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, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 (characterized)
to candidate AZOBR_RS03960 AZOBR_RS03960 dihydrolipoamide dehydrogenase

Query= SwissProt::P31023
         (501 letters)



>FitnessBrowser__azobra:AZOBR_RS03960
          Length = 466

 Score =  579 bits (1492), Expect = e-170
 Identities = 283/463 (61%), Positives = 349/463 (75%), Gaps = 3/463 (0%)

Query: 39  DVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 98
           DVV++GGGPGGYV AI+AAQLGFK  C+EKR ALGGTCLNVGCIPSKALL +S  Y EAK
Sbjct: 7   DVVVVGGGPGGYVCAIRAAQLGFKVACVEKRSALGGTCLNVGCIPSKALLAASEKYEEAK 66

Query: 99  HSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPSEIS 158
           H  A  G+KV  VE+DL  M+  KDK V   T GIE LFKKNK+ ++KG G+  +P+ + 
Sbjct: 67  HGLAKFGIKVDGVELDLPGMLSHKDKVVKENTGGIEFLFKKNKIAWLKGAGRITAPNTVE 126

Query: 159 VDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLVVIGAGY 218
           V   EG  T+   K I+IATGS+V  LPG+ IDE+KIVSSTGAL L E+PK+LVVIG G 
Sbjct: 127 V---EGVGTITASKAIVIATGSEVTPLPGIEIDEQKIVSSTGALELPEVPKRLVVIGGGV 183

Query: 219 IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGVDTS 278
           IGLE+GSVWGR+G+EVTVVEF   I+PTMD E+ KQ QR L KQGM FKL +KV G   +
Sbjct: 184 IGLELGSVWGRLGAEVTVVEFLDRILPTMDGEVSKQMQRILGKQGMTFKLGSKVTGAKVT 243

Query: 279 GDGVKLTVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNERFST 338
             GV L+VEP+AGG    I+ADVVLV+ GR  FT+GL LD +GVE D  GR+ + + F T
Sbjct: 244 NTGVTLSVEPAAGGTAEEIKADVVLVAIGRRAFTNGLGLDAVGVEMDNRGRVKIGKHFET 303

Query: 339 NVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASVGKT 398
           NV G+YAIGDV+ GPMLAHKAEE+GVA  E LAG+ GHV++D VPGVVYT PEVA+VGKT
Sbjct: 304 NVPGIYAIGDVVEGPMLAHKAEEEGVALAELLAGQAGHVNHDLVPGVVYTWPEVAAVGKT 363

Query: 399 EEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGELIH 458
           EE++K  G  Y+ GKFPF AN RA+A    +G VKI+A+  TDK+LGVH++ PN  E++ 
Sbjct: 364 EEELKAAGTAYKAGKFPFTANGRARASGTTDGFVKILADARTDKVLGVHMVGPNVSEMVA 423

Query: 459 EAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHI 501
           E A+A+++ AS+EDIAR CHAHPT+SE  KEAA+A   + +HI
Sbjct: 424 ELAVAMEFSASAEDIARTCHAHPTLSEVTKEAALAVDGRALHI 466


Lambda     K      H
   0.315    0.133    0.370 

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: 715
Number of extensions: 31
Number of successful extensions: 2
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: 501
Length of database: 466
Length adjustment: 34
Effective length of query: 467
Effective length of database: 432
Effective search space:   201744
Effective search space used:   201744
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

Align candidate AZOBR_RS03960 AZOBR_RS03960 (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.28281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-180  586.2  11.0   2.5e-180  586.0  11.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS03960  AZOBR_RS03960 dihydrolipoamide d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS03960  AZOBR_RS03960 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.0  11.0  2.5e-180  2.5e-180       2     461 .]       6     466 .]       5     466 .] 0.97

  Alignments for each domain:
  == domain 1  score: 586.0 bits;  conditional E-value: 2.5e-180
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgi 68 
                                               +dvvv+GgGpgGYv+Airaaqlg+kva+vek + lGGtClnvGCiP+KalL+++e +ee+k+ ++++gi
  lcl|FitnessBrowser__azobra:AZOBR_RS03960   6 FDVVVVGGGPGGYVCAIRAAQLGFKVACVEKrSALGGTCLNVGCIPSKALLAASEKYEEAKHgLAKFGI 74 
                                               8******************************899*********************************** PP

                                 TIGR01350  69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniii 137
                                               +v++v+ldl  +l +k+kvvk+ +gG+++L+kknk+  +kG ++++ +++vev++    +    k+i+i
  lcl|FitnessBrowser__azobra:AZOBR_RS03960  75 KVDGVELDLPGMLSHKDKVVKENTGGIEFLFKKNKIAWLKGAGRITAPNTVEVEGVG--TITASKAIVI 141
                                               *******************************************************98..4678999*** PP

                                 TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206
                                               AtGse++ lp+ +e de+ +++s++alel+evp++lv++GgGviG+E++s++ +lG++vtv+e+ldril
  lcl|FitnessBrowser__azobra:AZOBR_RS03960 142 ATGSEVTPLPG-IEIDEQKIVSSTGALELPEVPKRLVVIGGGVIGLELGSVWGRLGAEVTVVEFLDRIL 209
                                               ***********.********************************************************* PP

                                 TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnle 272
                                               p++d evsk++++ l k+g++++ ++kvt  + ++  v+  ve   + ++e+++a+ vLva+Gr++ ++
  lcl|FitnessBrowser__azobra:AZOBR_RS03960 210 PTMDGEVSKQMQRILGKQGMTFKLGSKVTGAKVTNTGVTlsVEPAAGgTAEEIKADVVLVAIGRRAFTN 278
                                               *****************************666666666644666655699******************* PP

                                 TIGR01350 273 elgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidyka 341
                                               +lgl+++gve+d+rg++k+ ++++tnvpgiyaiGDv++++mLAh+A++egv  ae +ag++  ++++++
  lcl|FitnessBrowser__azobra:AZOBR_RS03960 279 GLGLDAVGVEMDNRGRVKIGKHFETNVPGIYAIGDVVEGPMLAHKAEEEGVALAELLAGQAG-HVNHDL 346
                                               ***********************************************************998.9***** PP

                                 TIGR01350 342 vPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivg 410
                                               vP v+yt Peva+vG+tee++k++g+++k+gkfpf+ang+a+a++ tdGfvk+++d  t+++lG+h+vg
  lcl|FitnessBrowser__azobra:AZOBR_RS03960 347 VPGVVYTWPEVAAVGKTEEELKAAGTAYKAGKFPFTANGRARASGTTDGFVKILADARTDKVLGVHMVG 415
                                               ********************************************************************* PP

                                 TIGR01350 411 aeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               +++se+++ela+a+e+ +++e++a+t+h+HPtlsE++keaala+ g+a+h+
  lcl|FitnessBrowser__azobra:AZOBR_RS03960 416 PNVSEMVAELAVAMEFSASAEDIARTCHAHPTLSEVTKEAALAVDGRALHI 466
                                               ***********************************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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: 7.49
//
[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