GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Pseudomonas simiae WCS417

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate GFF871 PS417_04420 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__WCS417:GFF871
          Length = 440

 Score =  399 bits (1026), Expect = e-116
 Identities = 211/428 (49%), Positives = 281/428 (65%), Gaps = 1/428 (0%)

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

Query: 62  EKTGIAVTEAE-IDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
                 +   E ++ A     A   EAL++A  R+  +H +Q      YT+A G  LG +
Sbjct: 67  ASMSDLILPRERLELALTRITAPQREALEVAAARVRSYHEKQKQDSWSYTEADGTVLGQK 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  ++ + L T+ R E    
Sbjct: 247 VVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASINKLLPTMDRAEIIEK 306

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

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY  G NHVLPT+ +ARFSS L V D+ KR+S++    +    LG  A  +AR E L AH
Sbjct: 367 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSPQGASELGKTASVLARGESLSAH 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: 494
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: 440
Length adjustment: 32
Effective length of query: 398
Effective length of database: 408
Effective search space:   162384
Effective search space used:   162384
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 GFF871 PS417_04420 (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.1374059.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.4e-166  540.6   0.1   1.5e-166  540.4   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF871  PS417_04420 histidinol dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF871  PS417_04420 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.4   0.1  1.5e-166  1.5e-166       1     393 []      39     433 ..      39     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 540.4 bits;  conditional E-value: 1.5e-166
                          TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 
                                        v +ii++vr++Gd+Al+++t++fd++   ++++l +++e+le al+++++  +eale aa++++++hekq+++s++
  lcl|FitnessBrowser__WCS417:GFF871  39 VLDIIKAVRERGDAALVDFTRQFDGLdvaSMSDLILPRERLELALTRITAPQREALEVAAARVRSYHEKQKQDSWS 114
                                        679**********************9666788999***************************************** PP

                          TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvde 149
                                        +++++g++lgqkv+pl+r+glYvPgGka+ypS+vlm+a+pAkvAgv+e+v+v P+  +g++n+ vlaaa ++gvd+
  lcl|FitnessBrowser__WCS417:GFF871 115 YTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVTEVVMVVPTP-RGEINELVLAAACIAGVDR 189
                                        *******************************************************6.9****************** PP

                          TIGR00069 150 vykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsq 225
                                        v+++GGaqa+aalayGte+vpkvdk+vGPGniyV++AK++vfg+vgidmiaGPsE+lv++d +++p+++a+Dl+sq
  lcl|FitnessBrowser__WCS417:GFF871 190 VFTIGGAQAVAALAYGTESVPKVDKVVGPGNIYVATAKRHVFGQVGIDMIAGPSEILVVCDGQTDPDWIAMDLFSQ 265
                                        **************************************************************************** PP

                          TIGR00069 226 aEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkd 301
                                        aEHdedaqailv++++e+++kv +++++ l +++r+ei+eks++ +ga+ilv+d+e+a+e++n++ApEHLel ++d
  lcl|FitnessBrowser__WCS417:GFF871 266 AEHDEDAQAILVSPDAEFLDKVAASINKLLPTMDRAEIIEKSINGRGALILVRDMEQAIEVANRIAPEHLELSVAD 341
                                        **************************************************************************** PP

                          TIGR00069 302 peellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeavekl 377
                                        p+++l++i++aG++f+G++t+ealgdy+aGpnhvLPTsgtArf+s+l+v+dF+kr+s++ +s ++++el+++++ l
  lcl|FitnessBrowser__WCS417:GFF871 342 PQAWLPSIRHAGAIFMGRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSPQGASELGKTASVL 417
                                        **************************************************************************** PP

                          TIGR00069 378 aeaEgLeaHaeavevR 393
                                        a+ E L+aHa+++e R
  lcl|FitnessBrowser__WCS417:GFF871 418 ARGESLSAHARSAEYR 433
                                        ************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (440 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: 30.47
//
[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