Alignments for a candidate for hisD in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Acidovorax sp. GW101-3H11

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Ac3H11_4724 Histidinol dehydrogenase (EC 1.1.1.23)

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4724
          Length = 460

 Score =  392 bits (1006), Expect = e-113
 Identities = 210/444 (47%), Positives = 284/444 (63%), Gaps = 20/444 (4%)

Query: 5   LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEK- 63
           L   D DFE+KF   L    +    +++ V +I+  V++ GD+A+L+Y+ RFD +     
Sbjct: 10  LSTADADFEKKFQQCLHWSADTDAAIEQRVADILADVQKRGDAAVLEYTARFDGLSAPNM 69

Query: 64  TGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDR---YTDALGVELGSR 120
             + +T+A+  AAFDA P +  +AL+ A  R+  +H  Q         Y D  G  LG +
Sbjct: 70  AALELTQADFKAAFDAIPQAQRDALQAAAKRVRSYHEAQKKASGESWSYRDEDGTLLGQK 129

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAP---------------- 164
            T ++ VG+YVPGG A+YPSS+LMNA+PA VAGV  I+MVVP P                
Sbjct: 130 VTPLDRVGIYVPGGKAAYPSSLLMNAIPAHVAGVQEIIMVVPTPVRGSVATGGTGEGTST 189

Query: 165 DGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIV 224
            G  N LVL AA +AGV+  + +GGAQA+AALAYGT T+  V KI GPGNAYVA+AK+ V
Sbjct: 190 KGERNELVLAAAYVAGVTRAFTIGGAQAVAALAYGTATVPKVDKITGPGNAYVASAKKRV 249

Query: 225 FGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEA 284
           FGTVGIDMIAGPSE+L++AD    PDW+A DL +QAEHD  AQSIL+  D A+  AV+  
Sbjct: 250 FGTVGIDMIAGPSEILVLADGSTPPDWVAMDLFSQAEHDELAQSILLCPDAAYLDAVQRE 309

Query: 285 VERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIR 344
           ++R L T+ R E  + S    GA+IL KD E+A  ++NRIA EHLE++  D   + P +R
Sbjct: 310 IDRLLPTMPRAEIIAKSLTGRGALILTKDMEEACAISNRIAPEHLEVSSTDPHRWEPLLR 369

Query: 345 NAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRAL 404
           +AG+IF+G YT E +GDY  G NHVLPT+ +ARFSS L V D+ KR+SL+++     + L
Sbjct: 370 HAGAIFLGAYTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSLIEVSEAGAQVL 429

Query: 405 GPAAIEIARAEGLDAHAQSVAIRL 428
           G  A E+A  EGL AHAQ+  +RL
Sbjct: 430 GKIAAELAYGEGLQAHAQAAEMRL 453


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: 508
Number of extensions: 23
Number of successful extensions: 3
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: 460
Length adjustment: 32
Effective length of query: 398
Effective length of database: 428
Effective search space:   170344
Effective search space used:   170344
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 Ac3H11_4724 (Histidinol dehydrogenase (EC 1.1.1.23))
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.16093.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   9.6e-158  511.4   0.3   6.7e-157  508.7   0.3    1.9  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724  Histidinol dehydrogenase (EC 1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724  Histidinol dehydrogenase (EC 1.1.1.23)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.7   0.3  6.7e-157  6.7e-157       1     393 []      39     452 ..      39     452 .. 0.95

  Alignments for each domain:
  == domain 1  score: 508.7 bits;  conditional E-value: 6.7e-157
                                        TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaen 59 
                                                      v++i++dv+k+Gd+A+leyt +fd++   ++++l+++++++++a +a++++ ++al++aa++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724  39 VADILADVQKRGDAAVLEYTARFDGLsapNMAALELTQADFKAAFDAIPQAQRDALQAAAKR 100
                                                      789**********************977788899**************************** PP

                                        TIGR00069  60 iekfhekqlpes...veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAg 118
                                                      ++++he+q+++s   +++++e+g+llgqkv+pl+rvg+YvPgGkaaypS++lm+a+pA+vAg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724 101 VRSYHEAQKKASgesWSYRDEDGTLLGQKVTPLDRVGIYVPGGKAAYPSSLLMNAIPAHVAG 162
                                                      ********9876677*********************************************** PP

                                        TIGR00069 119 vkeivvvtPpk...............kdgkvnpavlaaakllgvdevykvGGaqaiaalayG 165
                                                      v+ei++v P+                ++g+ n+ vlaaa ++gv++ +++GGaqa+aalayG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724 163 VQEIIMVVPTPvrgsvatggtgegtsTKGERNELVLAAAYVAGVTRAFTIGGAQAVAALAYG 224
                                                      *******996422333333333333246778999**************************** PP

                                        TIGR00069 166 tetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqaE 227
                                                      t+tvpkvdki+GPGn+yV+ AKk vfg+vgidmiaGPsE+lv+ad s+ p++va+Dl+sqaE
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724 225 TATVPKVDKITGPGNAYVASAKKRVFGTVGIDMIAGPSEILVLADGSTPPDWVAMDLFSQAE 286
                                                      ************************************************************** PP

                                        TIGR00069 228 Hdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289
                                                      Hde aq+il++++++ +++v++e+++ l +++r+ei+ ksl+ +ga+il++d+eea+++sn+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724 287 HDELAQSILLCPDAAYLDAVQREIDRLLPTMPRAEIIAKSLTGRGALILTKDMEEACAISNR 348
                                                      ************************************************************** PP

                                        TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsve 351
                                                      +ApEHLe+  +dp+++ + +++aG++flG+yt+e+lgdy+aGpnhvLPTsgtArf+s+l+v+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724 349 IAPEHLEVSSTDPHRWEPLLRHAGAIFLGAYTSESLGDYCAGPNHVLPTSGTARFSSPLGVY 410
                                                      ************************************************************** PP

                                        TIGR00069 352 dFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                                      dF+kr+s++e+s+++++ l++ +++la  EgL+aHa+a+e+R
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4724 411 DFQKRSSLIEVSEAGAQVLGKIAAELAYGEGLQAHAQAAEMR 452
                                                      ***************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (460 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 3.17
//
[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:

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