS07315 465 -FFDASVIPSVAYTDPEVAWVGVTEDEAKAKGIKIEKGHFPWAASGRAVANGRSEGFTKLLFDAETHR 531
                                                .9****************************************************************** PP

                                  TIGR01350 403 ilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgk 457
                                                i+G  ivg++a ++i e+ala+e+++ + ++ ktihpHPtl+E +  aa+ a g+
  lcl|FitnessBrowser__HerbieS:HSERO_RS07315 532 IIGGGIVGTHAGDMIGEVALAIEMGADAVDIGKTIHPHPTLGESLGMAAEVAEGH 586
                                                ************************************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (596 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: 00:00:00.01
# Mc/sec: 14.93
//
[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