Alignments for a candidate for hisD in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Halomonas desiderata SP1

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate WP_086508840.1 BZY95_RS04815 histidinol dehydrogenase

Query= curated2:Q9RH05
         (430 letters)



>NCBI__GCF_002151265.1:WP_086508840.1
          Length = 436

 Score =  291 bits (745), Expect = 3e-83
 Identities = 165/413 (39%), Positives = 249/413 (60%), Gaps = 5/413 (1%)

Query: 21  DERRESEGDVSRDVSAIIADVKKRGDVAIAELTQKFDRHDLNKGGWQLTQEEIKKACDSL 80
           + R E++  V   V   +  ++ RGD A+ EL++KFDR   +   ++L+Q EI++A   L
Sbjct: 12  EARAEADRKVRETVEQTLQAIETRGDEAVRELSEKFDRW--SPATFRLSQAEIERAISEL 69

Query: 81  PSELMDALKLAATRIRYCHENQLP--ESSEMTDAAGVRMGVRWQAVEAAGLYVPGGRAAY 138
            ++ +D ++ A  +IR   E QL   +  E+    GV +G +   V + G YVPGG    
Sbjct: 70  TAQELDDIRFAQAQIRRFAEAQLASMQDVEVETRPGVVLGHKHIPVNSVGCYVPGGAYPM 129

Query: 139 CSSVLMNAVPAKVAGVKRLVMVTPTPDGFVNPAVIAAAVISEVDEIWKIGGAQAVAALAL 198
            +S  M+ + AKVAGVKR++   P   G  +PA++AA  ++  DEI  +GG QAV A+A+
Sbjct: 130 VASAHMSVLTAKVAGVKRVIAAAPPYQGKPHPAIVAAMHLAGADEILVLGGVQAVGAMAI 189

Query: 199 GTEKIKPVDVVVGPGNAWVAEAKRQLYGQVGIDMVAGPSEIVVVADKDNDPEWLAADLLS 258
           GTE I+ VD++VGPGNA+VAEAKRQL+G+VGID+ AGP+E +V+AD+  D    A DLL 
Sbjct: 190 GTESIEAVDMLVGPGNAFVAEAKRQLFGRVGIDLFAGPTETLVIADETVDGLLCATDLLG 249

Query: 259 QAEHDPTSQSILISDSEDLIEKTIEAVGRRLEKLETQKVARESWDKHGATILVQSLDEAP 318
           QAEH PTS + L+++SE L + T+ A+   L KL T ++AR++W+ +G  I+  S +E  
Sbjct: 250 QAEHGPTSPAALLTNSEALAKATLTAIDELLAKLPTAEIARQAWNDYGEVIVCDSHEEML 309

Query: 319 ALVDRLAPEHLELAVADPDALFANVHHSGSVFLGRYTPEAIGDYVGGPNHVLPTGRRARF 378
            + D +A EH+++   DP+     + + G++FLG  T  A GD V G NH LPT + AR+
Sbjct: 310 QVADEMAYEHVQVMTEDPNLYLDRLTNYGALFLGPRTNVAYGDKVIGTNHTLPTRKAARY 369

Query: 379 SSGLSVIDFMKRTTYLN-CSQEALSKIGPAAVTLAKAEGLPAHAESVISRLNK 430
           + GL V  F+K  TY    + EA ++IG     L   EG   H E    R+ +
Sbjct: 370 TGGLWVGKFLKTCTYQKVLTDEASAEIGSYCSRLCALEGFAGHGEQANERVRR 422


Lambda     K      H
   0.316    0.132    0.377 

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: 439
Number of extensions: 15
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: 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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_086508840.1 BZY95_RS04815 (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.32257.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.1e-139  449.1   0.4   9.5e-139  448.9   0.4    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508840.1  BZY95_RS04815 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508840.1  BZY95_RS04815 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.9   0.4  9.5e-139  9.5e-139       1     393 []      25     419 ..      25     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 448.9 bits;  conditional E-value: 9.5e-139
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlp 69 
                                               v++ +++++++GdeA++e++ekfd+++++++r+s++e+e+a ++++++  ++++ a+++i++f+e+ql+
  lcl|NCBI__GCF_002151265.1:WP_086508840.1  25 VEQTLQAIETRGDEAVRELSEKFDRWSPATFRLSQAEIERAISELTAQELDDIRFAQAQIRRFAEAQLA 93 
                                               788899*************************************************************97 PP

                                 TIGR00069  70 es..veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                               +   vevet++gv+lg+k  p+++vg+YvPgG +++++++ m +++AkvAgvk++++++Pp  +gk +p
  lcl|NCBI__GCF_002151265.1:WP_086508840.1  94 SMqdVEVETRPGVVLGHKHIPVNSVGCYVPGGAYPMVASAHMSVLTAKVAGVKRVIAAAPPY-QGKPHP 161
                                               64459********************************************************6.9***** PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                               a++aa++l+g+de++ +GG+qa++a+a Gte++++vd++vGPGn++V++AK+++fg+vgid++aGP+E 
  lcl|NCBI__GCF_002151265.1:WP_086508840.1 162 AIVAAMHLAGADEILVLGGVQAVGAMAIGTESIEAVDMLVGPGNAFVAEAKRQLFGRVGIDLFAGPTET 230
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               lviade+ +  l+a+Dll qaEH++++ a+l+t+se+la+++ ++++e l++l+++eia+++++++g++
  lcl|NCBI__GCF_002151265.1:WP_086508840.1 231 LVIADETVDGLLCATDLLGQAEHGPTSPAALLTNSEALAKATLTAIDELLAKLPTAEIARQAWNDYGEV 299
                                               ********************************************************************* PP

                                 TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                               i++d+ ee+l++++e+A EH++++t+dp+ +l++++n+G++flG+ t +a+gd+v G+nh+LPT ++Ar
  lcl|NCBI__GCF_002151265.1:WP_086508840.1 300 IVCDSHEEMLQVADEMAYEHVQVMTEDPNLYLDRLTNYGALFLGPRTNVAYGDKVIGTNHTLPTRKAAR 368
                                               ********************************************************************* PP

                                 TIGR00069 344 fasglsvedFlkrisvqel.skealeelaeaveklaeaEgLeaHaeavevR 393
                                               +++gl+v +Flk++++q++ + ea +e+++ +++l+++Eg++ H e ++ R
  lcl|NCBI__GCF_002151265.1:WP_086508840.1 369 YTGGLWVGKFLKTCTYQKVlTDEASAEIGSYCSRLCALEGFAGHGEQANER 419
                                               *****************963788999*******************998776 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: 10.25
//
[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