Alignments for a candidate for hisD in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Sphingomonas koreensis DSMZ 15582

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Ga0059261_1281 Ga0059261_1281 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Korea:Ga0059261_1281
          Length = 428

 Score =  486 bits (1251), Expect = e-142
 Identities = 249/424 (58%), Positives = 311/424 (73%)

Query: 5   LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64
           L  T+P F Q F   +  +RE   DV R VR IV  VR EGD+AL  ++R+FDR DL +T
Sbjct: 4   LSTTEPGFAQAFRELVDARREADADVARDVRTIVASVRDEGDAALHAFTRKFDRHDLNET 63

Query: 65  GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAI 124
           G  + +A+  AAFDA      +AL+LA DRI  +H +Q P D   TDA GV  G+RW A+
Sbjct: 64  GWRIEKADCAAAFDALEPKLRDALQLAADRITAYHEKQKPADSDTTDAAGVRTGARWQAV 123

Query: 125 EAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEI 184
           EA G+YVPGG A+YPSSVLMNA+PAKVAGVDR+VMV P PDG +NPLVL AA +AGV EI
Sbjct: 124 EAAGVYVPGGRAAYPSSVLMNAIPAKVAGVDRLVMVTPTPDGEVNPLVLAAAHIAGVDEI 183

Query: 185 YRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVAD 244
           +RVGGAQAIAALAYGT  I  V  I GPGNA+VA AKR ++G VGIDM+AGPSE++++AD
Sbjct: 184 WRVGGAQAIAALAYGTGRIAAVDVITGPGNAWVAEAKRQLYGVVGIDMVAGPSEIVVIAD 243

Query: 245 KDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRD 304
             N+P+WIAADLL+Q+EHD  +QSIL+T+D  FA  V EAV+ Q+ TL+    A  SW  
Sbjct: 244 GKNDPEWIAADLLSQSEHDPTSQSILLTDDAIFAGKVAEAVDLQIGTLSTKGVARQSWDA 303

Query: 305 FGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVG 364
            GA+IL    ++AIPL N++A EHLE+A  D +A   R+R+AGS+F+G  TPE IGDYV 
Sbjct: 304 NGAIILTGSLDEAIPLVNKLAPEHLELACDDPDALFARVRHAGSVFLGRMTPEAIGDYVA 363

Query: 365 GCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSV 424
           G NHVLPT R ARF+SGLSVLD+MKRTS L L +  L A+GPAA+ +A AEGL AHA+SV
Sbjct: 364 GPNHVLPTGRRARFASGLSVLDFMKRTSFLALDAAGLAAIGPAAVALAEAEGLPAHARSV 423

Query: 425 AIRL 428
           ++RL
Sbjct: 424 SLRL 427


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: 512
Number of extensions: 22
Number of successful extensions: 1
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 Ga0059261_1281 Ga0059261_1281 (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.24607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-162  524.8   0.1   9.7e-162  524.6   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1281  Ga0059261_1281 histidinol dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1281  Ga0059261_1281 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.6   0.1  9.7e-162  9.7e-162       1     393 []      33     426 ..      33     426 .. 0.99

  Alignments for each domain:
  == domain 1  score: 524.6 bits;  conditional E-value: 9.7e-162
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                               v++i+++vr+eGd+Al+++t+kfd+   + +  r++++++++a +a++++l++al+laa++i+++hekq
  lcl|FitnessBrowser__Korea:Ga0059261_1281  33 VRTIVASVRDEGDAALHAFTRKFDRHdlNETGWRIEKADCAAAFDALEPKLRDALQLAADRITAYHEKQ 101
                                               899**********************95566678************************************ PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                               +p++  +++++gv +g +++++e++g+YvPgG+aaypS+vlm+a+pAkvAgv+++v+vtP+  dg+vnp
  lcl|FitnessBrowser__Korea:Ga0059261_1281 102 KPADSDTTDAAGVRTGARWQAVEAAGVYVPGGRAAYPSSVLMNAIPAKVAGVDRLVMVTPTP-DGEVNP 169
                                               *************************************************************6.****** PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                                vlaaa+++gvde+++vGGaqaiaalayGt  + +vd+i+GPGn++V++AK++++g vgidm+aGPsE+
  lcl|FitnessBrowser__Korea:Ga0059261_1281 170 LVLAAAHIAGVDEIWRVGGAQAIAALAYGTGRIAAVDVITGPGNAWVAEAKRQLYGVVGIDMVAGPSEI 238
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               +viad + +pe++aaDllsq EHd+++q+il+t+++ +a kv e+v+ q+ +l++k +a++s++ ngai
  lcl|FitnessBrowser__Korea:Ga0059261_1281 239 VVIADGKNDPEWIAADLLSQSEHDPTSQSILLTDDAIFAGKVAEAVDLQIGTLSTKGVARQSWDANGAI 307
                                               ********************************************************************* PP

                                 TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                               il+ +l+ea+ l+n++ApEHLel+++dp +l  ++++aGsvflG++tpea+gdyvaGpnhvLPT++ Ar
  lcl|FitnessBrowser__Korea:Ga0059261_1281 308 ILTGSLDEAIPLVNKLAPEHLELACDDPDALFARVRHAGSVFLGRMTPEAIGDYVAGPNHVLPTGRRAR 376
                                               ********************************************************************* PP

                                 TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               fasglsv dF+kr+s+  l+ ++l+++++a+++laeaEgL aHa++v+ R
  lcl|FitnessBrowser__Korea:Ga0059261_1281 377 FASGLSVLDFMKRTSFLALDAAGLAAIGPAAVALAEAEGLPAHARSVSLR 426
                                               ***********************************************998 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.95
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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