Alignments for a candidate for hisD in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Phaeobacter inhibens BS107

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate GFF3068 PGA1_c31190 histidinol dehydrogenase HisD

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Phaeo:GFF3068
          Length = 433

 Score =  512 bits (1319), Expect = e-150
 Identities = 258/429 (60%), Positives = 326/429 (75%)

Query: 1   MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60
           M   L  +D  F+Q FA  L  KRE S DVD  V +I+  VR  GD+AL++ + +FDR+ 
Sbjct: 1   MPVFLNASDAGFDQAFATLLGAKREDSPDVDAVVADIIADVRTRGDAALIELTAKFDRLQ 60

Query: 61  LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
           L    + +++AEIDAA          AL+LA +RI  +H RQ+P+   + D  G  LG R
Sbjct: 61  LTADQLRISDAEIDAAIQDVSTEERVALELAVERIRAYHLRQMPQGAEWQDDAGASLGWR 120

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
           W+A+ A GLYVPGG ASYPSSVLMNA+PAKVAGV+R+ +VVP PDG +NPLVL+AARL+G
Sbjct: 121 WSAVSAAGLYVPGGLASYPSSVLMNAVPAKVAGVERLAVVVPTPDGQINPLVLLAARLSG 180

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V EIYRVGGAQA+AALAYGTE+I PV KI GPGNA+VAAAKR VFG VGIDMIAGPSE+L
Sbjct: 181 VDEIYRVGGAQAVAALAYGTESIAPVDKITGPGNAFVAAAKRRVFGKVGIDMIAGPSEIL 240

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           ++ADKDN+PDWIA DLL+QAEHD +AQSIL+T+DEAF  +V +AVE +L TL R+  A  
Sbjct: 241 VIADKDNDPDWIALDLLSQAEHDESAQSILITDDEAFGRSVADAVEARLQTLERSAIAGP 300

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           SWRD+GAVI+V D + A  L+NRIA EHLE+ VADA A   +  +AG+IF+G YTPE IG
Sbjct: 301 SWRDYGAVIVVPDLDVAAQLSNRIAPEHLELCVADARALSEKTIHAGAIFLGQYTPEAIG 360

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY+GG NHVLPTARSARFSSGLSV+D++KRT+L ++  + LRA+GPAA  +A++E L+AH
Sbjct: 361 DYIGGPNHVLPTARSARFSSGLSVMDFLKRTTLSEMTPDALRAIGPAAETLAKSESLEAH 420

Query: 421 AQSVAIRLN 429
             S+  RL+
Sbjct: 421 GLSIRARLD 429


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: 549
Number of extensions: 18
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: 433
Length adjustment: 32
Effective length of query: 398
Effective length of database: 401
Effective search space:   159598
Effective search space used:   159598
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 GFF3068 PGA1_c31190 (histidinol dehydrogenase HisD)
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.15016.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.1e-162  525.2   0.1     7e-162  525.0   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3068  PGA1_c31190 histidinol dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3068  PGA1_c31190 histidinol dehydrogenase HisD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.0   0.1    7e-162    7e-162       1     393 []      34     427 ..      34     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 525.0 bits;  conditional E-value: 7e-162
                          TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesvev 74 
                                        v++ii+dvr++Gd+Al+e+t kfd++  ++++lr+s++e+++a + v+ e + alela+e+i+++h +q+p+  e 
  lcl|FitnessBrowser__Phaeo:GFF3068  34 VADIIADVRTRGDAALIELTAKFDRLqlTADQLRISDAEIDAAIQDVSTEERVALELAVERIRAYHLRQMPQGAEW 109
                                        789*********************9877899********************************************* PP

                          TIGR00069  75 eteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdev 150
                                        ++ +g  lg ++ +++++glYvPgG a+ypS+vlm+avpAkvAgv++++vv P+  dg++np vl aa+l gvde+
  lcl|FitnessBrowser__Phaeo:GFF3068 110 QDDAGASLGWRWSAVSAAGLYVPGGLASYPSSVLMNAVPAKVAGVERLAVVVPTP-DGQINPLVLLAARLSGVDEI 184
                                        ******************************************************6.******************** PP

                          TIGR00069 151 ykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqa 226
                                        y+vGGaqa+aalayGte++ +vdki+GPGn++V+aAK+ vfg+vgidmiaGPsE+lviad++ +p+++a+Dllsqa
  lcl|FitnessBrowser__Phaeo:GFF3068 185 YRVGGAQAVAALAYGTESIAPVDKITGPGNAFVAAAKRRVFGKVGIDMIAGPSEILVIADKDNDPDWIALDLLSQA 260
                                        **************************************************************************** PP

                          TIGR00069 227 EHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdp 302
                                        EHde+aq+il+t++e++ ++v ++ve++l++ler+ ia  s++++ga+i+v dl+ a++lsn++ApEHLel+++d+
  lcl|FitnessBrowser__Phaeo:GFF3068 261 EHDESAQSILITDDEAFGRSVADAVEARLQTLERSAIAGPSWRDYGAVIVVPDLDVAAQLSNRIAPEHLELCVADA 336
                                        **************************************************************************** PP

                          TIGR00069 303 eellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeavekla 378
                                        ++l +k  +aG++flG+ytpea+gdy+ GpnhvLPT+++Arf+sglsv+dFlkr+++ e++ +al+++++a+e+la
  lcl|FitnessBrowser__Phaeo:GFF3068 337 RALSEKTIHAGAIFLGQYTPEAIGDYIGGPNHVLPTARSARFSSGLSVMDFLKRTTLSEMTPDALRAIGPAAETLA 412
                                        **************************************************************************** PP

                          TIGR00069 379 eaEgLeaHaeavevR 393
                                        + E LeaH  ++++R
  lcl|FitnessBrowser__Phaeo:GFF3068 413 KSESLEAHGLSIRAR 427
                                        ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (433 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: 00:00:00.01
# Mc/sec: 13.01
//
[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