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.3637357.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 33.26
//
[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:

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:

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:

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:

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