Alignments for a candidate for hisD in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Desulfovibrio oxyclinae DSM 11498

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_018123249.1 B149_RS0100770 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000375485.1:WP_018123249.1
          Length = 436

 Score =  324 bits (831), Expect = 3e-93
 Identities = 181/413 (43%), Positives = 252/413 (61%), Gaps = 4/413 (0%)

Query: 19  FLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFD 78
           +L  +++    VD  VREI+D +R  GD+AL++Y+ +FD   + +  + V E  I  A D
Sbjct: 20  WLDRRKDPDTKVDGIVREILDTIRSRGDTALVEYTAKFDCPKITREQLTVPEEIILGALD 79

Query: 79  AAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASY 138
           + PA   + L  A D +   H +Q       T   G  LG     ++ VGLYVPGG    
Sbjct: 80  SIPAEDKDILAEAIDNVRIFHEKQRENSWWTTAEDGTILGQMVRPVDRVGLYVPGGKGGE 139

Query: 139 P---SSVLMNAMPAKVAGVDRIVMVVPA-PDGNLNPLVLVAARLAGVSEIYRVGGAQAIA 194
               SS++MNA+PA+VAGV+ I +  P   DG LNP +L  A L G+ EI+  G A AI 
Sbjct: 140 TPLISSLIMNAIPAQVAGVESIAVTSPPREDGTLNPYILATAALLGLKEIHLSGSAWAIG 199

Query: 195 ALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAA 254
           ALAYGTE+I P   I GPGN +VA AK  + G +GIDM+AGPSE+ I+AD   NP+W+AA
Sbjct: 200 ALAYGTESIAPCDVIAGPGNIFVATAKSQLIGQIGIDMVAGPSEIAILADDSANPEWLAA 259

Query: 255 DLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDF 314
           D+L+QAEHD  A SIL+T+    A    E ++ Q   L R E A+ +  D+GA I+V+D 
Sbjct: 260 DMLSQAEHDPLAASILVTDSPELAEKTCEQLKLQTAELPRGEIAAKALADWGATIIVEDL 319

Query: 315 EDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTAR 374
                L NRIA EHLE+++AD  + +  IR+AG+IF+G ++PE +GDY  G NHVLPT R
Sbjct: 320 VTGADLINRIAPEHLELSLADPWSHLGAIRHAGAIFMGHHSPEPVGDYFAGPNHVLPTLR 379

Query: 375 SARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           + RFSS LSV ++ K++S++      +   G     +AR EGL+AHA+SV  R
Sbjct: 380 TVRFSSALSVQNFCKKSSVIAASPSYVAEHGDKIARLARLEGLEAHARSVECR 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: 444
Number of extensions: 20
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 WP_018123249.1 B149_RS0100770 (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.16788.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-153  496.3   0.0   4.2e-153  496.1   0.0    1.0  1  lcl|NCBI__GCF_000375485.1:WP_018123249.1  B149_RS0100770 histidinol dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018123249.1  B149_RS0100770 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.1   0.0  4.2e-153  4.2e-153       1     393 []      35     432 ..      35     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 496.1 bits;  conditional E-value: 4.2e-153
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                               v+ei++ +r++Gd+Al+eyt kfd    + e+l+v+ee +  al+++++e k+ l++a++n++ fhekq
  lcl|NCBI__GCF_000375485.1:WP_018123249.1  35 VREILDTIRSRGDTALVEYTAKFDCPkiTREQLTVPEEIILGALDSIPAEDKDILAEAIDNVRIFHEKQ 103
                                               899*********************7655899************************************** PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGk...aaypStvlmtavpAkvAgvkeivvvtPpkkdgk 133
                                               +++s+ ++ e+g++lgq+vrp++rvglYvPgGk   ++++S+++m+a+pA+vAgv++i+v++Pp++dg+
  lcl|NCBI__GCF_000375485.1:WP_018123249.1 104 RENSWWTTAEDGTILGQMVRPVDRVGLYVPGGKggeTPLISSLIMNAIPAQVAGVESIAVTSPPREDGT 172
                                               ******************************9876669******************************** PP

                                 TIGR00069 134 vnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGP 202
                                               +np +la+a+llg++e+   G a ai+alayGte++ ++d+i+GPGni+V++AK ++ g++gidm+aGP
  lcl|NCBI__GCF_000375485.1:WP_018123249.1 173 LNPYILATAALLGLKEIHLSGSAWAIGALAYGTESIAPCDVIAGPGNIFVATAKSQLIGQIGIDMVAGP 241
                                               ********************************************************************* PP

                                 TIGR00069 203 sEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekn 271
                                               sE++++ad+sanpe++aaD+lsqaEHd+ a++ilvt+s elaek+ e+++ q++el+r eia k+l++ 
  lcl|NCBI__GCF_000375485.1:WP_018123249.1 242 SEIAILADDSANPEWLAADMLSQAEHDPLAASILVTDSPELAEKTCEQLKLQTAELPRGEIAAKALADW 310
                                               ********************************************************************* PP

                                 TIGR00069 272 gaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsg 340
                                               ga i+v+dl   ++l+n++ApEHLel  +dp++ l  i++aG++f+G+++pe++gdy+aGpnhvLPT +
  lcl|NCBI__GCF_000375485.1:WP_018123249.1 311 GATIIVEDLVTGADLINRIAPEHLELSLADPWSHLGAIRHAGAIFMGHHSPEPVGDYFAGPNHVLPTLR 379
                                               ********************************************************************* PP

                                 TIGR00069 341 tArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               t rf+s+lsv++F+k++sv+ +s + ++e ++++++la++EgLeaHa++ve R
  lcl|NCBI__GCF_000375485.1:WP_018123249.1 380 TVRFSSALSVQNFCKKSSVIAASPSYVAEHGDKIARLARLEGLEAHARSVECR 432
                                               **************************************************998 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.25
//
[ok]

This GapMind analysis is from Apr 10 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