Alignments for a candidate for hisD in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Marinobacter adhaerens HP15

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate GFF2484 HP15_2428 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Marino:GFF2484
          Length = 434

 Score =  396 bits (1017), Expect = e-115
 Identities = 207/428 (48%), Positives = 280/428 (65%), Gaps = 1/428 (0%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +T L  +  DF    A  L+    V   V+ +VR I+  V+  GD A+L+++ +FDR+ +
Sbjct: 5   ITRLNASQSDFNDALAKLLAWDDSVDHQVNESVRHILHEVKTRGDQAVLEFTEKFDRLKV 64

Query: 62  EKTG-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
                + + ++ +  A DA P     AL+ A +RI  +H RQ  K  +Y D  G  LG +
Sbjct: 65  GSVAELEMDQSRLQQALDAIPQDQRVALEKAAERIRDYHERQNQKSWQYEDEDGTVLGQK 124

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
            T ++  GLYVPGG A+YPSSVLMNA+PAKVAGV  +VMVVP PDG +N +VL +A +AG
Sbjct: 125 VTPLDRAGLYVPGGKAAYPSSVLMNAIPAKVAGVSEVVMVVPTPDGVVNDMVLASAAIAG 184

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V  ++ VGGAQA+ ALA+GTETI  V KIVGPGN +VA AKR VFG VGIDMIAGPSE+L
Sbjct: 185 VDRVFTVGGAQAVGALAFGTETIPAVDKIVGPGNIFVATAKREVFGVVGIDMIAGPSEIL 244

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           +++D   +PDWIA DL +QAEHD  AQSIL++ D  F  AVE ++ + L T+ R +    
Sbjct: 245 VISDGKTDPDWIAMDLFSQAEHDEQAQSILISPDAEFLDAVEASINKLLPTMERADIIRT 304

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           S  D  A+I V D + A  ++NRIA EHLE++V D EA +  IR+AG+IF+G YT E +G
Sbjct: 305 SMTDRAALIHVTDLKQAAEVSNRIAPEHLELSVEDPEAMLDDIRHAGAIFMGRYTAEALG 364

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY  G NHVLPT+ +ARFSS L V D+ KR+S++   +     +G  A  +AR EGL AH
Sbjct: 365 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIGFSAAGADRMGRVASVLARGEGLTAH 424

Query: 421 AQSVAIRL 428
           A+S   R+
Sbjct: 425 ARSAEYRI 432


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: 481
Number of extensions: 23
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: 434
Length adjustment: 32
Effective length of query: 398
Effective length of database: 402
Effective search space:   159996
Effective search space used:   159996
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 GFF2484 HP15_2428 (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.759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.5e-166  538.8   0.6   5.2e-166  538.7   0.6    1.0  1  lcl|FitnessBrowser__Marino:GFF2484  HP15_2428 histidinol dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2484  HP15_2428 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.7   0.6  5.2e-166  5.2e-166       1     393 []      37     431 ..      37     431 .. 0.99

  Alignments for each domain:
  == domain 1  score: 538.7 bits;  conditional E-value: 5.2e-166
                           TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesv 72 
                                         v++i+++v+++Gd+A+le+tekfd++   ++++l++ +++l++al+a++++ + ale+aae+i+++he+q ++s+
  lcl|FitnessBrowser__Marino:GFF2484  37 VRHILHEVKTRGDQAVLEFTEKFDRLkvgSVAELEMDQSRLQQALDAIPQDQRVALEKAAERIRDYHERQNQKSW 111
                                         799*********************997777889****************************************** PP

                           TIGR00069  73 eveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgv 147
                                         ++e+e+g++lgqkv+pl+r+glYvPgGkaaypS+vlm+a+pAkvAgv+e+v+v P+  dg vn+ vla a+++gv
  lcl|FitnessBrowser__Marino:GFF2484 112 QYEDEDGTVLGQKVTPLDRAGLYVPGGKAAYPSSVLMNAIPAKVAGVSEVVMVVPTP-DGVVNDMVLASAAIAGV 185
                                         ********************************************************6.***************** PP

                           TIGR00069 148 devykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDl 222
                                         d+v++vGGaqa++ala+Gtet+p+vdkivGPGni+V++AK++vfg vgidmiaGPsE+lvi+d +++p+++a+Dl
  lcl|FitnessBrowser__Marino:GFF2484 186 DRVFTVGGAQAVGALAFGTETIPAVDKIVGPGNIFVATAKREVFGVVGIDMIAGPSEILVISDGKTDPDWIAMDL 260
                                         *************************************************************************** PP

                           TIGR00069 223 lsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLel 297
                                         +sqaEHde+aq+il+++++e++++ve+++++ l ++er++i+++s+++++a+i v dl++a+e+sn++ApEHLel
  lcl|FitnessBrowser__Marino:GFF2484 261 FSQAEHDEQAQSILISPDAEFLDAVEASINKLLPTMERADIIRTSMTDRAALIHVTDLKQAAEVSNRIAPEHLEL 335
                                         *************************************************************************** PP

                           TIGR00069 298 qtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelae 372
                                          ++dpe++l++i++aG++f+G+yt+ealgdy+aGpnhvLPTsgtArf+s+l+v+dF+kr+s++ +s ++++++++
  lcl|FitnessBrowser__Marino:GFF2484 336 SVEDPEAMLDDIRHAGAIFMGRYTAEALGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIGFSAAGADRMGR 410
                                         *************************************************************************** PP

                           TIGR00069 373 aveklaeaEgLeaHaeavevR 393
                                          ++ la+ EgL+aHa+++e R
  lcl|FitnessBrowser__Marino:GFF2484 411 VASVLARGEGLTAHARSAEYR 431
                                         *****************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (434 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: 10.63
//
[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