Alignments for a candidate for lpd in Herbaspirillum seropedicae SmR1

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.32629.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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.93
//
[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:

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