GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Xenophilus azovorans DSM 13620

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_038208762.1 Q392_RS14285 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000745855.1:WP_038208762.1
          Length = 463

 Score =  389 bits (998), Expect = e-112
 Identities = 208/444 (46%), Positives = 288/444 (64%), Gaps = 20/444 (4%)

Query: 5   LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64
           L      FE  F A L    +    +++ V +I+  V+R GD+A+L+Y+RRFD +     
Sbjct: 10  LSTASASFEADFKARLHWSADTDAAIEQRVADILADVQRRGDAAVLEYTRRFDGLAAGSM 69

Query: 65  G-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDR---YTDALGVELGSR 120
             + +T+A+  AAF++ PA+  +AL+ A +R+  +H  Q         Y DA G  LG +
Sbjct: 70  AQLELTQADFRAAFESLPAAQRDALRSAAERVRSYHEAQKKASGESWTYRDADGTLLGQK 129

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAP---------------- 164
            T ++ VG+YVPGG A+YPSS+LMNA+PA VAGV  I+MVVP P                
Sbjct: 130 VTPLDRVGIYVPGGKAAYPSSLLMNAIPAHVAGVQEIIMVVPTPAKGSVATGGSGTEPAA 189

Query: 165 DGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIV 224
            G  N LVL AA +AGV+  + +GGAQA+AALAYGT T+  V KI GPGNAYVAAAKR V
Sbjct: 190 QGERNVLVLAAAHVAGVTRAFTIGGAQAVAALAYGTATVPAVDKITGPGNAYVAAAKRRV 249

Query: 225 FGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEA 284
           FGTVGIDMIAGPSE+L++AD    PDW+A DL +QAEHD  AQSIL++ D A+  AV+  
Sbjct: 250 FGTVGIDMIAGPSEILVLADGSTPPDWVAMDLFSQAEHDELAQSILLSPDAAYIDAVQRE 309

Query: 285 VERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIR 344
           ++R L  + R +  +AS    GA+I  +D E+A  ++NRIA EHLE++  +   + P +R
Sbjct: 310 IDRLLPDMPRAQIIAASLTGRGALIHTRDMEEACAISNRIAPEHLEVSSREPHRWEPLLR 369

Query: 345 NAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRAL 404
           +AG+IF+G +T E +GDY  G NHVLPT+ +ARFSS L V D+ KR+SL+++  +  +AL
Sbjct: 370 HAGAIFLGAFTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSLIEVSEQGAQAL 429

Query: 405 GPAAIEIARAEGLDAHAQSVAIRL 428
           GP A E+A  EGL AHA++  +RL
Sbjct: 430 GPIAAELAYGEGLQAHARAAEMRL 453


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: 531
Number of extensions: 26
Number of successful extensions: 4
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: 463
Length adjustment: 33
Effective length of query: 397
Effective length of database: 430
Effective search space:   170710
Effective search space used:   170710
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_038208762.1 Q392_RS14285 (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.3857076.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-156  508.1   0.3     2e-155  503.8   0.3    2.0  1  NCBI__GCF_000745855.1:WP_038208762.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038208762.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.8   0.3    2e-155    2e-155       1     393 []      39     452 ..      39     452 .. 0.95

  Alignments for each domain:
  == domain 1  score: 503.8 bits;  conditional E-value: 2e-155
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 
                                           v++i++dv+++Gd+A+leyt++fd++   ++++l+++++++++a e+++++ ++al+ aae+++++he+q+++
  NCBI__GCF_000745855.1:WP_038208762.1  39 VADILADVQRRGDAAVLEYTRRFDGLaagSMAQLELTQADFRAAFESLPAAQRDALRSAAERVRSYHEAQKKA 111
                                           789**********************98888999*************************************987 PP

                             TIGR00069  71 s...veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkv...... 134
                                           s   +++++++g+llgqkv+pl+rvg+YvPgGkaaypS++lm+a+pA+vAgv+ei++v P+  +g+v      
  NCBI__GCF_000745855.1:WP_038208762.1 112 SgesWTYRDADGTLLGQKVTPLDRVGIYVPGGKAAYPSSLLMNAIPAHVAGVQEIIMVVPTPAKGSVatggsg 184
                                           6677******************************************************997655544122222 PP

                             TIGR00069 135 .........npavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidm 198
                                                    n  vlaaa+++gv++ +++GGaqa+aalayGt+tvp+vdki+GPGn+yV+aAK+ vfg+vgidm
  NCBI__GCF_000745855.1:WP_038208762.1 185 tepaaqgerNVLVLAAAHVAGVTRAFTIGGAQAVAALAYGTATVPAVDKITGPGNAYVAAAKRRVFGTVGIDM 257
                                           2111111115679************************************************************ PP

                             TIGR00069 199 iaGPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekn 271
                                           iaGPsE+lv+ad s+ p++va+Dl+sqaEHde aq+il++++++ +++v++e+++ l +++r++i+ +sl+ +
  NCBI__GCF_000745855.1:WP_038208762.1 258 IAGPSEILVLADGSTPPDWVAMDLFSQAEHDELAQSILLSPDAAYIDAVQREIDRLLPDMPRAQIIAASLTGR 330
                                           ************************************************************************* PP

                             TIGR00069 272 gaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArf 344
                                           ga+i ++d+eea+++sn++ApEHLe+  ++p+++ + +++aG++flG+ t+e+lgdy+aGpnhvLPTsgtArf
  NCBI__GCF_000745855.1:WP_038208762.1 331 GALIHTRDMEEACAISNRIAPEHLEVSSREPHRWEPLLRHAGAIFLGAFTSESLGDYCAGPNHVLPTSGTARF 403
                                           ************************************************************************* PP

                             TIGR00069 345 asglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                           +s+l+v+dF+kr+s++e+s++++++l++ +++la  EgL+aHa+a+e+R
  NCBI__GCF_000745855.1:WP_038208762.1 404 SSPLGVYDFQKRSSLIEVSEQGAQALGPIAAELAYGEGLQAHARAAEMR 452
                                           **********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (463 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: 14.66
//
[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