Alignments for a candidate for hisD in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Sinorhizobium fredii NGR234

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_164924165.1 NGR_RS12475 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000018545.1:WP_164924165.1
          Length = 434

 Score =  620 bits (1600), Expect = 0.0
 Identities = 317/429 (73%), Positives = 362/429 (84%)

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

Query: 61  LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
              T +AV+ AEIDAA DA     + ALK+A  RIE HH RQLPKDD Y D +GV LGSR
Sbjct: 61  FSVTPMAVSAAEIDAAIDAVEPEVLGALKVAATRIEAHHRRQLPKDDLYEDKMGVGLGSR 120

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
           WTAI+AVGLYVPGGTASYPSSVLMNA+PAKVAGV RIVMVVP   G +NP VL AARLAG
Sbjct: 121 WTAIDAVGLYVPGGTASYPSSVLMNALPAKVAGVPRIVMVVPTRGGAINPAVLAAARLAG 180

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V EIYR+GGAQA+A+LAYGTETI PVAKI+GPGNAYVAAAKR VFGTVGIDMIAGPSEVL
Sbjct: 181 VEEIYRIGGAQAVASLAYGTETIAPVAKIMGPGNAYVAAAKRQVFGTVGIDMIAGPSEVL 240

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

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           SWRDFGAVILV D + A+PLANRIAAEHLE+A+AD ++ VP+IRNAG+IFIG +TPEVIG
Sbjct: 301 SWRDFGAVILVPDLDKAVPLANRIAAEHLELAMADPDSMVPKIRNAGAIFIGRHTPEVIG 360

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DYVGG NHVLPTARSARFSSGL VLDYMKRTS+L+LG EQLR LGPAAI +A++EGL+AH
Sbjct: 361 DYVGGSNHVLPTARSARFSSGLGVLDYMKRTSILRLGPEQLRILGPAAIALAKSEGLEAH 420

Query: 421 AQSVAIRLN 429
           A+SVAIRLN
Sbjct: 421 ARSVAIRLN 429


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: 595
Number of extensions: 14
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 WP_164924165.1 NGR_RS12475 (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.4083761.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-163  530.5   1.3   1.8e-163  530.3   1.3    1.0  1  NCBI__GCF_000018545.1:WP_164924165.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_164924165.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.3   1.3  1.8e-163  1.8e-163       1     393 []      34     427 ..      34     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 530.3 bits;  conditional E-value: 1.8e-163
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                           v++ii+dvr++Gd+Al +y+ +fd+v  +++ ++vs++e+++a +av++e+  al+ aa++ie+ h++qlp++
  NCBI__GCF_000018545.1:WP_164924165.1  34 VRAIIDDVRARGDAALADYSARFDGVdfSVTPMAVSAAEIDAAIDAVEPEVLGALKVAATRIEAHHRRQLPKD 106
                                           799**********************988899****************************************** PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                             +e++ gv lg +++++++vglYvPgG+a+ypS+vlm+a+pAkvAgv++iv+v P++  g +npavlaaa+l
  NCBI__GCF_000018545.1:WP_164924165.1 107 DLYEDKMGVGLGSRWTAIDAVGLYVPGGTASYPSSVLMNALPAKVAGVPRIVMVVPTR-GGAINPAVLAAARL 178
                                           *********************************************************6.99************ PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                           +gv+e+y++GGaqa+a layGtet+ +v ki+GPGn+yV+aAK++vfg+vgidmiaGPsEvlviad++ +p++
  NCBI__GCF_000018545.1:WP_164924165.1 179 AGVEEIYRIGGAQAVASLAYGTETIAPVAKIMGPGNAYVAAAKRQVFGTVGIDMIAGPSEVLVIADRDNDPDW 251
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290
                                           +aaDll+qaEHd+ aqail+t+++++ ++ve++ve+ql++l+r+e+a++s+++ ga+ilv dl++a+ l+n++
  NCBI__GCF_000018545.1:WP_164924165.1 252 IAADLLAQAEHDAGAQAILITDDAAFGASVEQAVERQLKTLPRSETATASWRDFGAVILVPDLDKAVPLANRI 324
                                           ************************************************************************* PP

                             TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqels 363
                                           A+EHLel+++dp ++++ki+naG++f+G++tpe +gdyv G+nhvLPT+++Arf+sgl+v d++kr+s+ +l 
  NCBI__GCF_000018545.1:WP_164924165.1 325 AAEHLELAMADPDSMVPKIRNAGAIFIGRHTPEVIGDYVGGSNHVLPTARSARFSSGLGVLDYMKRTSILRLG 397
                                           ************************************************************************* PP

                             TIGR00069 364 kealeelaeaveklaeaEgLeaHaeavevR 393
                                            e+l+ l++a+++la+ EgLeaHa++v++R
  NCBI__GCF_000018545.1:WP_164924165.1 398 PEQLRILGPAAIALAKSEGLEAHARSVAIR 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 16.49
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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