GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Thiohalospira halophila DSM 15071 HL 3

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_093427940.1 BM272_RS06415 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_900112605.1:WP_093427940.1
          Length = 437

 Score =  399 bits (1026), Expect = e-116
 Identities = 212/423 (50%), Positives = 286/423 (67%), Gaps = 2/423 (0%)

Query: 8   TDPD-FEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGI 66
           TD D F+      L+ +    + V+  VR+I+  VR  GD+A+++ + R DR D      
Sbjct: 9   TDEDGFDAALDRLLAWEEGTDDRVEGIVRDILTDVRTRGDTAVVEQTNRLDRRDAATMAD 68

Query: 67  AVTEAE-IDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIE 125
               AE +  A +A P++  +AL+ A +RI  +H  Q  +  +YT+A G  LG + T ++
Sbjct: 69  LELPAERLQRALEALPSAQRQALETAAERIRGYHRHQCQESWQYTEADGTVLGQQVTPMD 128

Query: 126 AVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIY 185
             GLYVPGG A+YPSSVLMNA+PAKVAGV  +VMVVPAPDG LN LVL AA +AGV  ++
Sbjct: 129 RAGLYVPGGKAAYPSSVLMNALPAKVAGVGELVMVVPAPDGELNDLVLAAAAVAGVDRVF 188

Query: 186 RVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADK 245
            +GGAQA+AALAYGTET+  V KIVGPGN +VA AKR+VFGTVGIDMIAGPSE+L+V D 
Sbjct: 189 TLGGAQAVAALAYGTETVPAVDKIVGPGNIFVATAKRMVFGTVGIDMIAGPSEILVVCDG 248

Query: 246 DNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDF 305
           + +P+W+A DL +QAEHD  AQ+IL+  D A+   V EA++R L T+ R     +S    
Sbjct: 249 ETDPEWVAVDLFSQAEHDEDAQAILVCPDAAYLDRVAEAMDRLLPTMGRETIIRSSLAAR 308

Query: 306 GAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGG 365
           GA+I  +D +DA  + NR+A EHLE++VA+ EA   ++R+AG+IF+G YT E +GDY  G
Sbjct: 309 GALIQCRDLDDAAAVINRVAPEHLELSVAEPEALAAKVRHAGAIFLGRYTSESLGDYCAG 368

Query: 366 CNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVA 425
            NHVLPT+R+ARFSS L V D+ KR+SL+   +    ALGP A  +A  EGL AHA++  
Sbjct: 369 PNHVLPTSRTARFSSPLGVYDFQKRSSLIGCSAAGAAALGPTAAALADGEGLGAHAEAAR 428

Query: 426 IRL 428
            RL
Sbjct: 429 RRL 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: 542
Number of extensions: 25
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 430
Length of database: 437
Length adjustment: 32
Effective length of query: 398
Effective length of database: 405
Effective search space:   161190
Effective search space used:   161190
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_093427940.1 BM272_RS06415 (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.26833.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-161  523.3   0.2   2.7e-161  523.1   0.2    1.0  1  NCBI__GCF_900112605.1:WP_093427940.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093427940.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.1   0.2  2.7e-161  2.7e-161       1     393 []      36     430 ..      36     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.1 bits;  conditional E-value: 2.7e-161
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 
                                           v++i++dvr++Gd+A++e t+++d+    ++++l++++e+l++alea++++ ++ale+aae+i+ +h++q +e
  NCBI__GCF_900112605.1:WP_093427940.1  36 VRDILTDVRTRGDTAVVEQTNRLDRRdaaTMADLELPAERLQRALEALPSAQRQALETAAERIRGYHRHQCQE 108
                                           899*********************976668889**************************************** PP

                             TIGR00069  71 sveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaak 143
                                           s+++++++g++lgq+v+p++r+glYvPgGkaaypS+vlm+a+pAkvAgv e+v+v P   dg++n+ vlaaa+
  NCBI__GCF_900112605.1:WP_093427940.1 109 SWQYTEADGTVLGQQVTPMDRAGLYVPGGKAAYPSSVLMNALPAKVAGVGELVMVVPAP-DGELNDLVLAAAA 180
                                           **********************************************************6.************* PP

                             TIGR00069 144 llgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpe 216
                                           ++gvd+v+++GGaqa+aalayGtetvp+vdkivGPGni+V++AK++vfg+vgidmiaGPsE+lv++d +++pe
  NCBI__GCF_900112605.1:WP_093427940.1 181 VAGVDRVFTLGGAQAVAALAYGTETVPAVDKIVGPGNIFVATAKRMVFGTVGIDMIAGPSEILVVCDGETDPE 253
                                           ************************************************************************* PP

                             TIGR00069 217 lvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289
                                           +va+Dl+sqaEHdedaqailv+++++ +++v e++++ l ++ r++i+++sl+ +ga+i ++dl++a++++n+
  NCBI__GCF_900112605.1:WP_093427940.1 254 WVAVDLFSQAEHDEDAQAILVCPDAAYLDRVAEAMDRLLPTMGRETIIRSSLAARGALIQCRDLDDAAAVINR 326
                                           ************************************************************************* PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           +ApEHLel +++pe+l+ k+++aG++flG+yt+e+lgdy+aGpnhvLPTs+tArf+s+l+v+dF+kr+s++ +
  NCBI__GCF_900112605.1:WP_093427940.1 327 VAPEHLELSVAEPEALAAKVRHAGAIFLGRYTSESLGDYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSLIGC 399
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           s +++++l++++++la+ EgL aHaea++ R
  NCBI__GCF_900112605.1:WP_093427940.1 400 SAAGAAALGPTAAALADGEGLGAHAEAARRR 430
                                           ***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (437 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.29
//
[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:

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:

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:

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:

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