Alignments for a candidate for hisD in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Pseudomonas fluorescens FW300-N1B4

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Pf1N1B4_1066 Histidinol dehydrogenase (EC 1.1.1.23)

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066
          Length = 441

 Score =  394 bits (1011), Expect = e-114
 Identities = 207/428 (48%), Positives = 280/428 (65%), Gaps = 1/428 (0%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +  L   DPDF       LS +    + V++ V +I+  VR  GD+AL++++++FD + +
Sbjct: 7   IRRLNAADPDFAHHLDHLLSWESVSDDSVNQRVLDIIKAVRERGDAALVEFTQKFDGLQV 66

Query: 62  EKTGIAVTEAE-IDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
                 +   E ++ A     A   EAL+ A  R+  +H +Q      YT+A G  LG +
Sbjct: 67  ASMADLILPRERLELALTRITAPQREALEKAATRVRSYHEKQKQDSWSYTEADGTVLGQK 126

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

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V  ++ +GGAQA+AALAYGTE++  V K+VGPGN YVA AKR VFG VGIDMIAGPSE+L
Sbjct: 187 VDRVFTIGGAQAVAALAYGTESVPKVDKVVGPGNIYVATAKRHVFGQVGIDMIAGPSEIL 246

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           +V D   +PDWIA DL +QAEHD  AQ+IL++ D  F   V  ++ + L T+ R E    
Sbjct: 247 VVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASIAKLLPTMERAEIIET 306

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           S    GA+I V+D E AI +ANRIA EHLE++VAD +A++P+IR+AG+IF+G +T E +G
Sbjct: 307 SINGRGALIKVRDMEQAIEVANRIAPEHLELSVADPQAWLPQIRHAGAIFMGRHTSEALG 366

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY  G NHVLPT+ +ARFSS L V D+ KR+S++    +    LG  A  +AR E L AH
Sbjct: 367 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSEQGASELGKTASVLARGESLTAH 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: 486
Number of extensions: 26
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: 441
Length adjustment: 32
Effective length of query: 398
Effective length of database: 409
Effective search space:   162782
Effective search space used:   162782
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 Pf1N1B4_1066 (Histidinol dehydrogenase (EC 1.1.1.23))
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.22834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   9.1e-167  541.1   0.4     1e-166  540.9   0.4    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066  Histidinol dehydrogenase (EC 1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066  Histidinol dehydrogenase (EC 1.1.1.23)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.9   0.4    1e-166    1e-166       1     393 []      39     433 ..      39     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 540.9 bits;  conditional E-value: 1e-166
                                      TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaenie 61 
                                                    v +ii++vr++Gd+Al+e+t+kfd++   ++++l +++e+le al+++++  +eale+aa++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066  39 VLDIIKAVRERGDAALVEFTQKFDGLqvaSMADLILPRERLELALTRITAPQREALEKAATRVR 102
                                                    679*********************99556677889***************************** PP

                                      TIGR00069  62 kfhekqlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvv 125
                                                    ++hekq+++s+++++++g++lgqkv+pl+r+glYvPgGka+ypS+vlm+a+pAkvAgv+e+v+v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066 103 SYHEKQKQDSWSYTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVSEVVMV 166
                                                    **************************************************************** PP

                                      TIGR00069 126 tPpkkdgkvnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKkl 189
                                                     P+  +g++n+ vlaaa ++gvd+v+++GGaqa+aalayGte+vpkvdk+vGPGniyV++AK++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066 167 VPTP-RGEINELVLAAACIAGVDRVFTIGGAQAVAALAYGTESVPKVDKVVGPGNIYVATAKRH 229
                                                    ***6.9********************************************************** PP

                                      TIGR00069 190 vfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeevee 253
                                                    vfg+vgidmiaGPsE+lv++d +++p+++a+Dl+sqaEHdedaqailv++++e+++kv +++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066 230 VFGQVGIDMIAGPSEILVVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASIAK 293
                                                    **************************************************************** PP

                                      TIGR00069 254 qleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvfl 317
                                                     l ++er+ei+e+s++ +ga+i v+d+e+a+e++n++ApEHLel ++dp+++l++i++aG++f+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066 294 LLPTMERAEIIETSINGRGALIKVRDMEQAIEVANRIAPEHLELSVADPQAWLPQIRHAGAIFM 357
                                                    **************************************************************** PP

                                      TIGR00069 318 GeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaE 381
                                                    G++t+ealgdy+aGpnhvLPTsgtArf+s+l+v+dF+kr+s++ +s+++++el+++++ la+ E
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066 358 GRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSEQGASELGKTASVLARGE 421
                                                    **************************************************************** PP

                                      TIGR00069 382 gLeaHaeavevR 393
                                                     L+aHa+++e R
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1066 422 SLTAHARSAEYR 433
                                                    ********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (441 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: 00:00:00.02
# Mc/sec: 7.38
//
[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