Alignments for a candidate for hisD in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Desulfitobacterium hafniense DCB-2

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_015943471.1 DHAF_RS07445 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000021925.1:WP_015943471.1
          Length = 426

 Score =  366 bits (939), Expect = e-106
 Identities = 198/401 (49%), Positives = 269/401 (67%), Gaps = 5/401 (1%)

Query: 30  VDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDAAPASTVEALK 89
           ++  V EI+  +++EGDSAL   + +FD +DL  +G+ V   E+  A+       + AL+
Sbjct: 25  LEHKVAEILSEIKKEGDSALYALTEKFDGVDLRPSGLRVRAEELVKAYSQVDEEFLAALR 84

Query: 90  LARDRIEKHHARQLPKDDRYTDAL--GVELGSRWTAIEAVGLYVPGGTASYPSSVLMNAM 147
           LA+++I  +H +Q  K   + DA   G  LG     ++ VG+YVPGGTA+YPSSVLMNA+
Sbjct: 85  LAKEKITSYHEKQ--KRTSWLDAQEDGSILGQLLLPLKRVGIYVPGGTAAYPSSVLMNAV 142

Query: 148 PAKVAGVDRIVMVVPA-PDGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPV 206
           PA VAGV+ IVMV P   DG+L P VLVAA  AGV+EIY+VGGAQAIAALA+GT  I PV
Sbjct: 143 PAVVAGVEEIVMVSPPRKDGSLLPEVLVAAAEAGVTEIYKVGGAQAIAALAFGTGEISPV 202

Query: 207 AKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAA 266
            KI GPGN YV  AK+ VFGTV IDM+AGPSE+LI+AD+   P+ +AADLL+QAEHD  A
Sbjct: 203 DKITGPGNIYVTLAKKQVFGTVDIDMLAGPSEILILADESAQPEELAADLLSQAEHDPLA 262

Query: 267 QSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAA 326
            SIL++ D          VERQL  L R + A ASW  +GA ILVKD  + + L N+IA 
Sbjct: 263 SSILVSPDRKVLEETVAEVERQLKLLPRQDIARASWETYGAAILVKDLAEGMNLVNQIAP 322

Query: 327 EHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLD 386
           EH E+ + +  +++ R+RNAG++F+G ++PE +GDY  G NHVLPT  +ARF S L+V  
Sbjct: 323 EHFELVIKEPYSWLGRVRNAGAVFLGRFSPEPVGDYFAGPNHVLPTGGTARFYSPLNVDT 382

Query: 387 YMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           +MK+ S++    + L+  G     +AR EGL+AHA++V  R
Sbjct: 383 FMKKVSVISYSEKALQRDGKHIAHLARKEGLEAHARAVEAR 423


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: 437
Number of extensions: 16
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: 426
Length adjustment: 32
Effective length of query: 398
Effective length of database: 394
Effective search space:   156812
Effective search space used:   156812
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_015943471.1 DHAF_RS07445 (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.6229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.1e-170  551.4   0.0     8e-170  551.2   0.0    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015943471.1  DHAF_RS07445 histidinol dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015943471.1  DHAF_RS07445 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.2   0.0    8e-170    8e-170       1     393 []      29     423 ..      29     423 .. 0.99

  Alignments for each domain:
  == domain 1  score: 551.2 bits;  conditional E-value: 8e-170
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                               v+ei+++++keGd+Al+++tekfd+v  +++ lrv +eel +a+++vdee+ +al+la+e+i+++hekq
  lcl|NCBI__GCF_000021925.1:WP_015943471.1  29 VAEILSEIKKEGDSALYALTEKFDGVdlRPSGLRVRAEELVKAYSQVDEEFLAALRLAKEKITSYHEKQ 97 
                                               789**********************9778889************************************* PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                               +++s+   +e+g++lgq++ pl+rvg+YvPgG+aaypS+vlm+avpA vAgv+eiv+v+Pp+kdg++ p
  lcl|NCBI__GCF_000021925.1:WP_015943471.1  98 KRTSWLDAQEDGSILGQLLLPLKRVGIYVPGGTAAYPSSVLMNAVPAVVAGVEEIVMVSPPRKDGSLLP 166
                                               ********************************************************************* PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                               +vl+aa+ +gv+e+ykvGGaqaiaala+Gt ++++vdki+GPGniyVt AKk+vfg+v+idm+aGPsE+
  lcl|NCBI__GCF_000021925.1:WP_015943471.1 167 EVLVAAAEAGVTEIYKVGGAQAIAALAFGTGEISPVDKITGPGNIYVTLAKKQVFGTVDIDMLAGPSEI 235
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               l++adesa+pe +aaDllsqaEHd+ a++ilv+++++++e++ +eve+ql+ l+r++ia++s+e++ga 
  lcl|NCBI__GCF_000021925.1:WP_015943471.1 236 LILADESAQPEELAADLLSQAEHDPLASSILVSPDRKVLEETVAEVERQLKLLPRQDIARASWETYGAA 304
                                               ********************************************************************* PP

                                 TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                               ilv+dl+e ++l+n++ApEH el +k+p ++l +++naG+vflG+ +pe++gdy+aGpnhvLPT+gtAr
  lcl|NCBI__GCF_000021925.1:WP_015943471.1 305 ILVKDLAEGMNLVNQIAPEHFELVIKEPYSWLGRVRNAGAVFLGRFSPEPVGDYFAGPNHVLPTGGTAR 373
                                               ********************************************************************* PP

                                 TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               f+s+l+v++F+k++sv+++s++al++ ++++++la+ EgLeaHa+ave+R
  lcl|NCBI__GCF_000021925.1:WP_015943471.1 374 FYSPLNVDTFMKKVSVISYSEKALQRDGKHIAHLARKEGLEAHARAVEAR 423
                                               ************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (426 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.57
//
[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