Alignments for a candidate for hisD in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Thioalkalivibrio denitrificans ALJD

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_077278003.1 B1C78_RS04755 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_002000365.1:WP_077278003.1
          Length = 432

 Score =  416 bits (1070), Expect = e-121
 Identities = 219/428 (51%), Positives = 295/428 (68%), Gaps = 1/428 (0%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +  L  +D DF Q+  A L+ +    E V   VREI++RVR EGD+ALL+Y+RRFDR ++
Sbjct: 4   INRLSTSDADFRQRLDALLAWEGVSDETVLATVREILNRVRDEGDAALLEYTRRFDRREI 63

Query: 62  -EKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
            +   + +    ++ A  A  +  +EAL+ A  RI ++  RQ     +YT+  G  LG +
Sbjct: 64  SDAADLEIPLFRLEQARTAISSEQLEALETAAARIRRYSERQRLSSWQYTEEDGTVLGQQ 123

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
            T ++ VGLYVPGG A+YPSSVLMNA+PAKVAGV+ ++MVVP PDG +N LVL AA +AG
Sbjct: 124 VTPLDRVGLYVPGGKAAYPSSVLMNAIPAKVAGVEELIMVVPTPDGEVNELVLAAAAVAG 183

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V  ++ VGGAQA+AALAYGT+T+  V KIVGPGN YVA AKR+VFG VGIDMIAGPSE+L
Sbjct: 184 VDRVFAVGGAQAVAALAYGTDTVPAVDKIVGPGNIYVATAKRMVFGAVGIDMIAGPSEIL 243

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           ++ D   +PDWIA DL +QAEHD  AQS+L++ D+AF   V E++++ L  + R +   A
Sbjct: 244 VICDGQTDPDWIAMDLFSQAEHDEDAQSLLVSPDKAFLDRVAESMDKLLADMPREDIIRA 303

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           S    GA+I V D ++A+ LAN IA EHLE++V++ E    RIR+AG+IF+G YT E +G
Sbjct: 304 SLAARGALIQVADMDEAVDLANLIAPEHLELSVSEPERMAGRIRHAGAIFMGRYTAEAVG 363

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY  G NHVLPT+R+ARFSS L V D+ KR+SL+   +E    LG  A  +AR EGL AH
Sbjct: 364 DYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSLINCSAEGAATLGRTASRLARGEGLVAH 423

Query: 421 AQSVAIRL 428
           A+S   R+
Sbjct: 424 ARSAEYRI 431


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: 498
Number of extensions: 21
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_077278003.1 B1C78_RS04755 (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.4074349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-166  540.3   0.0   1.8e-166  540.2   0.0    1.0  1  NCBI__GCF_002000365.1:WP_077278003.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002000365.1:WP_077278003.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.2   0.0  1.8e-166  1.8e-166       1     393 []      36     430 ..      36     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 540.2 bits;  conditional E-value: 1.8e-166
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 
                                           v+ei+++vr+eGd+Alleyt++fd+    ++++l+++  +le+a++a+++e  eale+aa++i+++ e+q+ +
  NCBI__GCF_002000365.1:WP_077278003.1  36 VREILNRVRDEGDAALLEYTRRFDRReisDAADLEIPLFRLEQARTAISSEQLEALETAAARIRRYSERQRLS 108
                                           89**********************986677889**************************************** PP

                             TIGR00069  71 sveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaak 143
                                           s+++++e+g++lgq+v+pl+rvglYvPgGkaaypS+vlm+a+pAkvAgv+e+++v P+  dg+vn+ vlaaa+
  NCBI__GCF_002000365.1:WP_077278003.1 109 SWQYTEEDGTVLGQQVTPLDRVGLYVPGGKAAYPSSVLMNAIPAKVAGVEELIMVVPTP-DGEVNELVLAAAA 180
                                           **********************************************************6.************* PP

                             TIGR00069 144 llgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpe 216
                                           ++gvd+v++vGGaqa+aalayGt+tvp+vdkivGPGniyV++AK++vfg vgidmiaGPsE+lvi+d +++p+
  NCBI__GCF_002000365.1:WP_077278003.1 181 VAGVDRVFAVGGAQAVAALAYGTDTVPAVDKIVGPGNIYVATAKRMVFGAVGIDMIAGPSEILVICDGQTDPD 253
                                           ************************************************************************* PP

                             TIGR00069 217 lvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289
                                           ++a+Dl+sqaEHdedaq++lv+++++++++v e++++ l++++r++i+++sl+ +ga+i v+d++ea++l+n 
  NCBI__GCF_002000365.1:WP_077278003.1 254 WIAMDLFSQAEHDEDAQSLLVSPDKAFLDRVAESMDKLLADMPREDIIRASLAARGALIQVADMDEAVDLANL 326
                                           ************************************************************************* PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           +ApEHLel +++pe+++ +i++aG++f+G+yt+ea+gdy+aGpnhvLPTs+tArf+s+l+v+dF+kr+s++++
  NCBI__GCF_002000365.1:WP_077278003.1 327 IAPEHLELSVSEPERMAGRIRHAGAIFMGRYTAEAVGDYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSLINC 399
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           s e++++l++++++la+ EgL aHa+++e R
  NCBI__GCF_002000365.1:WP_077278003.1 400 SAEGAATLGRTASRLARGEGLVAHARSAEYR 430
                                           ***************************9988 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.87
//
[ok]

This GapMind analysis is from Jul 25 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 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