GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Azorhizobium caulinodans ORS 571

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012171673.1 AZC_RS16245 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000010525.1:WP_012171673.1
          Length = 430

 Score =  552 bits (1422), Expect = e-162
 Identities = 285/418 (68%), Positives = 327/418 (78%), Gaps = 1/418 (0%)

Query: 12  FEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEA 71
           F   FA FL+ KRE S DV  AV +I+  VR  GD+AL+DYSR FDR++LE   I VTEA
Sbjct: 12  FPDAFATFLASKREASTDVAVAVADIIAGVRARGDAALIDYSRTFDRVELEGR-IRVTEA 70

Query: 72  EIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYV 131
           EI+AA    P  T EALK A+ RIE HHARQLP D+RYTDA+GVELG RWT ++AVGLYV
Sbjct: 71  EIEAALAEVPQDTFEALKFAKARIEAHHARQLPADERYTDAVGVELGQRWTPVDAVGLYV 130

Query: 132 PGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRVGGAQ 191
           PGGTA+YPSSVLMNA+PAKVAGV R+ MVVP+PDG + PLVL AARLAGV E+YRVGGAQ
Sbjct: 131 PGGTAAYPSSVLMNAVPAKVAGVPRVAMVVPSPDGVIAPLVLAAARLAGVDEVYRVGGAQ 190

Query: 192 AIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDW 251
           A+AALAYGTETI PV KIVGPGNAYVAAAKR VFG VGIDMIAGPSEVLI+AD + N  W
Sbjct: 191 AVAALAYGTETIAPVDKIVGPGNAYVAAAKRQVFGKVGIDMIAGPSEVLILADGNANAAW 250

Query: 252 IAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILV 311
           IAADLLAQAEHD AAQSIL+T+    A AV  AVE QL TL R E A ASWRD GA+ILV
Sbjct: 251 IAADLLAQAEHDAAAQSILVTDSPVLADAVTRAVEAQLTTLPRREIAEASWRDHGAIILV 310

Query: 312 KDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLP 371
              ++A+PL +R+A EHLEI   DA+A   RIR+AG+IF+G YTPE IGDYVGG NHVLP
Sbjct: 311 GSMDEALPLVDRVAPEHLEIHADDADALADRIRHAGAIFVGAYTPEAIGDYVGGTNHVLP 370

Query: 372 TARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRLN 429
           TARSARFSSGL V D++KRTS+LK     L  +GPAA+ +A  E LDAH +S+ IR N
Sbjct: 371 TARSARFSSGLGVYDFLKRTSILKCSPASLNVIGPAAVRLAEVERLDAHGRSILIRTN 428


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: 586
Number of extensions: 22
Number of successful extensions: 2
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: 430
Length adjustment: 32
Effective length of query: 398
Effective length of database: 398
Effective search space:   158404
Effective search space used:   158404
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_012171673.1 AZC_RS16245 (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.666145.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-167  542.5   3.5   3.9e-167  542.4   3.5    1.0  1  NCBI__GCF_000010525.1:WP_012171673.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012171673.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.4   3.5  3.9e-167  3.9e-167       1     393 []      34     426 ..      34     426 .. 0.99

  Alignments for each domain:
  == domain 1  score: 542.4 bits;  conditional E-value: 3.9e-167
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkle.slrvseeeleealeavdeelkealelaaeniekfhekqlpesv 72 
                                           v++ii+ vr++Gd+Al++y+++fd+v+le ++rv+e+e+e+al++v++++ eal+ a+++ie+ h++qlp++ 
  NCBI__GCF_000010525.1:WP_012171673.1  34 VADIIAGVRARGDAALIDYSRTFDRVELEgRIRVTEAEIEAALAEVPQDTFEALKFAKARIEAHHARQLPADE 106
                                           789***********************87658****************************************** PP

                             TIGR00069  73 eveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakll 145
                                            ++++ gv lgq+++p+++vglYvPgG+aaypS+vlm+avpAkvAgv+++++v P   dg ++p vlaaa+l+
  NCBI__GCF_000010525.1:WP_012171673.1 107 RYTDAVGVELGQRWTPVDAVGLYVPGGTAAYPSSVLMNAVPAKVAGVPRVAMVVPSP-DGVIAPLVLAAARLA 178
                                           ********************************************************6.*************** PP

                             TIGR00069 146 gvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelv 218
                                           gvdevy+vGGaqa+aalayGtet+ +vdkivGPGn+yV+aAK++vfg+vgidmiaGPsEvl++ad +an++++
  NCBI__GCF_000010525.1:WP_012171673.1 179 GVDEVYRVGGAQAVAALAYGTETIAPVDKIVGPGNAYVAAAKRQVFGKVGIDMIAGPSEVLILADGNANAAWI 251
                                           ************************************************************************* PP

                             TIGR00069 219 aaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyA 291
                                           aaDll+qaEHd+ aq+ilvt+s  la++v+++ve+ql++l+r+eiae+s++++gaiilv +++eal l++++A
  NCBI__GCF_000010525.1:WP_012171673.1 252 AADLLAQAEHDAAAQSILVTDSPVLADAVTRAVEAQLTTLPRREIAEASWRDHGAIILVGSMDEALPLVDRVA 324
                                           ************************************************************************* PP

                             TIGR00069 292 pEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelsk 364
                                           pEHLe++++d+ +l+++i++aG++f+G+ytpea+gdyv G+nhvLPT+++Arf+sgl+v+dFlkr+s+ ++s 
  NCBI__GCF_000010525.1:WP_012171673.1 325 PEHLEIHADDADALADRIRHAGAIFVGAYTPEAIGDYVGGTNHVLPTARSARFSSGLGVYDFLKRTSILKCSP 397
                                           ************************************************************************* PP

                             TIGR00069 365 ealeelaeaveklaeaEgLeaHaeavevR 393
                                           ++l+ +++a+++lae+E L+aH +++ +R
  NCBI__GCF_000010525.1:WP_012171673.1 398 ASLNVIGPAAVRLAEVERLDAHGRSILIR 426
                                           **************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (430 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: 25.32
//
[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