Alignments for a candidate for hisD in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Methylomonas methanica MC09

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_337998544.1 METME_RS03475 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000214665.1:WP_337998544.1
          Length = 428

 Score =  398 bits (1023), Expect = e-115
 Identities = 209/425 (49%), Positives = 280/425 (65%), Gaps = 1/425 (0%)

Query: 5   LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64
           L  T+PDF +     L+       D+ + V EI+  VR+ GD AL+DY+ RFDR +    
Sbjct: 4   LDSTNPDFARDLQQRLAWDASDDLDIHQRVLEIIANVRKSGDQALIDYTNRFDRTNFTTA 63

Query: 65  G-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTA 123
           G + + +A +  A+D+ P    +AL+ A +R+  +  +Q  +  ++T+A G  LG + T 
Sbjct: 64  GELELDKAALKHAWDSLPDDQAQALQTAAERVRAYAEQQKLQSWQFTEADGTVLGQKVTP 123

Query: 124 IEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSE 183
           ++  GLYVPGG A+YPSSVLMNA+PAKVAGV  ++MVVP P G  N +VL AA +AGV  
Sbjct: 124 LDKAGLYVPGGKAAYPSSVLMNAIPAKVAGVGELIMVVPTPGGETNAMVLAAAYIAGVDR 183

Query: 184 IYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVA 243
           ++ +GGAQA+AALAYGTET+  V KIVGPGN YVA AK++VFG VGIDMIAGPSE+LI+ 
Sbjct: 184 VFTIGGAQAVAALAYGTETVPAVDKIVGPGNIYVATAKKLVFGQVGIDMIAGPSEILIIC 243

Query: 244 DKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWR 303
           D   +PDWIA DL +QAEHD  AQSIL++++  F   VE ++ + L  + R E   AS  
Sbjct: 244 DGQTHPDWIAMDLFSQAEHDENAQSILISDNSEFLDQVEASINKLLPEMERAEIIRASMT 303

Query: 304 DFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYV 363
             GA I V    DA  +ANRIA EHLE++VAD EA   +IRNAG+IF+G YT E +GDY 
Sbjct: 304 GRGAFIKVASLADAAEVANRIAPEHLELSVADPEALAAQIRNAGAIFMGRYTAEALGDYC 363

Query: 364 GGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQS 423
            G NHVLPT+ +AR+SS L V D+ KR+SL+   +     LG  A  +AR E L AHA+S
Sbjct: 364 AGPNHVLPTSSTARYSSPLGVYDFQKRSSLINCSAAGASELGKIASVLARGESLTAHARS 423

Query: 424 VAIRL 428
              R+
Sbjct: 424 AEYRI 428


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: 456
Number of extensions: 16
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: 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 WP_337998544.1 METME_RS03475 (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.4162502.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-162  527.0   1.7     2e-162  526.9   1.7    1.0  1  NCBI__GCF_000214665.1:WP_337998544.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214665.1:WP_337998544.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.9   1.7    2e-162    2e-162       1     393 []      33     427 ..      33     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 526.9 bits;  conditional E-value: 2e-162
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 
                                           v eii++vrk+Gd+Al++yt++fd++   ++ +l++ ++ l++a+++++++  +al++aae++++++e+q+ +
  NCBI__GCF_000214665.1:WP_337998544.1  33 VLEIIANVRKSGDQALIDYTNRFDRTnftTAGELELDKAALKHAWDSLPDDQAQALQTAAERVRAYAEQQKLQ 105
                                           679*********************98777888***************************************** PP

                             TIGR00069  71 sveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaak 143
                                           s++ ++++g++lgqkv+pl+++glYvPgGkaaypS+vlm+a+pAkvAgv e+++v P+   g+ n+ vlaaa 
  NCBI__GCF_000214665.1:WP_337998544.1 106 SWQFTEADGTVLGQKVTPLDKAGLYVPGGKAAYPSSVLMNAIPAKVAGVGELIMVVPTP-GGETNAMVLAAAY 177
                                           **********************************************************6.9************ PP

                             TIGR00069 144 llgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpe 216
                                           ++gvd+v+++GGaqa+aalayGtetvp+vdkivGPGniyV++AKklvfg+vgidmiaGPsE+l+i+d +++p+
  NCBI__GCF_000214665.1:WP_337998544.1 178 IAGVDRVFTIGGAQAVAALAYGTETVPAVDKIVGPGNIYVATAKKLVFGQVGIDMIAGPSEILIICDGQTHPD 250
                                           ************************************************************************* PP

                             TIGR00069 217 lvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289
                                           ++a+Dl+sqaEHde+aq+il+++++e++++ve+++++ l e+er+ei+++s++ +ga i v++l++a+e++n+
  NCBI__GCF_000214665.1:WP_337998544.1 251 WIAMDLFSQAEHDENAQSILISDNSEFLDQVEASINKLLPEMERAEIIRASMTGRGAFIKVASLADAAEVANR 323
                                           ************************************************************************* PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           +ApEHLel ++dpe+l+ +i+naG++f+G+yt+ealgdy+aGpnhvLPTs tAr++s+l+v+dF+kr+s++++
  NCBI__GCF_000214665.1:WP_337998544.1 324 IAPEHLELSVADPEALAAQIRNAGAIFMGRYTAEALGDYCAGPNHVLPTSSTARYSSPLGVYDFQKRSSLINC 396
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           s ++++el++ ++ la+ E L+aHa+++e R
  NCBI__GCF_000214665.1:WP_337998544.1 397 SAAGASELGKIASVLARGESLTAHARSAEYR 427
                                           ***************************9988 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.82
//
[ok]

This GapMind analysis is from Jul 25 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:

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