GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Chlorobaculum parvum NCIB 8327

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012502672.1 CPAR_RS07305 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000020505.1:WP_012502672.1
          Length = 428

 Score =  334 bits (857), Expect = 3e-96
 Identities = 185/422 (43%), Positives = 257/422 (60%), Gaps = 3/422 (0%)

Query: 8   TDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIA 67
           T P  E      L+       +  + V EI+ RVR EGD A+LDY+ RF  + LE   + 
Sbjct: 6   TFPQDEAALKEQLNRTVSFDPEAQKTVDEILHRVRTEGDKAILDYTERFQGVRLES--MM 63

Query: 68  VTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAV 127
           V + EIDAA+  +    +  L+ A   I   H  +  K   Y    GV LG R T +E  
Sbjct: 64  VPQEEIDAAYAESDPEFISILEEAYANITAFHRNEAEKSFFYEQKGGVILGQRVTPMEKA 123

Query: 128 GLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAP-DGNLNPLVLVAARLAGVSEIYR 186
            LYVPGG A+YPSSVLMNA PA+VAGVD I M  P   +G +NP +L AA++AG++ +YR
Sbjct: 124 LLYVPGGKAAYPSSVLMNAAPAQVAGVDEIYMTTPCDAEGKVNPHILAAAKVAGITSVYR 183

Query: 187 VGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKD 246
           +GGAQA+AA AYGT +I  V  + GPGN YVA AK+ VFG V ID IAGPSEV+++AD+ 
Sbjct: 184 LGGAQAVAAFAYGTASIPKVDIVTGPGNKYVALAKKQVFGHVSIDSIAGPSEVVVIADEK 243

Query: 247 NNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFG 306
            +P++I  D+ AQAEHD  A ++L+T   A A AV+EA  R   T+ R E  + +  D G
Sbjct: 244 ADPEFIVMDMFAQAEHDPDASAVLITPSAAVAKAVQEAAARLASTMLRGEVITKALTDNG 303

Query: 307 AVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGC 366
            +++    ++A  +++ IA EHLE+ V +    +P +R+AG+IF+G ++ E +GDY  G 
Sbjct: 304 GIVVTNSMQEACKVSDMIAPEHLELHVENPWEILPDLRHAGAIFMGPWSCETVGDYFAGP 363

Query: 367 NHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAI 426
           NH LPT  +ARF S LSV D++K TS++     +L   G      A  EGL AHA++V +
Sbjct: 364 NHTLPTNGTARFFSPLSVRDFVKHTSIIAWSKGELGRAGEKIARFADHEGLQAHAEAVRV 423

Query: 427 RL 428
           RL
Sbjct: 424 RL 425


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: 396
Number of extensions: 20
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: 428
Length adjustment: 32
Effective length of query: 398
Effective length of database: 396
Effective search space:   157608
Effective search space used:   157608
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_012502672.1 CPAR_RS07305 (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.1319074.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-166  540.8   2.3   1.3e-166  540.6   2.3    1.0  1  NCBI__GCF_000020505.1:WP_012502672.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020505.1:WP_012502672.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.6   2.3  1.3e-166  1.3e-166       1     393 []      32     424 ..      32     424 .. 1.00

  Alignments for each domain:
  == domain 1  score: 540.6 bits;  conditional E-value: 1.3e-166
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 
                                           v ei+++vr+eGd+A+l+yte+f++v+les+ v++ee+++a+++ d+e+++ le+a++ni++fh+++ ++s++
  NCBI__GCF_000020505.1:WP_012502672.1  32 VDEILHRVRTEGDKAILDYTERFQGVRLESMMVPQEEIDAAYAESDPEFISILEEAYANITAFHRNEAEKSFF 104
                                           789********************************************************************** PP

                             TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllg 146
                                           +e++ gv+lgq+v+p+e++ lYvPgGkaaypS+vlm+a pA+vAgv+ei+++tP + +gkvnp++laaak++g
  NCBI__GCF_000020505.1:WP_012502672.1 105 YEQKGGVILGQRVTPMEKALLYVPGGKAAYPSSVLMNAAPAQVAGVDEIYMTTPCDAEGKVNPHILAAAKVAG 177
                                           ************************************************************************* PP

                             TIGR00069 147 vdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelva 219
                                           +++vy++GGaqa+aa+ayGt+++pkvd+++GPGn+yV+ AKk+vfg+v+id+iaGPsEv+viade+a+pe+++
  NCBI__GCF_000020505.1:WP_012502672.1 178 ITSVYRLGGAQAVAAFAYGTASIPKVDIVTGPGNKYVALAKKQVFGHVSIDSIAGPSEVVVIADEKADPEFIV 250
                                           ************************************************************************* PP

                             TIGR00069 220 aDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyAp 292
                                           +D+++qaEHd+da+a+l+t+s+++a++v+e+ ++ ++++ r e+++k+l++ng i+++++++ea+++s+ +Ap
  NCBI__GCF_000020505.1:WP_012502672.1 251 MDMFAQAEHDPDASAVLITPSAAVAKAVQEAAARLASTMLRGEVITKALTDNGGIVVTNSMQEACKVSDMIAP 323
                                           ************************************************************************* PP

                             TIGR00069 293 EHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelske 365
                                           EHLel++++p+e+l+++++aG++f+G++++e++gdy+aGpnh+LPT+gtArf s+lsv+dF+k++s++  sk 
  NCBI__GCF_000020505.1:WP_012502672.1 324 EHLELHVENPWEILPDLRHAGAIFMGPWSCETVGDYFAGPNHTLPTNGTARFFSPLSVRDFVKHTSIIAWSKG 396
                                           ************************************************************************* PP

                             TIGR00069 366 aleelaeaveklaeaEgLeaHaeavevR 393
                                           +l + +e+++++a+ EgL+aHaeav+vR
  NCBI__GCF_000020505.1:WP_012502672.1 397 ELGRAGEKIARFADHEGLQAHAEAVRVR 424
                                           **************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (428 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: 17.05
//
[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