GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Burkholderia phytofirmans PsJN

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate BPHYT_RS17710 BPHYT_RS17710 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__BFirm:BPHYT_RS17710
          Length = 440

 Score =  396 bits (1018), Expect = e-115
 Identities = 209/432 (48%), Positives = 291/432 (67%), Gaps = 5/432 (1%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +  L  T PDF++   A L+ +    E ++R+V +I++ V+  GD+A+L+Y++RFDR++ 
Sbjct: 5   IRKLDSTAPDFQKSLHAVLAFEASEDEAIERSVAQILNDVKARGDAAVLEYTQRFDRVEA 64

Query: 62  EKT-GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDD----RYTDALGVE 116
           +    + +  +E++AA +        AL+ A  R+  +H +Q  +      +YT+A G  
Sbjct: 65  KSVDALELPMSELEAALENLEPKRRAALEAAAARVRGYHEKQKIECGSHSWQYTEADGTV 124

Query: 117 LGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAA 176
           LG + T ++  G+YVPGG A+YPSSVLMNA+PA+VAGV  IVMVVP PDG  NPLVL AA
Sbjct: 125 LGQKVTPLDRAGIYVPGGKAAYPSSVLMNAIPARVAGVREIVMVVPTPDGVKNPLVLAAA 184

Query: 177 RLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGP 236
            L GV  ++ +GGAQA+ ALAYGT TI  V KI GPGNAYVA+AKR VFGTVGIDMIAGP
Sbjct: 185 LLGGVDRVFTIGGAQAVGALAYGTATIPAVDKICGPGNAYVASAKRRVFGTVGIDMIAGP 244

Query: 237 SEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTE 296
           SE+L++ D   +P W+A DL +QAEHD  AQSIL+  D+AF   V++A++  L T+ R +
Sbjct: 245 SEILVLCDGTTDPRWVAMDLFSQAEHDELAQSILLCPDDAFIGRVKDAIDELLPTMPRRD 304

Query: 297 TASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTP 356
               S  D GA+I V+D E A  +AN IA EHLEI+  +   +   IR+AG+IF+G YT 
Sbjct: 305 VIRKSLEDRGALIKVRDMEQACAIANDIAPEHLEISALEPHHWGQLIRHAGAIFLGRYTS 364

Query: 357 EVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEG 416
           E +GDY  G NHVLPT+R+ARFSS L V D+ KR+S++++ +E  + LG  A E+A  EG
Sbjct: 365 ESLGDYCAGPNHVLPTSRTARFSSPLGVYDFFKRSSVIEVSAEGAQTLGEIAAELAYGEG 424

Query: 417 LDAHAQSVAIRL 428
           L AHA+S   R+
Sbjct: 425 LQAHARSAEYRM 436


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: 455
Number of extensions: 23
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: 430
Length of database: 440
Length adjustment: 32
Effective length of query: 398
Effective length of database: 408
Effective search space:   162384
Effective search space used:   162384
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 BPHYT_RS17710 BPHYT_RS17710 (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.24977.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     4e-161  522.6   0.0   4.6e-161  522.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS17710  BPHYT_RS17710 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS17710  BPHYT_RS17710 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  522.3   0.0  4.6e-161  4.6e-161       1     393 []      37     435 ..      37     435 .. 0.98

  Alignments for each domain:
  == domain 1  score: 522.3 bits;  conditional E-value: 4.6e-161
                                TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                              v++i++dv+++Gd+A+leyt++fd+v   ++++l+++ +ele+ale+++++ ++ale+aa++++ +hekq
  lcl|FitnessBrowser__BFirm:BPHYT_RS17710  37 VAQILNDVKARGDAAVLEYTQRFDRVeakSVDALELPMSELEAALENLEPKRRAALEAAAARVRGYHEKQ 106
                                              789***********************666667899*********************************** PP

                                TIGR00069  68 lpes....veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgk 133
                                              + e     +++++++g++lgqkv+pl+r+g+YvPgGkaaypS+vlm+a+pA+vAgv+eiv+v P+  dg 
  lcl|FitnessBrowser__BFirm:BPHYT_RS17710 107 KIECgshsWQYTEADGTVLGQKVTPLDRAGIYVPGGKAAYPSSVLMNAIPARVAGVREIVMVVPTP-DGV 175
                                              95433345*********************************************************6.*** PP

                                TIGR00069 134 vnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPs 203
                                               np vlaaa l gvd+v+++GGaqa++alayGt+t+p+vdki+GPGn+yV+ AK+ vfg+vgidmiaGPs
  lcl|FitnessBrowser__BFirm:BPHYT_RS17710 176 KNPLVLAAALLGGVDRVFTIGGAQAVGALAYGTATIPAVDKICGPGNAYVASAKRRVFGTVGIDMIAGPS 245
                                              ********************************************************************** PP

                                TIGR00069 204 EvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273
                                              E+lv++d +++p++va+Dl+sqaEHde aq+il++++++++ +v+++++e l +++r+++++ksle++ga
  lcl|FitnessBrowser__BFirm:BPHYT_RS17710 246 EILVLCDGTTDPRWVAMDLFSQAEHDELAQSILLCPDDAFIGRVKDAIDELLPTMPRRDVIRKSLEDRGA 315
                                              ********************************************************************** PP

                                TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                              +i v+d+e+a++++n++ApEHLe+ + +p+++ + i++aG++flG+yt+e+lgdy+aGpnhvLPTs+tAr
  lcl|FitnessBrowser__BFirm:BPHYT_RS17710 316 LIKVRDMEQACAIANDIAPEHLEISALEPHHWGQLIRHAGAIFLGRYTSESLGDYCAGPNHVLPTSRTAR 385
                                              ********************************************************************** PP

                                TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                              f+s+l+v+dF+kr+sv+e+s e++++l+e +++la  EgL+aHa+++e R
  lcl|FitnessBrowser__BFirm:BPHYT_RS17710 386 FSSPLGVYDFFKRSSVIEVSAEGAQTLGEIAAELAYGEGLQAHARSAEYR 435
                                              **********************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (440 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: 9.61
//
[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