Alignments for a candidate for hisD in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Pseudomonas stutzeri RCH2

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate GFF3235 Psest_3298 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__psRCH2:GFF3235
          Length = 436

 Score =  410 bits (1053), Expect = e-119
 Identities = 217/428 (50%), Positives = 285/428 (66%), Gaps = 1/428 (0%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +  L   D DF +     LS +    E V+  V EI+  VR  GD+AL++ ++RFD + +
Sbjct: 7   IRRLNAADADFARHLDHLLSWESVSDEGVNERVLEIIKAVRERGDAALVELTQRFDGLQV 66

Query: 62  EKTG-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
                + +  A ++ A +    +  EAL++A +R+  +H RQ      YT+A G  LG +
Sbjct: 67  ASMADLILPRARLEQALERITPAQREALEIAAERVSSYHERQKQDSWTYTEADGTVLGQK 126

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
            T ++  GLYVPGG ASYPSSVLMNA+PAKVAGV  +VMVVP P G LN LVL AA +AG
Sbjct: 127 VTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVPEVVMVVPTPRGELNELVLAAACIAG 186

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V  ++ +GGAQA+AALAYGTE++ PV KIVGPGN YVA AKR VFG VGIDMIAGPSE+L
Sbjct: 187 VDRVFTIGGAQAVAALAYGTESVPPVDKIVGPGNIYVATAKRHVFGKVGIDMIAGPSEIL 246

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           +V D   +PDWIA DL +QAEHD  AQSIL++ D  F   V E++ R L TL R + A  
Sbjct: 247 VVCDGQTDPDWIAMDLFSQAEHDEDAQSILVSPDAEFLDRVAESIARLLPTLERADIART 306

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           S    GA+ILV D + AI +ANRIA EHLE++VA+ E ++P+IR+AG+IF+G YT E +G
Sbjct: 307 SIEGRGALILVADMQQAIEVANRIAPEHLELSVAEPEQWLPQIRHAGAIFMGRYTAEALG 366

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY  G NHVLPT+ +ARFSS L V D+ KR+S++   +E    LG  A  +AR E L AH
Sbjct: 367 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIINCSAEGASTLGKVASVLARGESLTAH 426

Query: 421 AQSVAIRL 428
           A+S   R+
Sbjct: 427 ARSAEYRI 434


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: 502
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: 436
Length adjustment: 32
Effective length of query: 398
Effective length of database: 404
Effective search space:   160792
Effective search space used:   160792
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 GFF3235 Psest_3298 (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.18713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.1e-168  544.8   0.2   8.2e-168  544.6   0.2    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3235  Psest_3298 histidinol dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3235  Psest_3298 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.6   0.2  8.2e-168  8.2e-168       1     393 []      39     433 ..      39     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 544.6 bits;  conditional E-value: 8.2e-168
                           TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesv 72 
                                         v eii++vr++Gd+Al+e+t++fd++   ++++l +++++le+ale+++++ +eale aae+++++he+q+++s+
  lcl|FitnessBrowser__psRCH2:GFF3235  39 VLEIIKAVRERGDAALVELTQRFDGLqvaSMADLILPRARLEQALERITPAQREALEIAAERVSSYHERQKQDSW 113
                                         679*********************99556677889**************************************** PP

                           TIGR00069  73 eveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgv 147
                                         ++++++g++lgqkv+pl+r+glYvPgGka+ypS+vlm+a+pAkvAgv+e+v+v P+  +g++n+ vlaaa ++gv
  lcl|FitnessBrowser__psRCH2:GFF3235 114 TYTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVPEVVMVVPTP-RGELNELVLAAACIAGV 187
                                         ********************************************************6.9**************** PP

                           TIGR00069 148 devykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDl 222
                                         d+v+++GGaqa+aalayGte+vp+vdkivGPGniyV++AK++vfg+vgidmiaGPsE+lv++d +++p+++a+Dl
  lcl|FitnessBrowser__psRCH2:GFF3235 188 DRVFTIGGAQAVAALAYGTESVPPVDKIVGPGNIYVATAKRHVFGKVGIDMIAGPSEILVVCDGQTDPDWIAMDL 262
                                         *************************************************************************** PP

                           TIGR00069 223 lsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLel 297
                                         +sqaEHdedaq+ilv++++e++++v e++++ l +ler++ia++s+e +ga+ilv+d+++a+e++n++ApEHLel
  lcl|FitnessBrowser__psRCH2:GFF3235 263 FSQAEHDEDAQSILVSPDAEFLDRVAESIARLLPTLERADIARTSIEGRGALILVADMQQAIEVANRIAPEHLEL 337
                                         *************************************************************************** PP

                           TIGR00069 298 qtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelae 372
                                          +++pe++l++i++aG++f+G+yt+ealgdy+aGpnhvLPTsgtArf+s+l+v+dF+kr+s++++s e++++l++
  lcl|FitnessBrowser__psRCH2:GFF3235 338 SVAEPEQWLPQIRHAGAIFMGRYTAEALGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIINCSAEGASTLGK 412
                                         *************************************************************************** PP

                           TIGR00069 373 aveklaeaEgLeaHaeavevR 393
                                          ++ la+ E L+aHa+++e R
  lcl|FitnessBrowser__psRCH2:GFF3235 413 VASVLARGESLTAHARSAEYR 433
                                         *****************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (436 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: 9.59
//
[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