GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Streptacidiphilus oryzae TH49

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_037581586.1 BS73_RS28925 histidinol dehydrogenase

Query= SwissProt::P9WNW9
         (444 letters)



>NCBI__GCF_000744815.1:WP_037581586.1
          Length = 435

 Score =  553 bits (1426), Expect = e-162
 Identities = 292/437 (66%), Positives = 336/437 (76%), Gaps = 8/437 (1%)

Query: 7   VLTRIDLRGAELTAAELRAALPRGGADVEAVLPTVRPIVAAVAERGAEAALDFGASFDGV 66
           +++RIDLRG+     + RA LPR   DVEA L  VRPI   V  RG EA ++    FDGV
Sbjct: 1   MISRIDLRGS---TDDPRALLPRAELDVEAALEKVRPICEDVHHRGVEALIEITERFDGV 57

Query: 67  RPHAIRVPDAALDAALAGLDCDVCEALQVMVERTRAVHSGQRRTDVTTTLGPGATVTERW 126
           R    RVP   L  ALA LD  V  AL+V +ER R VH  QRRTD TT + PG TVTERW
Sbjct: 58  RLTTTRVPVEELHKALAELDPKVRAALEVSIERARKVHREQRRTDHTTQVVPGGTVTERW 117

Query: 127 VPVERVGLYVPGGNAVYPSSVVMNVVPAQAAGVDSLVVASPPQAQWDGMPHPTILAAARL 186
           VPVERVGLYVPGG AVYPSSVVMNVVPAQ AGV+SL V SPPQ  +DG+PHPTILAA  L
Sbjct: 118 VPVERVGLYVPGGRAVYPSSVVMNVVPAQEAGVESLAVTSPPQPDFDGLPHPTILAACAL 177

Query: 187 LGVDEVWAVGGAQAVALLAYGGTDTDGAALTPVDMITGPGNIYVTAAKRLCRSRVGIDAE 246
           LGVDEV+AVGGAQAVA+ AYG  +       PV+++TGPGNI+V AAKRL + R+GIDAE
Sbjct: 178 LGVDEVYAVGGAQAVAMFAYGTEEC-----RPVNLVTGPGNIWVAAAKRLLKGRIGIDAE 232

Query: 247 AGPTEIAILADHTADPVHVAADLISQAEHDELAASVLVTPSEDLADATDAELAGQLQTTV 306
           AGPTEIAILAD TADP HVAAD+ISQAEHD LAA+VLVT S  LADA + EL  Q++ T 
Sbjct: 233 AGPTEIAILADSTADPRHVAADMISQAEHDPLAAAVLVTDSLALADAVEKELEPQVRATK 292

Query: 307 HRERVTAALTGRQSAIVLVDDVDAAVLVVNAYAAEHLEIQTADAPQVASRIRSAGAIFVG 366
           H ER+  AL GRQS IVLVDD+D  + VV+AYAAEHLEIQTADA  VA+R+R+AGAIF+G
Sbjct: 293 HSERIATALDGRQSGIVLVDDIDQGLKVVDAYAAEHLEIQTADAHAVAARVRNAGAIFIG 352

Query: 367 PWSPVSLGDYCAGSNHVLPTAGCARHSSGLSVQTFLRGIHVVEYTEAALKDVSGHVITLA 426
            W+PVSLGDY AGSNHVLPT GCA HSSGLSVQ+FLRGIHVV+Y+  AL +V+GHV+ LA
Sbjct: 353 AWAPVSLGDYAAGSNHVLPTGGCACHSSGLSVQSFLRGIHVVDYSREALAEVAGHVVNLA 412

Query: 427 TAEDLPAHGEAVRRRFE 443
            AEDLP HG+A+R RFE
Sbjct: 413 NAEDLPGHGDAIRARFE 429


Lambda     K      H
   0.317    0.132    0.383 

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: 545
Number of extensions: 14
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: 444
Length of database: 435
Length adjustment: 32
Effective length of query: 412
Effective length of database: 403
Effective search space:   166036
Effective search space used:   166036
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_037581586.1 BS73_RS28925 (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.243784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-149  484.5   2.8   1.6e-149  484.3   2.8    1.0  1  NCBI__GCF_000744815.1:WP_037581586.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037581586.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.3   2.8  1.6e-149  1.6e-149       1     393 []      32     427 ..      32     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 484.3 bits;  conditional E-value: 1.6e-149
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 
                                           v++i+edv+++G eAl+e+te+fd+v+l++ rv+ eel++al+++d+++++ale ++e+ +k+h++q++++++
  NCBI__GCF_000744815.1:WP_037581586.1  32 VRPICEDVHHRGVEALIEITERFDGVRLTTTRVPVEELHKALAELDPKVRAALEVSIERARKVHREQRRTDHT 104
                                           799********************************************************************** PP

                             TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkk..dgkvnpavlaaakl 144
                                           ++  +g +++++++p+ervglYvPgG+a ypS+v+m++vpA+ Agv++++v++Pp+   dg  +p++laa++l
  NCBI__GCF_000744815.1:WP_037581586.1 105 TQVVPGGTVTERWVPVERVGLYVPGGRAVYPSSVVMNVVPAQEAGVESLAVTSPPQPdfDGLPHPTILAACAL 177
                                           *******************************************************7756899*********** PP

                             TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                           lgvdevy+vGGaqa+a++ayGte++++v+ ++GPGni+V+aAK+l+ g++gid  aGP+E++++ad++a+p++
  NCBI__GCF_000744815.1:WP_037581586.1 178 LGVDEVYAVGGAQAVAMFAYGTEECRPVNLVTGPGNIWVAAAKRLLKGRIGIDAEAGPTEIAILADSTADPRH 250
                                           ************************************************************************* PP

                             TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslek.ngaiilvddleealelsne 289
                                           vaaD++sqaEHd+ a+a+lvt+s +la++ve+e+e q+++++++e + ++l+  ++ i+lvdd+++ l+++++
  NCBI__GCF_000744815.1:WP_037581586.1 251 VAADMISQAEHDPLAAAVLVTDSLALADAVEKELEPQVRATKHSERIATALDGrQSGIVLVDDIDQGLKVVDA 323
                                           ***************************************************976899**************** PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           yA+EHLe+qt+d+++++ +++naG++f+G+++p++lgdy+aG+nhvLPT+g+A ++sglsv++Fl+ i+v+++
  NCBI__GCF_000744815.1:WP_037581586.1 324 YAAEHLEIQTADAHAVAARVRNAGAIFIGAWAPVSLGDYAAGSNHVLPTGGCACHSSGLSVQSFLRGIHVVDY 396
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           s+eal+e+a +v++la+aE+L  H +a+++R
  NCBI__GCF_000744815.1:WP_037581586.1 397 SREALAEVAGHVVNLANAEDLPGHGDAIRAR 427
                                           ****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (435 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: 29.96
//
[ok]

This GapMind analysis is from Jul 26 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:

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