Alignments for a candidate for hisD in Maridesulfovibrio zosterae DSM 11974

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Maridesulfovibrio zosterae DSM 11974

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_027722801.1 H589_RS0115100 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000425265.1:WP_027722801.1
          Length = 434

 Score =  311 bits (796), Expect = 3e-89
 Identities = 175/403 (43%), Positives = 247/403 (61%), Gaps = 4/403 (0%)

Query: 30  VDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDAAPASTVEALK 89
           VD  V++I+  V+  G+ AL++Y++++D  +  +  + V+   +  A+       +E ++
Sbjct: 31  VDGIVKDILANVKNNGNQALIEYTQKYDCPEFTQEMLKVSLDSVRLAYAEVETEDLEIIE 90

Query: 90  LARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASYP---SSVLMNA 146
            A   I   H +Q+ +    T   G  LG     ++ VGLYVPGG        SS++MNA
Sbjct: 91  EAIRNIRNFHRKQVEESWWTTGEDGTILGQLVRPVDRVGLYVPGGQGGETPLISSMIMNA 150

Query: 147 MPAKVAGVDRIVMVVPA-PDGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRP 205
           +PA+VAGV  I ++ P   DG LNP +L  A++ G+ EIY  G A AI ALAYGT+TI P
Sbjct: 151 VPAQVAGVKEIAVISPPRKDGTLNPYILATAQVLGIKEIYASGSAWAIGALAYGTQTIAP 210

Query: 206 VAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTA 265
              I GPGN +VA AK  + G VGIDMIAGPSEV I+AD +++P W+AADLL+QAEHD  
Sbjct: 211 CDVIAGPGNIFVATAKGQLVGEVGIDMIAGPSEVAILADGNSDPAWLAADLLSQAEHDPL 270

Query: 266 AQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIA 325
           A SIL+T D+     V+  ++RQ   L R+E A  S  D+GA++ V D +  I   N +A
Sbjct: 271 AASILITWDKDLGAKVKAELKRQADLLPRSEIAFKSLEDWGAIVTVPDRDTGINFVNNMA 330

Query: 326 AEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVL 385
            EHLE+A  D  + +  I++AG+IF+G +TPE +GDY  G NHVLPT  +ARFSS LSV 
Sbjct: 331 PEHLELAFEDPWSALGLIKHAGAIFMGHFTPEPVGDYFAGPNHVLPTVGTARFSSALSVE 390

Query: 386 DYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428
            + K+TSL+      +   G     +AR EGL+AHA+SV  RL
Sbjct: 391 TFTKKTSLIYTDQNYVTRHGGKIARLARLEGLEAHARSVETRL 433


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: 425
Number of extensions: 24
Number of successful extensions: 5
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: 434
Length adjustment: 32
Effective length of query: 398
Effective length of database: 402
Effective search space:   159996
Effective search space used:   159996
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_027722801.1 H589_RS0115100 (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.523813.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.8e-158  511.6   0.0   9.9e-158  511.4   0.0    1.0  1  NCBI__GCF_000425265.1:WP_027722801.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027722801.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.4   0.0  9.9e-158  9.9e-158       1     393 []      35     432 ..      35     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 511.4 bits;  conditional E-value: 9.9e-158
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 
                                           vk+i+++v+++G++Al+eyt+k+d    ++e l+vs ++++ a+++v+ e  e +e+a++ni++fh+kq++es
  NCBI__GCF_000425265.1:WP_027722801.1  35 VKDILANVKNNGNQALIEYTQKYDCPefTQEMLKVSLDSVRLAYAEVETEDLEIIEEAIRNIRNFHRKQVEES 107
                                           89**********************87668999***************************************** PP

                             TIGR00069  72 veveteegvllgqkvrplervglYvPgGk...aaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaa 141
                                           + ++ e+g++lgq+vrp++rvglYvPgG+   ++++S+++m+avpA+vAgvkei+v++Pp+kdg++np +la+
  NCBI__GCF_000425265.1:WP_027722801.1 108 WWTTGEDGTILGQLVRPVDRVGLYVPGGQggeTPLISSMIMNAVPAQVAGVKEIAVISPPRKDGTLNPYILAT 180
                                           **************************9765559**************************************** PP

                             TIGR00069 142 akllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesan 214
                                           a++lg++e+y+ G a ai+alayGt+t+ ++d+i+GPGni+V++AK +++gevgidmiaGPsEv+++ad +++
  NCBI__GCF_000425265.1:WP_027722801.1 181 AQVLGIKEIYASGSAWAIGALAYGTQTIAPCDVIAGPGNIFVATAKGQLVGEVGIDMIAGPSEVAILADGNSD 253
                                           ************************************************************************* PP

                             TIGR00069 215 pelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealels 287
                                           p+++aaDllsqaEHd+ a++il+t +++l +kv++e+++q++ l+r+eia ksle+ gai++v d +  ++++
  NCBI__GCF_000425265.1:WP_027722801.1 254 PAWLAADLLSQAEHDPLAASILITWDKDLGAKVKAELKRQADLLPRSEIAFKSLEDWGAIVTVPDRDTGINFV 326
                                           ************************************************************************* PP

                             TIGR00069 288 neyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvq 360
                                           n++ApEHLel+ +dp++ l  ik+aG++f+G+ tpe++gdy+aGpnhvLPT gtArf+s+lsve+F+k++s++
  NCBI__GCF_000425265.1:WP_027722801.1 327 NNMAPEHLELAFEDPWSALGLIKHAGAIFMGHFTPEPVGDYFAGPNHVLPTVGTARFSSALSVETFTKKTSLI 399
                                           ************************************************************************* PP

                             TIGR00069 361 elskealeelaeaveklaeaEgLeaHaeavevR 393
                                           +++++ +++ + ++++la++EgLeaHa++ve+R
  NCBI__GCF_000425265.1:WP_027722801.1 400 YTDQNYVTRHGGKIARLARLEGLEAHARSVETR 432
                                           *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (434 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: 21.61
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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