Alignments for a candidate for hisD in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Sinorhizobium meliloti 1021

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate SMc02307 SMc02307 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Smeli:SMc02307
          Length = 434

 Score =  628 bits (1620), Expect = 0.0
 Identities = 323/430 (75%), Positives = 361/430 (83%)

Query: 1   MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60
           M   L   D  FE+ FAAFL+ KREVSEDV+  VR I+D VR  GD+AL DYS RFD ID
Sbjct: 1   MAIRLNYLDTSFERDFAAFLTTKREVSEDVNAVVRAIIDDVRARGDAALADYSARFDGID 60

Query: 61  LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
              TG+AVT AEIDAA  A     + ALK+A  RIE HH RQLPKDD Y D +GV LGSR
Sbjct: 61  FTVTGMAVTSAEIDAAIHAVAPEVLGALKVAATRIEAHHRRQLPKDDIYEDQMGVGLGSR 120

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
           WT I+AVGLYVPGGTASYPSSVLMNA+PAKVAGV RIVMVVPA  G++NP VL AARLAG
Sbjct: 121 WTPIDAVGLYVPGGTASYPSSVLMNALPAKVAGVPRIVMVVPASGGSINPAVLAAARLAG 180

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V EIYR+GGAQA+AALAYGTETI PVAKIVGPGNAYVAAAKR VFGTVGIDMIAGPSEVL
Sbjct: 181 VEEIYRIGGAQAVAALAYGTETIEPVAKIVGPGNAYVAAAKRQVFGTVGIDMIAGPSEVL 240

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           ++AD+DN+PDWIAADLLAQAEHD  AQ+IL+T+D AF  AVE+AVERQL TL R ETA+A
Sbjct: 241 VIADRDNDPDWIAADLLAQAEHDAGAQAILITDDAAFGDAVEKAVERQLKTLPRAETAAA 300

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           SWRDFGAVILV DF+ A+PLANRIA EHLE+A AD +A VP IRNAG+IFIG +TPEVIG
Sbjct: 301 SWRDFGAVILVPDFDKAVPLANRIAPEHLELATADPDAMVPAIRNAGAIFIGRHTPEVIG 360

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DYVGG NHVLPTARSARFSSGL VLDY+KRTS+L+LG +QLR LGPAAI +AR+EGL+AH
Sbjct: 361 DYVGGSNHVLPTARSARFSSGLGVLDYVKRTSILRLGPDQLRILGPAAIALARSEGLEAH 420

Query: 421 AQSVAIRLNL 430
           A+SVAIRLNL
Sbjct: 421 ARSVAIRLNL 430


Lambda     K      H
   0.318    0.134    0.375 

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: 627
Number of extensions: 22
Number of successful extensions: 1
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: 430
Length of database: 434
Length adjustment: 32
Effective length of query: 398
Effective length of database: 402
Effective search space:   159996
Effective search space used:   159996
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate SMc02307 SMc02307 (histidinol dehydrogenase)
to HMM TIGR00069 (hisD: histidinol dehydrogenase (EC 1.1.1.23))

# 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.aa/TIGR00069.hmm
# target sequence database:        /tmp/gapView.13004.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00069  [M=393]
Accession:   TIGR00069
Description: hisD: histidinol 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.1e-165  534.5   1.4   1.1e-164  534.3   1.4    1.0  1  lcl|FitnessBrowser__Smeli:SMc02307  SMc02307 histidinol dehydrogenas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02307  SMc02307 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.3   1.4  1.1e-164  1.1e-164       1     393 []      34     427 ..      34     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 534.3 bits;  conditional E-value: 1.1e-164
                           TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 
                                         v++ii+dvr++Gd+Al +y+ +fd++  +++ ++v+++e+++a +av +e+  al+ aa++ie+ h++qlp++  
  lcl|FitnessBrowser__Smeli:SMc02307  34 VRAIIDDVRARGDAALADYSARFDGIdfTVTGMAVTSAEIDAAIHAVAPEVLGALKVAATRIEAHHRRQLPKDDI 108
                                         799**********************988999******************************************9* PP

                           TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvd 148
                                         +e++ gv lg +++p+++vglYvPgG+a+ypS+vlm+a+pAkvAgv++iv+v P +  g++npavlaaa+l+gv+
  lcl|FitnessBrowser__Smeli:SMc02307 109 YEDQMGVGLGSRWTPIDAVGLYVPGGTASYPSSVLMNALPAKVAGVPRIVMVVPAS-GGSINPAVLAAARLAGVE 182
                                         *******************************************************6.99**************** PP

                           TIGR00069 149 evykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDll 223
                                         e+y++GGaqa+aalayGtet+++v kivGPGn+yV+aAK++vfg+vgidmiaGPsEvlviad++ +p+++aaDll
  lcl|FitnessBrowser__Smeli:SMc02307 183 EIYRIGGAQAVAALAYGTETIEPVAKIVGPGNAYVAAAKRQVFGTVGIDMIAGPSEVLVIADRDNDPDWIAADLL 257
                                         *************************************************************************** PP

                           TIGR00069 224 sqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelq 298
                                         +qaEHd+ aqail+t+++++ ++ve++ve+ql++l+r+e+a +s+++ ga+ilv d+++a+ l+n++ApEHLel+
  lcl|FitnessBrowser__Smeli:SMc02307 258 AQAEHDAGAQAILITDDAAFGDAVEKAVERQLKTLPRAETAAASWRDFGAVILVPDFDKAVPLANRIAPEHLELA 332
                                         *************************************************************************** PP

                           TIGR00069 299 tkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaea 373
                                         t+dp ++++ i+naG++f+G++tpe +gdyv G+nhvLPT+++Arf+sgl+v d++kr+s+ +l  ++l+ l++a
  lcl|FitnessBrowser__Smeli:SMc02307 333 TADPDAMVPAIRNAGAIFIGRHTPEVIGDYVGGSNHVLPTARSARFSSGLGVLDYVKRTSILRLGPDQLRILGPA 407
                                         *************************************************************************** PP

                           TIGR00069 374 veklaeaEgLeaHaeavevR 393
                                         +++la+ EgLeaHa++v++R
  lcl|FitnessBrowser__Smeli:SMc02307 408 AIALARSEGLEAHARSVAIR 427
                                         ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (434 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: 00:00:00.01
# Mc/sec: 9.29
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis