Alignments for a candidate for hisD in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Cupriavidus basilensis 4G11

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate RR42_RS18915 RR42_RS18915 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Cup4G11:RR42_RS18915
          Length = 445

 Score =  392 bits (1006), Expect = e-113
 Identities = 204/432 (47%), Positives = 289/432 (66%), Gaps = 5/432 (1%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +  L  T+  F  +    L+ +    + +DRAV +I+  V+  GD+A+L+Y++RFDR++ 
Sbjct: 11  IRRLDSTEQGFAAELRKVLAFEAGEDDAIDRAVAQILADVKARGDAAVLEYTQRFDRVEA 70

Query: 62  EK-TGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDD----RYTDALGVE 116
                + ++ A+++AA +        AL+ A  R+  +H +Q  +       YT++ G  
Sbjct: 71  SSMAALEISPAKLEAALEELEPKRRAALETAAARVRAYHEKQKIECGSHSWEYTESDGTV 130

Query: 117 LGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAA 176
           LG + T ++ VG+YVPGG A+YPSSVLMNA+PA+VAGV  ++MVVP P G  N LVL AA
Sbjct: 131 LGQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPARVAGVKEVIMVVPTPGGVRNELVLAAA 190

Query: 177 RLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGP 236
           ++AGV  ++ +GGAQA+ ALAYGT ++  V KIVGPGNAYVAAAKR VFGTVGIDMIAGP
Sbjct: 191 QIAGVDRVFTIGGAQAVGALAYGTGSLPQVDKIVGPGNAYVAAAKRRVFGTVGIDMIAGP 250

Query: 237 SEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTE 296
           SE+L++ D   +PDW+A DL +QAEHD  AQSIL+  D  +   VEE++ RQL ++ R +
Sbjct: 251 SEILVICDGTTDPDWVAMDLFSQAEHDELAQSILLCPDSNYLAQVEESIHRQLDSMPRRD 310

Query: 297 TASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTP 356
              AS    GA+I V+D ++A  +AN IA EHLEI+  +   +  +IR+AG+IF+G YT 
Sbjct: 311 VIRASLSGRGALIRVRDMDEACEIANAIAPEHLEISAENPRHWAEKIRHAGAIFLGRYTS 370

Query: 357 EVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEG 416
           E +GDY  G NHVLPT+R+ARFSS L V D+ KR+SL+++  +  + LG  A E+A  EG
Sbjct: 371 ESLGDYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSLIEVSEQGAQMLGQIAAELAYGEG 430

Query: 417 LDAHAQSVAIRL 428
           L AHA+S   RL
Sbjct: 431 LQAHARSAEYRL 442


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: 473
Number of extensions: 24
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: 445
Length adjustment: 32
Effective length of query: 398
Effective length of database: 413
Effective search space:   164374
Effective search space used:   164374
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 RR42_RS18915 RR42_RS18915 (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.14038.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-166  539.1   0.2   4.4e-166  538.9   0.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS18915  RR42_RS18915 histidinol dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS18915  RR42_RS18915 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.9   0.2  4.4e-166  4.4e-166       1     393 []      43     441 ..      43     441 .. 0.98

  Alignments for each domain:
  == domain 1  score: 538.9 bits;  conditional E-value: 4.4e-166
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 
                                               v++i++dv+++Gd+A+leyt++fd+v   ++++l++s ++le+ale+++++ ++ale+aa++++++hek
  lcl|FitnessBrowser__Cup4G11:RR42_RS18915  43 VAQILADVKARGDAAVLEYTQRFDRVeasSMAALEISPAKLEAALEELEPKRRAALETAAARVRAYHEK 111
                                               789***********************666667899********************************** PP

                                 TIGR00069  67 qlpes....veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkd 131
                                               q+ e     +e+++++g++lgqkv+pl+rvg+YvPgGkaaypS+vlm+a+pA+vAgvke+++v P+   
  lcl|FitnessBrowser__Cup4G11:RR42_RS18915 112 QKIECgshsWEYTESDGTVLGQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPARVAGVKEVIMVVPTP-G 179
                                               *95433345*********************************************************6.8 PP

                                 TIGR00069 132 gkvnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmia 200
                                               g  n+ vlaaa+++gvd+v+++GGaqa++alayGt ++p+vdkivGPGn+yV+aAK+ vfg+vgidmia
  lcl|FitnessBrowser__Cup4G11:RR42_RS18915 180 GVRNELVLAAAQIAGVDRVFTIGGAQAVGALAYGTGSLPQVDKIVGPGNAYVAAAKRRVFGTVGIDMIA 248
                                               999****************************************************************** PP

                                 TIGR00069 201 GPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksle 269
                                               GPsE+lvi+d +++p++va+Dl+sqaEHde aq+il++++++ +++vee++++ql++++r++++++sl+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18915 249 GPSEILVICDGTTDPDWVAMDLFSQAEHDELAQSILLCPDSNYLAQVEESIHRQLDSMPRRDVIRASLS 317
                                               ********************************************************************* PP

                                 TIGR00069 270 kngaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPT 338
                                                +ga+i v+d++ea+e++n++ApEHLe+ +++p+++++ki++aG++flG+yt+e+lgdy+aGpnhvLPT
  lcl|FitnessBrowser__Cup4G11:RR42_RS18915 318 GRGALIRVRDMDEACEIANAIAPEHLEISAENPRHWAEKIRHAGAIFLGRYTSESLGDYCAGPNHVLPT 386
                                               ********************************************************************* PP

                                 TIGR00069 339 sgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               s+tArf+s+l+v+dF+kr+s++e+s+++++ l++ +++la  EgL+aHa+++e R
  lcl|FitnessBrowser__Cup4G11:RR42_RS18915 387 SRTARFSSPLGVYDFQKRSSLIEVSEQGAQMLGQIAAELAYGEGLQAHARSAEYR 441
                                               ***************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (445 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: 12.82
//
[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