GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Sphingomonas koreensis DSMZ 15582

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Ga0059261_1281 Ga0059261_1281 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Korea:Ga0059261_1281
          Length = 428

 Score =  486 bits (1251), Expect = e-142
 Identities = 249/424 (58%), Positives = 311/424 (73%)

Query: 5   LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64
           L  T+P F Q F   +  +RE   DV R VR IV  VR EGD+AL  ++R+FDR DL +T
Sbjct: 4   LSTTEPGFAQAFRELVDARREADADVARDVRTIVASVRDEGDAALHAFTRKFDRHDLNET 63

Query: 65  GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAI 124
           G  + +A+  AAFDA      +AL+LA DRI  +H +Q P D   TDA GV  G+RW A+
Sbjct: 64  GWRIEKADCAAAFDALEPKLRDALQLAADRITAYHEKQKPADSDTTDAAGVRTGARWQAV 123

Query: 125 EAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEI 184
           EA G+YVPGG A+YPSSVLMNA+PAKVAGVDR+VMV P PDG +NPLVL AA +AGV EI
Sbjct: 124 EAAGVYVPGGRAAYPSSVLMNAIPAKVAGVDRLVMVTPTPDGEVNPLVLAAAHIAGVDEI 183

Query: 185 YRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVAD 244
           +RVGGAQAIAALAYGT  I  V  I GPGNA+VA AKR ++G VGIDM+AGPSE++++AD
Sbjct: 184 WRVGGAQAIAALAYGTGRIAAVDVITGPGNAWVAEAKRQLYGVVGIDMVAGPSEIVVIAD 243

Query: 245 KDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRD 304
             N+P+WIAADLL+Q+EHD  +QSIL+T+D  FA  V EAV+ Q+ TL+    A  SW  
Sbjct: 244 GKNDPEWIAADLLSQSEHDPTSQSILLTDDAIFAGKVAEAVDLQIGTLSTKGVARQSWDA 303

Query: 305 FGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVG 364
            GA+IL    ++AIPL N++A EHLE+A  D +A   R+R+AGS+F+G  TPE IGDYV 
Sbjct: 304 NGAIILTGSLDEAIPLVNKLAPEHLELACDDPDALFARVRHAGSVFLGRMTPEAIGDYVA 363

Query: 365 GCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSV 424
           G NHVLPT R ARF+SGLSVLD+MKRTS L L +  L A+GPAA+ +A AEGL AHA+SV
Sbjct: 364 GPNHVLPTGRRARFASGLSVLDFMKRTSFLALDAAGLAAIGPAAVALAEAEGLPAHARSV 423

Query: 425 AIRL 428
           ++RL
Sbjct: 424 SLRL 427


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: 512
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: 428
Length adjustment: 32
Effective length of query: 398
Effective length of database: 396
Effective search space:   157608
Effective search space used:   157608
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 Ga0059261_1281 Ga0059261_1281 (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.4978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-162  524.8   0.1   9.7e-162  524.6   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1281  Ga0059261_1281 histidinol dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1281  Ga0059261_1281 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.6   0.1  9.7e-162  9.7e-162       1     393 []      33     426 ..      33     426 .. 0.99

  Alignments for each domain:
  == domain 1  score: 524.6 bits;  conditional E-value: 9.7e-162
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                               v++i+++vr+eGd+Al+++t+kfd+   + +  r++++++++a +a++++l++al+laa++i+++hekq
  lcl|FitnessBrowser__Korea:Ga0059261_1281  33 VRTIVASVRDEGDAALHAFTRKFDRHdlNETGWRIEKADCAAAFDALEPKLRDALQLAADRITAYHEKQ 101
                                               899**********************95566678************************************ PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                               +p++  +++++gv +g +++++e++g+YvPgG+aaypS+vlm+a+pAkvAgv+++v+vtP+  dg+vnp
  lcl|FitnessBrowser__Korea:Ga0059261_1281 102 KPADSDTTDAAGVRTGARWQAVEAAGVYVPGGRAAYPSSVLMNAIPAKVAGVDRLVMVTPTP-DGEVNP 169
                                               *************************************************************6.****** PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                                vlaaa+++gvde+++vGGaqaiaalayGt  + +vd+i+GPGn++V++AK++++g vgidm+aGPsE+
  lcl|FitnessBrowser__Korea:Ga0059261_1281 170 LVLAAAHIAGVDEIWRVGGAQAIAALAYGTGRIAAVDVITGPGNAWVAEAKRQLYGVVGIDMVAGPSEI 238
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               +viad + +pe++aaDllsq EHd+++q+il+t+++ +a kv e+v+ q+ +l++k +a++s++ ngai
  lcl|FitnessBrowser__Korea:Ga0059261_1281 239 VVIADGKNDPEWIAADLLSQSEHDPTSQSILLTDDAIFAGKVAEAVDLQIGTLSTKGVARQSWDANGAI 307
                                               ********************************************************************* PP

                                 TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                               il+ +l+ea+ l+n++ApEHLel+++dp +l  ++++aGsvflG++tpea+gdyvaGpnhvLPT++ Ar
  lcl|FitnessBrowser__Korea:Ga0059261_1281 308 ILTGSLDEAIPLVNKLAPEHLELACDDPDALFARVRHAGSVFLGRMTPEAIGDYVAGPNHVLPTGRRAR 376
                                               ********************************************************************* PP

                                 TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               fasglsv dF+kr+s+  l+ ++l+++++a+++laeaEgL aHa++v+ R
  lcl|FitnessBrowser__Korea:Ga0059261_1281 377 FASGLSVLDFMKRTSFLALDAAGLAAIGPAAVALAEAEGLPAHARSVSLR 426
                                               ***********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (428 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: 00:00:00.02
# Mc/sec: 7.73
//
[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:

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