Alignments for a candidate for hisD in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Desulfovibrio vulgaris Hildenborough

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate 206223 DVU0796 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>MicrobesOnline__882:206223
          Length = 436

 Score =  350 bits (897), Expect = e-101
 Identities = 191/412 (46%), Positives = 257/412 (62%), Gaps = 4/412 (0%)

Query: 20  LSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDA 79
           L+G+ +  + V+  VR+I+  VR +GD AL +Y+RRFD  D     + VT  E+  A  +
Sbjct: 21  LAGRYDPDDAVEPVVRDILAAVRSKGDEALAEYTRRFDCPDFTPALLHVTSEEVAQAVAS 80

Query: 80  APASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASYP 139
            PA  +  ++ A D I   H  Q  +    T   G  LG + T ++  GLYVPGG     
Sbjct: 81  VPADDIAIIRQAADNIRSFHEAQKERSWFVTHDDGTILGQKVTPVDRAGLYVPGGKGGDT 140

Query: 140 ---SSVLMNAMPAKVAGVDRIVMVVPA-PDGNLNPLVLVAARLAGVSEIYRVGGAQAIAA 195
              SS+LMNA+PA+VAGV  I +  P  PDG LNP +L AA + G+++I R G A A+AA
Sbjct: 141 PLLSSLLMNAIPAQVAGVTSITVASPPRPDGTLNPHLLAAAHILGITDIIRAGSAWAVAA 200

Query: 196 LAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAAD 255
            A+GT+TI PV  I GPGN +V  AKR+V G V IDMIAGPSE+LI+AD    PDW+AAD
Sbjct: 201 FAFGTQTIAPVDVIAGPGNIFVTTAKRMVQGRVAIDMIAGPSEILILADATARPDWVAAD 260

Query: 256 LLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFE 315
           +L+QAEHD  A SIL+T + A A AV   +ERQL TL R + A  +  D+GAV++V D +
Sbjct: 261 MLSQAEHDPLASSILVTTEPALAEAVTAELERQLATLPRADIARKALADWGAVVVVPDMD 320

Query: 316 DAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARS 375
            A+ +ANR+A EHLE+  A        +R+AG++F+G Y+PE +GDY  G NHVLPT  +
Sbjct: 321 VAVAIANRVAPEHLEVLTAQPWELAGSLRHAGALFLGPYSPEPLGDYFAGPNHVLPTMGT 380

Query: 376 ARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           ARFSS LSV  + KRTS++            A   +AR EGL+AHA+S A R
Sbjct: 381 ARFSSALSVQTFCKRTSIIAASRAFAERNADAVARLARLEGLEAHARSAASR 432


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: 470
Number of extensions: 22
Number of successful extensions: 5
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: 436
Length adjustment: 32
Effective length of query: 398
Effective length of database: 404
Effective search space:   160792
Effective search space used:   160792
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 206223 DVU0796 (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.13032.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-161  523.8   0.2   1.9e-161  523.6   0.2    1.0  1  lcl|MicrobesOnline__882:206223  DVU0796 histidinol dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206223  DVU0796 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.6   0.2  1.9e-161  1.9e-161       1     393 []      35     432 ..      35     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.6 bits;  conditional E-value: 1.9e-161
                       TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesvevete 77 
                                     v++i+++vr++GdeAl eyt++fd    +++ l+v++ee+++a+++v+++ ++ +++aa+ni++fhe+q+++s++v++ 
  lcl|MicrobesOnline__882:206223  35 VRDILAAVRSKGDEALAEYTRRFDCPdfTPALLHVTSEEVAQAVASVPADDIAIIRQAADNIRSFHEAQKERSWFVTHD 113
                                     899*********************97668899*********************************************** PP

                       TIGR00069  78 egvllgqkvrplervglYvPgGk...aaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevykv 153
                                     +g++lgqkv+p++r+glYvPgGk   ++++S++lm+a+pA+vAgv++i+v++Pp+ dg++np++laaa++lg+++++++
  lcl|MicrobesOnline__882:206223 114 DGTILGQKVTPVDRAGLYVPGGKggdTPLLSSLLMNAIPAQVAGVTSITVASPPRPDGTLNPHLLAAAHILGITDIIRA 192
                                     ********************9886669**************************************************** PP

                       TIGR00069 154 GGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHdeda 232
                                     G a a+aa+a+Gt+t+ +vd+i+GPGni+Vt+AK++v+g+v+idmiaGPsE+l++ad++a p++vaaD+lsqaEHd+ a
  lcl|MicrobesOnline__882:206223 193 GSAWAVAAFAFGTQTIAPVDVIAGPGNIFVTTAKRMVQGRVAIDMIAGPSEILILADATARPDWVAADMLSQAEHDPLA 271
                                     ******************************************************************************* PP

                       TIGR00069 233 qailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpeellkkikn 311
                                     ++ilvtt+ +lae+v++e+e+ql++l+r++ia+k+l++ ga+++v d++ a++++n++ApEHLe+ t++p+el+ ++++
  lcl|MicrobesOnline__882:206223 272 SSILVTTEPALAEAVTAELERQLATLPRADIARKALADWGAVVVVPDMDVAVAIANRVAPEHLEVLTAQPWELAGSLRH 350
                                     ******************************************************************************* PP

                       TIGR00069 312 aGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeav 390
                                     aG++flG+y+pe+lgdy+aGpnhvLPT+gtArf+s+lsv++F+kr+s++ +s++ +e+ a+av++la++EgLeaHa+++
  lcl|MicrobesOnline__882:206223 351 AGALFLGPYSPEPLGDYFAGPNHVLPTMGTARFSSALSVQTFCKRTSIIAASRAFAERNADAVARLARLEGLEAHARSA 429
                                     ******************************************************************************9 PP

                       TIGR00069 391 evR 393
                                     + R
  lcl|MicrobesOnline__882:206223 430 ASR 432
                                     887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (436 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.42
//
[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