Alignments for a candidate for hisD in Enterococcus termitis LMG 8895

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Enterococcus termitis LMG 8895

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_069662106.1 BCR25_RS00385 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_001730305.1:WP_069662106.1
          Length = 426

 Score =  366 bits (939), Expect = e-106
 Identities = 192/428 (44%), Positives = 277/428 (64%), Gaps = 5/428 (1%)

Query: 5   LRQTDPDFEQKFAAFLSGKREVSED---VDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +++   D      A L+ +++  E+   ++  V++I+  V + GD AL +YS++FD++ L
Sbjct: 1   MKRLTGDASDVLTALLAERKQTQEETKEIEEQVKQIIQTVEQNGDQALKNYSKQFDQVVL 60

Query: 62  EKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRW 121
             T +AV+E EI+  +       + +L  A++ I  +H +Q   D   T+  GV  G   
Sbjct: 61  --TDLAVSEEEIEQGYQRVEPEVIASLIAAKENIISYHKKQKQYDFFDTEKAGVIRGQLV 118

Query: 122 TAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGV 181
             +E VG+YVPGGTA+YPSSVLMN +PAK+AGV  I+MV P     +  ++L AA++AGV
Sbjct: 119 LPLERVGVYVPGGTAAYPSSVLMNVLPAKIAGVKEIIMVTPPTTSGIPDVILAAAKIAGV 178

Query: 182 SEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLI 241
             I+++GGAQA+AALAYGTE+I  V KIVGPGN YVA AK+ VFG VGIDMIAGPSE+ I
Sbjct: 179 DNIFQIGGAQAVAALAYGTESIPKVDKIVGPGNVYVATAKKQVFGLVGIDMIAGPSEIGI 238

Query: 242 VADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASAS 301
           +AD   NP ++AADLL+QAEHDT A++IL+TN + FA  VE+ +E+QL TL R   A  +
Sbjct: 239 IADDTANPVYVAADLLSQAEHDTLARAILVTNSKRFADQVEKEIEQQLKTLPRKTIAEKA 298

Query: 302 WRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGD 361
             D G +I+V   E    + N IA EHLE+ ++D  +++  I++AGSIF+G Y  E +GD
Sbjct: 299 ISDHGRIIIVPTLEAMFTVMNEIAPEHLEVQLSDPMSYLHEIKHAGSIFLGAYASEPVGD 358

Query: 362 YVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHA 421
           Y  G NHVLPT+ +A+F S L V D++K + +     E L     A   +AR EGL+AHA
Sbjct: 359 YFSGTNHVLPTSGTAKFYSPLGVYDFVKYSQVTYYTKEALAQAKDAITTLARKEGLEAHA 418

Query: 422 QSVAIRLN 429
           +++  R N
Sbjct: 419 RAIDCRFN 426


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: 433
Number of extensions: 14
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: 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_069662106.1 BCR25_RS00385 (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.667934.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-173  561.6   7.0   6.2e-173  561.4   7.0    1.0  1  NCBI__GCF_001730305.1:WP_069662106.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069662106.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.4   7.0  6.2e-173  6.2e-173       1     393 []      33     424 ..      33     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 561.4 bits;  conditional E-value: 6.2e-173
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 
                                           vk+ii+ v+++Gd+Al++y+++fd+v l++l+vseee+e+ +++v++e++++l +a+eni ++h+kq++ +++
  NCBI__GCF_001730305.1:WP_069662106.1  33 VKQIIQTVEQNGDQALKNYSKQFDQVVLTDLAVSEEEIEQGYQRVEPEVIASLIAAKENIISYHKKQKQYDFF 105
                                           89*********************************************************************** PP

                             TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllg 146
                                            ++++gv+ gq+v plervg+YvPgG+aaypS+vlm+++pAk+Agvkei++vtPp+++g + + +laaak++g
  NCBI__GCF_001730305.1:WP_069662106.1 106 DTEKAGVIRGQLVLPLERVGVYVPGGTAAYPSSVLMNVLPAKIAGVKEIIMVTPPTTSG-IPDVILAAAKIAG 177
                                           *******************************************************8666.************* PP

                             TIGR00069 147 vdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelva 219
                                           vd+++++GGaqa+aalayGte++pkvdkivGPGn+yV++AKk+vfg vgidmiaGPsE+ +iad++anp +va
  NCBI__GCF_001730305.1:WP_069662106.1 178 VDNIFQIGGAQAVAALAYGTESIPKVDKIVGPGNVYVATAKKQVFGLVGIDMIAGPSEIGIIADDTANPVYVA 250
                                           ************************************************************************* PP

                             TIGR00069 220 aDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyAp 292
                                           aDllsqaEHd+ a+ailvt+s+++a++ve+e+e+ql++l+rk+iaek+++++g+ii+v +le ++ ++ne+Ap
  NCBI__GCF_001730305.1:WP_069662106.1 251 ADLLSQAEHDTLARAILVTNSKRFADQVEKEIEQQLKTLPRKTIAEKAISDHGRIIIVPTLEAMFTVMNEIAP 323
                                           ************************************************************************* PP

                             TIGR00069 293 EHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelske 365
                                           EHLe+q +dp+++l++ik+aGs+flG+y++e++gdy++G+nhvLPTsgtA+f+s+l+v+dF+k ++v++++ke
  NCBI__GCF_001730305.1:WP_069662106.1 324 EHLEVQLSDPMSYLHEIKHAGSIFLGAYASEPVGDYFSGTNHVLPTSGTAKFYSPLGVYDFVKYSQVTYYTKE 396
                                           ************************************************************************* PP

                             TIGR00069 366 aleelaeaveklaeaEgLeaHaeavevR 393
                                           al++ ++a+++la+ EgLeaHa+a++ R
  NCBI__GCF_001730305.1:WP_069662106.1 397 ALAQAKDAITTLARKEGLEAHARAIDCR 424
                                           *************************988 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.40
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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