Alignments for a candidate for hisD in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Thermithiobacillus tepidarius DSM 3134

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_028988607.1 G579_RS0100400 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000423825.1:WP_028988607.1
          Length = 432

 Score =  416 bits (1070), Expect = e-121
 Identities = 219/420 (52%), Positives = 285/420 (67%), Gaps = 1/420 (0%)

Query: 10  PDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTG-IAV 68
           PDF+Q           +   V+  VR+++  VR +GD A+LDY++RFDR+       + V
Sbjct: 9   PDFDQALRRLTDWDAGLDPAVEATVRDVLHAVREQGDRAVLDYTQRFDRLRANSLAELEV 68

Query: 69  TEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVG 128
             A++  A      +  EAL LA +RI  +H RQ+ +   Y++A G  LG R T +  VG
Sbjct: 69  PRAKLREALAGLAPADREALALAAERIRSYHERQVAESWEYSEADGTRLGQRVTPLARVG 128

Query: 129 LYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRVG 188
           +YVPGG A+YPSSVLMNA+PAKVAGV  I+MVVPAP G LNPLVL AA LAGV  ++ +G
Sbjct: 129 IYVPGGKAAYPSSVLMNAIPAKVAGVAEIIMVVPAPGGELNPLVLAAAELAGVDRVFTIG 188

Query: 189 GAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNN 248
           GAQA+AALAYGTET+  V KIVGPGN YVA AKR+VFG VGIDMIAGPSE+L+++D   +
Sbjct: 189 GAQAVAALAYGTETVPAVDKIVGPGNIYVATAKRMVFGRVGIDMIAGPSEILVISDGQTD 248

Query: 249 PDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAV 308
           PDW+A DLL+QAEHD  AQSIL++ D      V  +V++ L TL R   A  +W    A+
Sbjct: 249 PDWLAMDLLSQAEHDEQAQSILISWDADCLTRVAASVDKLLPTLEREAIARQAWDSRAAL 308

Query: 309 ILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNH 368
           ILV+D  +A  +A+RIA EHLE++VAD +A +P + NAG++F+G YT E +GDYV G NH
Sbjct: 309 ILVRDAAEACAVADRIAPEHLELSVADPDALLPALHNAGAVFMGRYTAEALGDYVAGPNH 368

Query: 369 VLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428
           VLPTA SARFSS L V D+ KRTS++   +     LG AA  +A  EGL AHA+S A R+
Sbjct: 369 VLPTAGSARFSSPLGVYDFQKRTSIIYASAVGADQLGRAAKRLAEGEGLTAHARSAAYRI 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: 556
Number of extensions: 24
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: 432
Length adjustment: 32
Effective length of query: 398
Effective length of database: 400
Effective search space:   159200
Effective search space used:   159200
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_028988607.1 G579_RS0100400 (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.1435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-165  536.1   0.3   3.7e-165  535.9   0.3    1.0  1  lcl|NCBI__GCF_000423825.1:WP_028988607.1  G579_RS0100400 histidinol dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000423825.1:WP_028988607.1  G579_RS0100400 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.9   0.3  3.7e-165  3.7e-165       1     393 []      33     427 ..      33     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 535.9 bits;  conditional E-value: 3.7e-165
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 
                                               v++++++vr++Gd+A+l+yt++fd++   +l++l+v++++l+eal+ + ++ +eal+laae+i+++he+
  lcl|NCBI__GCF_000423825.1:WP_028988607.1  33 VRDVLHAVREQGDRAVLDYTQRFDRLranSLAELEVPRAKLREALAGLAPADREALALAAERIRSYHER 101
                                               799**********************966677899*********************************** PP

                                 TIGR00069  67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvn 135
                                               q++es+e+++++g+ lgq+v+pl rvg+YvPgGkaaypS+vlm+a+pAkvAgv ei++v P    g++n
  lcl|NCBI__GCF_000423825.1:WP_028988607.1 102 QVAESWEYSEADGTRLGQRVTPLARVGIYVPGGKAAYPSSVLMNAIPAKVAGVAEIIMVVPAP-GGELN 169
                                               **************************************************************6.9**** PP

                                 TIGR00069 136 pavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204
                                               p vlaaa+l+gvd+v+++GGaqa+aalayGtetvp+vdkivGPGniyV++AK++vfg+vgidmiaGPsE
  lcl|NCBI__GCF_000423825.1:WP_028988607.1 170 PLVLAAAELAGVDRVFTIGGAQAVAALAYGTETVPAVDKIVGPGNIYVATAKRMVFGRVGIDMIAGPSE 238
                                               ********************************************************************* PP

                                 TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273
                                               +lvi+d +++p+++a+DllsqaEHde+aq+il++ +++ +++v ++v++ l +ler+ ia++++++++a
  lcl|NCBI__GCF_000423825.1:WP_028988607.1 239 ILVISDGQTDPDWLAMDLLSQAEHDEQAQSILISWDADCLTRVAASVDKLLPTLEREAIARQAWDSRAA 307
                                               ********************************************************************* PP

                                 TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342
                                               +ilv+d++ea+++++++ApEHLel ++dp +ll+ ++naG+vf+G+yt+ealgdyvaGpnhvLPT+g+A
  lcl|NCBI__GCF_000423825.1:WP_028988607.1 308 LILVRDAAEACAVADRIAPEHLELSVADPDALLPALHNAGAVFMGRYTAEALGDYVAGPNHVLPTAGSA 376
                                               ********************************************************************* PP

                                 TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               rf+s+l+v+dF+kr+s++++s  ++++l++a+++lae EgL+aHa++++ R
  lcl|NCBI__GCF_000423825.1:WP_028988607.1 377 RFSSPLGVYDFQKRTSIIYASAVGADQLGRAAKRLAEGEGLTAHARSAAYR 427
                                               ***********************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (432 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: 7.66
//
[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