Alignments for a candidate for lpd in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Azospirillum brasilense Sp245

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate AZOBR_RS14390 AZOBR_RS14390 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__azobra:AZOBR_RS14390
          Length = 465

 Score =  544 bits (1401), Expect = e-159
 Identities = 280/467 (59%), Positives = 343/467 (73%), Gaps = 3/467 (0%)

Query: 1   MAD-HFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEV 59
           MAD ++DLIV+GGGPGGYVAAIRAAQL L  A+VER +LGGICLNWGCIPTK+LLRSAEV
Sbjct: 1   MADMNYDLIVIGGGPGGYVAAIRAAQLGLSTAVVERENLGGICLNWGCIPTKALLRSAEV 60

Query: 60  YHEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGN 119
               ++A  YGL    P FDLDK++ RSR+VA +L  GVK LL+KNKV VI G  +L G 
Sbjct: 61  LRNAKHASEYGLVIQNPSFDLDKVVQRSRKVAGQLNGGVKHLLKKNKVAVIEGEAKLLGK 120

Query: 120 QQMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVI 179
            Q+ V           AK+IIIATGARAR LP +  DG  +WTY  A+ P   PK LLVI
Sbjct: 121 GQVAVTKGGAAVGTFGAKNIIIATGARARTLPGLEDDGNLVWTYRKAMTPNTTPKSLLVI 180

Query: 180 GSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQN 239
           GSGAIGIEFASFY + GA+V++VE   +ILP+ED E+SA+  K F+K+G+RI+T     N
Sbjct: 181 GSGAIGIEFASFYNELGAKVTVVEVMDRILPVEDEEISAFARKQFEKQGMRIITNGKAGN 240

Query: 240 LTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFG 299
           L    + VT  +  A+GK         I+A+G+  N EN+GL+   ++ DRG I  +   
Sbjct: 241 LRKGADSVTVAVE-ANGKTEDITVDRVILAVGIAPNTENLGLENTKVQTDRGHIKTNANC 299

Query: 300 RTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVAS 359
           +T+   V+AIGDV GAP LAHKASH+GVIA E IAG  H H L+ +NIPGCTY+ PQ+AS
Sbjct: 300 QTDEPGVYAIGDVTGAPWLAHKASHEGVIAVEHIAG-KHPHALDVRNIPGCTYSHPQIAS 358

Query: 360 VGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVT 419
           VGLTE+KA++ GY V++G FPFI NGKAIA G  DG VKTVFDA +G LLGAHMVGAEVT
Sbjct: 359 VGLTEKKAKEAGYEVRVGRFPFIGNGKAIALGEADGMVKTVFDAKTGELLGAHMVGAEVT 418

Query: 420 EMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466
           E+IQGYTVA+T+ETTE E+M+T+FPHPTLSE MHESVL AYGRA+HF
Sbjct: 419 ELIQGYTVAKTMETTEQELMQTVFPHPTLSEMMHESVLDAYGRAIHF 465


Lambda     K      H
   0.319    0.135    0.393 

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: 669
Number of extensions: 31
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: 466
Length of database: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS14390 AZOBR_RS14390 (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.16596.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-183  596.6   8.1   1.7e-183  596.4   8.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS14390  AZOBR_RS14390 dihydrolipoamide d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS14390  AZOBR_RS14390 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  596.4   8.1  1.7e-183  1.7e-183       1     461 []       5     465 .]       5     465 .] 0.99

  Alignments for each domain:
  == domain 1  score: 596.4 bits;  conditional E-value: 1.7e-183
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgie 69 
                                               +yd++viGgGpgGYvaAiraaqlgl++a+ve+e+lGG+Cln+GCiPtKalL+saev++++k+a+e+g+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS14390   5 NYDLIVIGGGPGGYVAAIRAAQLGLSTAVVERENLGGICLNWGCIPTKALLRSAEVLRNAKHASEYGLV 73 
                                               69******************************************************************* PP

                                 TIGR01350  70 venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniii 137
                                               ++n ++dl+k+++r++kv  +l+gGvk+Llkknkv vi+Geakll+k++v v+k  ++  +  akniii
  lcl|FitnessBrowser__azobra:AZOBR_RS14390  74 IQNPSFDLDKVVQRSRKVAGQLNGGVKHLLKKNKVAVIEGEAKLLGKGQVAVTKGGAAvGTFGAKNIII 142
                                               ******************************************************998878999****** PP

                                 TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206
                                               AtG++ r+lp+ le d+++v+t+++a++ +++p+sl+++G+G+iG+Efas++++lG+kvtv+e++dril
  lcl|FitnessBrowser__azobra:AZOBR_RS14390 143 ATGARARTLPG-LEDDGNLVWTYRKAMTPNTTPKSLLVIGSGAIGIEFASFYNELGAKVTVVEVMDRIL 210
                                               ***********.********************************************************* PP

                                 TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleel 274
                                               p++d+e+s +++k+++k+g++i+tn k  +++k +d+v+v  + + ++e +++++v++avG  pn+e+l
  lcl|FitnessBrowser__azobra:AZOBR_RS14390 211 PVEDEEISAFARKQFEKQGMRIITNGKAGNLRKGADSVTVAVEANgKTEDITVDRVILAVGIAPNTENL 279
                                               ***************************************877777789********************* PP

                                 TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavP 343
                                               gle++ v++d+ g ik++++++t  pg+yaiGDv+g + LAh+As+egv+a+e+iagk+++++d + +P
  lcl|FitnessBrowser__azobra:AZOBR_RS14390 280 GLENTKVQTDR-GHIKTNANCQTDEPGVYAIGDVTGAPWLAHKASHEGVIAVEHIAGKHPHALDVRNIP 347
                                               ********776.********************************************************* PP

                                 TIGR01350 344 sviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgae 412
                                                ++y++P++asvGlte++ake+g+ev+vg+fpf  ngka+al+e+dG+vk+++d ktge+lGah+vgae
  lcl|FitnessBrowser__azobra:AZOBR_RS14390 348 GCTYSHPQIASVGLTEKKAKEAGYEVRVGRFPFIGNGKAIALGEADGMVKTVFDAKTGELLGAHMVGAE 416
                                               ********************************************************************* PP

                                 TIGR01350 413 aseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               ++eli+  ++a ++e+t++el++t++pHPtlsE+++e++l+a+g+aih+
  lcl|FitnessBrowser__azobra:AZOBR_RS14390 417 VTELIQGYTVAKTMETTEQELMQTVFPHPTLSEMMHESVLDAYGRAIHF 465
                                               ***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 10.00
//
[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