Alignments for a candidate for hisD in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Derxia gummosa DSM 723

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_028312397.1 H566_RS0117145 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000482785.1:WP_028312397.1
          Length = 445

 Score =  404 bits (1038), Expect = e-117
 Identities = 212/437 (48%), Positives = 293/437 (67%), Gaps = 9/437 (2%)

Query: 1   MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60
           ++  L  +D DF  K    L+ + E    ++ AV  I+  VR+ GD A+LDY+R+FDR++
Sbjct: 5   LIHRLATSDADFTAKLDHLLAFEAETDAAIESAVASILADVRKRGDEAVLDYTRKFDRVE 64

Query: 61  L-EKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDD---RYTDALGVE 116
                 + +  AE+DAA  A PA    AL+ A +R+ ++HA QL K     +Y DA G  
Sbjct: 65  AGSMAALEIGRAELDAALAAIPAEVRAALEAAAERVREYHAIQLDKTAGSFQYHDADGTL 124

Query: 117 LGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAA 176
           LG + T ++ VGLYVPGG A+YPSS+LM+A+PA+VAGV  ++MV P P G  N  VL AA
Sbjct: 125 LGQKVTPLDRVGLYVPGGKAAYPSSILMDAVPARVAGVGELIMVTPTPGGVRNDTVLAAA 184

Query: 177 RLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGP 236
            +AGV  ++ +GGAQA+ ALAYGT T+  V KIVGPGNAYVA AKR VFG  GIDMIAGP
Sbjct: 185 AIAGVDRVFAIGGAQAVGALAYGTATVPKVDKIVGPGNAYVAEAKRRVFGVCGIDMIAGP 244

Query: 237 SEVLIVADKDNNP-----DWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHT 291
           SE+L++ D D        DW+A DL +QAEHD  AQ+IL+T   AFA  VE A+ R L T
Sbjct: 245 SEILVICDGDTAAIPQLADWVAIDLFSQAEHDELAQAILLTPSAAFADEVEAAIARLLPT 304

Query: 292 LARTETASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFI 351
           + R E  + S R+ GA+++V+D E+A  +ANR+A EH+E++VAD  A +P +++AG+IF+
Sbjct: 305 MPRREIIATSLRNRGAIVVVRDLEEAAAVANRVAPEHMEVSVADPHALLPLLKHAGAIFL 364

Query: 352 GGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEI 411
           G YT E +GDY  G NHVLPT+ +ARFSS L V D++KR+SL+ + +   + LG  A  +
Sbjct: 365 GRYTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFIKRSSLIDVSAAGAQKLGRIASTL 424

Query: 412 ARAEGLDAHAQSVAIRL 428
           A +EGL AHA++  +RL
Sbjct: 425 AHSEGLTAHARAAELRL 441


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: 506
Number of extensions: 28
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: 445
Length adjustment: 32
Effective length of query: 398
Effective length of database: 413
Effective search space:   164374
Effective search space used:   164374
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_028312397.1 H566_RS0117145 (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.4172809.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-160  519.2   2.2   4.8e-160  519.0   2.2    1.0  1  NCBI__GCF_000482785.1:WP_028312397.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_028312397.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.0   2.2  4.8e-160  4.8e-160       1     393 []      38     440 ..      38     440 .. 0.97

  Alignments for each domain:
  == domain 1  score: 519.0 bits;  conditional E-value: 4.8e-160
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 
                                           v++i++dvrk+GdeA+l+yt+kfd+v   ++++l++ ++el++al+a+++e+++ale+aae+++++h+ ql++
  NCBI__GCF_000482785.1:WP_028312397.1  38 VASILADVRKRGDEAVLDYTRKFDRVeagSMAALEIGRAELDAALAAIPAEVRAALEAAAERVREYHAIQLDK 110
                                           789***********************777778999************************************88 PP

                             TIGR00069  71 s...veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavla 140
                                           +   +++++++g+llgqkv+pl+rvglYvPgGkaaypS++lm avpA+vAgv e+++vtP+   g  n++vla
  NCBI__GCF_000482785.1:WP_028312397.1 111 TagsFQYHDADGTLLGQKVTPLDRVGLYVPGGKAAYPSSILMDAVPARVAGVGELIMVTPTP-GGVRNDTVLA 182
                                           767799*******************************************************6.8999****** PP

                             TIGR00069 141 aakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesa 213
                                           aa+++gvd+v+++GGaqa++alayGt+tvpkvdkivGPGn+yV++AK+ vfg +gidmiaGPsE+lvi+d ++
  NCBI__GCF_000482785.1:WP_028312397.1 183 AAAIAGVDRVFAIGGAQAVGALAYGTATVPKVDKIVGPGNAYVAEAKRRVFGVCGIDMIAGPSEILVICDGDT 255
                                           *********************************************************************9876 PP

                             TIGR00069 214 n.....pelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddle 281
                                                 +++va Dl+sqaEHde aqail+t+s+++a++ve+++++ l +++r+ei+ +sl+++gai++v+dle
  NCBI__GCF_000482785.1:WP_028312397.1 256 AaipqlADWVAIDLFSQAEHDELAQAILLTPSAAFADEVEAAIARLLPTMPRREIIATSLRNRGAIVVVRDLE 328
                                           52333358***************************************************************** PP

                             TIGR00069 282 ealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFl 354
                                           ea++++n++ApEH+e+ ++dp++ll+ +k+aG++flG+yt+e+lgdy+aGpnhvLPTsgtArf+s+l+v+dF+
  NCBI__GCF_000482785.1:WP_028312397.1 329 EAAAVANRVAPEHMEVSVADPHALLPLLKHAGAIFLGRYTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFI 401
                                           ************************************************************************* PP

                             TIGR00069 355 krisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                           kr+s++++s +++++l++ +++la+ EgL+aHa+a+e R
  NCBI__GCF_000482785.1:WP_028312397.1 402 KRSSLIDVSAAGAQKLGRIASTLAHSEGLTAHARAAELR 440
                                           ***********************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (445 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: 22.50
//
[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