GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Streptacidiphilus oryzae TH49

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate WP_037576905.1 BS73_RS27295 histidinol dehydrogenase

Query= curated2:Q9RH05
         (430 letters)



>NCBI__GCF_000744815.1:WP_037576905.1
          Length = 439

 Score =  258 bits (659), Expect = 3e-73
 Identities = 157/407 (38%), Positives = 228/407 (56%), Gaps = 16/407 (3%)

Query: 30  VSRDVSAIIADVKKRGDVAIAELTQKFDRHDLNKGGWQ-----LTQEEIKKACDSLPSEL 84
           V   VS +++D++K G  A+   +++ D       GWQ     ++  E+K+  DSL  EL
Sbjct: 34  VVETVSRMLSDIEKNGMDAVLRYSRELD-------GWQGGDVEISAAELKRTGDSLSPEL 86

Query: 85  MDALKLAATRIRY--CHENQLPESSEMTDAAGVRMGVRWQAVEAAGLYVPGGRAAYCSSV 142
             AL   A R R     + +  +  E     GV  G ++  V   G Y+P G     +S 
Sbjct: 87  RQALAAGAERTRLFAVEQREHLQDFETELIPGVVTGQKYLPVPRVGAYLPAGNFPILASA 146

Query: 143 LMNAVPAKVAGVKRLVMVTP-TPDGFVNPAVIAAAVISEVDEIWKIGGAQAVAALALGTE 201
            M    AK A V  ++  TP T +   +PAV+ AA +S VD  + +GG QA+AA+A G  
Sbjct: 147 FMTVGVAKAADVPTVLACTPPTAEQGGHPAVLYAAYLSGVDRAFALGGVQALAAMAFGLL 206

Query: 202 KIKPVDVVVGPGNAWVAEAKRQLYGQVGIDMVAGPSEIVVVADKDNDPEWLAADLLSQAE 261
             +P D++VG GNA+V EAKRQL+G+VGID++AGPSE+ V+AD+  DPE +AADLL QAE
Sbjct: 207 GDQPADMLVGAGNAYVTEAKRQLFGRVGIDLLAGPSEVAVIADETADPELVAADLLGQAE 266

Query: 262 HDPTSQSILISDSEDLIEKTIEAVGRRLEKLETQKVARESWDKHGATILVQSLDEAPALV 321
           H   S + L++ S +L    +E V ++L +L T+ +A  +W  HG   + +    A  L+
Sbjct: 267 HGRQSPASLVTTSRELGLAVLEEVEKQLRQLPTRDIAEPAWRDHGTVYVAEDRQTAVELM 326

Query: 322 DRLAPEHLELAVADPDALFANVHHSGSVFLGRYTPEAIGDY-VGGPNHVLPTGRRARFSS 380
           D LAPEHLE+  AD D    N+ + GS+FLG ++  A  D  + G NHVLPTGR AR S+
Sbjct: 327 DLLAPEHLEVISADDDYYHQNLKNYGSIFLGAWSTVAYSDKGIAGTNHVLPTGRGARASA 386

Query: 381 GLSVIDFMKRTTYLNCSQEALSKIGPAAVTLAKAEGLPAHAESVISR 427
           GLSV  F+K  T+   S EA   +      ++  EG+ AH  +   R
Sbjct: 387 GLSVSRFLKPLTFQKVSAEATPDLAAHVEAISDFEGMAAHRATATLR 433


Lambda     K      H
   0.316    0.132    0.377 

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: 461
Number of extensions: 18
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: 430
Length of database: 439
Length adjustment: 32
Effective length of query: 398
Effective length of database: 407
Effective search space:   161986
Effective search space used:   161986
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: 51 (24.3 bits)

Align candidate WP_037576905.1 BS73_RS27295 (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.240127.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-131  425.2   0.0   1.7e-131  425.0   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037576905.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037576905.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.0   0.0  1.7e-131  1.7e-131       1     393 []      38     433 ..      38     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 425.0 bits;  conditional E-value: 1.7e-131
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes.. 71 
                                           v+++++d++k+G +A+l+y++++d+++  ++++s++el++  +++++el++al++ ae+ + f+ +q+++   
  NCBI__GCF_000744815.1:WP_037576905.1  38 VSRMLSDIEKNGMDAVLRYSRELDGWQGGDVEISAAELKRTGDSLSPELRQALAAGAERTRLFAVEQREHLqd 110
                                           78899**********************************************************9999865334 PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144
                                           +e+e  +gv++gqk+ p+ rvg+Y+P+G+ + +++++mt+  Ak A v++++++tPp+ ++  +pavl+aa l
  NCBI__GCF_000744815.1:WP_037576905.1 111 FETELIPGVVTGQKYLPVPRVGAYLPAGNFPILASAFMTVGVAKAADVPTVLACTPPTAEQGGHPAVLYAAYL 183
                                           99999****************************************************98888*********** PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                            gvd+ +++GG+qa+aa+a+G+   +++d++vG Gn+yVt+AK+++fg+vgid++aGPsEv+viade+a+pel
  NCBI__GCF_000744815.1:WP_037576905.1 184 SGVDRAFALGGVQALAAMAFGLLGDQPADMLVGAGNAYVTEAKRQLFGRVGIDLLAGPSEVAVIADETADPEL 256
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290
                                           vaaDll qaEH++++ a lvtts+el  +v eeve+ql++l++++iae +++++g++ +++d + a+el++ +
  NCBI__GCF_000744815.1:WP_037576905.1 257 VAADLLGQAEHGRQSPASLVTTSRELGLAVLEEVEKQLRQLPTRDIAEPAWRDHGTVYVAEDRQTAVELMDLL 329
                                           ************************************************************************* PP

                             TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdy.vaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           ApEHLe+  +d   + +++kn+Gs+flG+++++a++d+ +aG+nhvLPT++ Ar+++glsv++Flk +++q++
  NCBI__GCF_000744815.1:WP_037576905.1 330 APEHLEVISADDDYYHQNLKNYGSIFLGAWSTVAYSDKgIAGTNHVLPTGRGARASAGLSVSRFLKPLTFQKV 402
                                           *************************************989********************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           s ea+ +la +ve+++++Eg++aH+++++ R
  NCBI__GCF_000744815.1:WP_037576905.1 403 SAEATPDLAAHVEAISDFEGMAAHRATATLR 433
                                           *************************998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (439 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.14
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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