Alignments for a candidate for hisD in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Pseudomonas fluorescens GW456-L13

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate PfGW456L13_5000 Histidinol dehydrogenase (EC 1.1.1.23)

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000
          Length = 445

 Score =  396 bits (1017), Expect = e-115
 Identities = 207/428 (48%), Positives = 282/428 (65%), Gaps = 1/428 (0%)

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

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

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
            T ++  GLYVPGG ASYPSSVLMNA+PAKVAGV  +VMVVP P G +N LVL AA +AG
Sbjct: 127 VTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVTEVVMVVPTPRGEINELVLAAACIAG 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  ++ + + T+ R      
Sbjct: 247 VVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASIAKLMPTMERAAIIET 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: 506
Number of extensions: 25
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: 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 PfGW456L13_5000 (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.24870.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   5.8e-166  538.5   0.6   6.7e-166  538.3   0.6    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000  Histidinol dehydrogenase (EC 1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000  Histidinol dehydrogenase (EC 1.1.1.23)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.3   0.6  6.7e-166  6.7e-166       1     393 []      39     433 ..      39     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 538.3 bits;  conditional E-value: 6.7e-166
                                               TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkea 52 
                                                             v +ii++vr++Gd+Al+++t++fd++   ++++l +++e+le al++++ + +ea
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000  39 VLDIIKAVRERGDAALVDFTRQFDGLdvkSMADLILPRERLELALTRITVAQREA 93 
                                                             679**********************9555666788******************** PP

                                               TIGR00069  53 lelaaeniekfhekqlpesveveteegvllgqkvrplervglYvPgGkaaypStv 107
                                                             le aa++++++hekq+++s+++++++g++lgqkv+pl+r+glYvPgGka+ypS+v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000  94 LEVAAARVRSYHEKQKQDSWSYTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSV 148
                                                             ******************************************************* PP

                                               TIGR00069 108 lmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevykvGGaqaiaal 162
                                                             lm+a+pAkvAgv+e+v+v P+  +g++n+ vlaaa ++gvd+v+++GGaqa+aal
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000 149 LMNAIPAKVAGVTEVVMVVPTP-RGEINELVLAAACIAGVDRVFTIGGAQAVAAL 202
                                                             *********************6.9******************************* PP

                                               TIGR00069 163 ayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217
                                                             ayGte+vpkvdk+vGPGniyV++AK++vfg+vgidmiaGPsE+lv++d +++p++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000 203 AYGTESVPKVDKVVGPGNIYVATAKRHVFGQVGIDMIAGPSEILVVCDGQTDPDW 257
                                                             ******************************************************* PP

                                               TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekng 272
                                                             +a+Dl+sqaEHdedaqailv++++e+++kv +++++ + ++er+ i+e+s++ +g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000 258 IAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASIAKLMPTMERAAIIETSINGRG 312
                                                             ******************************************************* PP

                                               TIGR00069 273 aiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgd 327
                                                             a+i v+d+e+a+e++n++ApEHLel ++dp+++l++i++aG++f+G++t+ealgd
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000 313 ALIKVRDMEQAIEVANRIAPEHLELSVADPQAWLPQIRHAGAIFMGRHTSEALGD 367
                                                             ******************************************************* PP

                                               TIGR00069 328 yvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEg 382
                                                             y+aGpnhvLPTsgtArf+s+l+v+dF+kr+s++ +s+++++el+++++ la+ E 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000 368 YCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSEQGASELGKTASVLARGES 422
                                                             ******************************************************* PP

                                               TIGR00069 383 LeaHaeavevR 393
                                                             L+aHa+++e R
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5000 423 LTAHARSAEYR 433
                                                             *******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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.10
//
[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