Alignments for a candidate for hisD in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Herbaspirillum seropedicae SmR1

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate HSERO_RS20345 HSERO_RS20345 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__HerbieS:HSERO_RS20345
          Length = 438

 Score =  398 bits (1022), Expect = e-115
 Identities = 208/432 (48%), Positives = 285/432 (65%), Gaps = 5/432 (1%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +  L   D  F  + +A L+ +    E +DRA   I+  V+  GD+A+L+Y++RFDR+  
Sbjct: 5   IRKLDSADAGFRDQLSAVLAFEASEDEAIDRAAATILADVKARGDAAVLEYTQRFDRLQA 64

Query: 62  EKTG-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDR----YTDALGVE 116
                + + +  + AA    P +   AL+ A DR+  +H RQ  +       Y +A G E
Sbjct: 65  ASVAALEIGKDALQAALAGLPEARRHALQTAADRVRAYHERQKKECGSDGFLYREADGTE 124

Query: 117 LGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAA 176
           LG + T ++ VG+YVPGG A+YPSSVLMNA+PAKVAGV  ++MVVP PDG  N LVL AA
Sbjct: 125 LGQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPAKVAGVQEVIMVVPTPDGVKNELVLAAA 184

Query: 177 RLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGP 236
            +AGV  ++ +GGAQA+ ALAYGT TI  V KIVGPGNAYVAAAKR VFG VGIDMIAGP
Sbjct: 185 AIAGVDRVFTIGGAQAVGALAYGTATIPQVDKIVGPGNAYVAAAKRRVFGVVGIDMIAGP 244

Query: 237 SEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTE 296
           SE+L++ D   +PDWIA DL +QAEHD  AQSIL+  D  +   VE ++ R L  + R +
Sbjct: 245 SEILVICDGATDPDWIAMDLFSQAEHDELAQSILLCPDADYIAKVEASINRLLDDMPRKD 304

Query: 297 TASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTP 356
               S  D GA++ V+D  +A  +AN IAAEHLEI+  +A+ +  +IR+AG++F+G ++ 
Sbjct: 305 VIRTSLTDRGALVKVRDMAEACEIANMIAAEHLEISAQEAQQWADQIRHAGAMFLGRFSS 364

Query: 357 EVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEG 416
           E +GDY  G NHVLPT+R+ARFSS L V D+ KR+S++++  E  + LG  A E+A  EG
Sbjct: 365 ESLGDYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSIIRVSEEGAQTLGKIAAELAYGEG 424

Query: 417 LDAHAQSVAIRL 428
           L AHA+S  +RL
Sbjct: 425 LQAHARSAELRL 436


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: 491
Number of extensions: 26
Number of successful extensions: 3
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: 438
Length adjustment: 32
Effective length of query: 398
Effective length of database: 406
Effective search space:   161588
Effective search space used:   161588
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 HSERO_RS20345 HSERO_RS20345 (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.2058.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.5e-161  522.4   1.3   5.2e-161  522.2   1.3    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20345  HSERO_RS20345 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20345  HSERO_RS20345 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  522.2   1.3  5.2e-161  5.2e-161       2     393 .]      38     435 ..      37     435 .. 0.98

  Alignments for each domain:
  == domain 1  score: 522.2 bits;  conditional E-value: 5.2e-161
                                  TIGR00069   2 keiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 
                                                ++i++dv+++Gd+A+leyt++fd++   ++++l++ ++ l++al+ ++e+ ++al++aa++++++he+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20345  38 ATILADVKARGDAAVLEYTQRFDRLqaaSVAALEIGKDALQAALAGLPEARRHALQTAADRVRAYHER 105
                                                589********************99656677899********************************** PP

                                  TIGR00069  67 qlpes....veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkk 130
                                                q++e     + +++++g+ lgqkv+pl+rvg+YvPgGkaaypS+vlm+a+pAkvAgv+e+++v P+  
  lcl|FitnessBrowser__HerbieS:HSERO_RS20345 106 QKKECgsdgFLYREADGTELGQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPAKVAGVQEVIMVVPTP- 172
                                                *98855667999******************************************************6. PP

                                  TIGR00069 131 dgkvnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidm 198
                                                dg  n+ vlaaa+++gvd+v+++GGaqa++alayGt+t+p+vdkivGPGn+yV+aAK+ vfg vgidm
  lcl|FitnessBrowser__HerbieS:HSERO_RS20345 173 DGVKNELVLAAAAIAGVDRVFTIGGAQAVGALAYGTATIPQVDKIVGPGNAYVAAAKRRVFGVVGIDM 240
                                                ******************************************************************** PP

                                  TIGR00069 199 iaGPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaek 266
                                                iaGPsE+lvi+d  ++p+++a+Dl+sqaEHde aq+il++++++ ++kve+++++ l++++rk+++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS20345 241 IAGPSEILVICDGATDPDWIAMDLFSQAEHDELAQSILLCPDADYIAKVEASINRLLDDMPRKDVIRT 308
                                                ******************************************************************** PP

                                  TIGR00069 267 slekngaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnh 334
                                                sl+++ga++ v+d++ea+e++n +A+EHLe+ ++++++++++i++aG++flG+ ++e+lgdy+aGpnh
  lcl|FitnessBrowser__HerbieS:HSERO_RS20345 309 SLTDRGALVKVRDMAEACEIANMIAAEHLEISAQEAQQWADQIRHAGAMFLGRFSSESLGDYCAGPNH 376
                                                ******************************************************************** PP

                                  TIGR00069 335 vLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                                vLPTs+tArf+s+l+v+dF+kr+s++++s+e++++l++ +++la  EgL+aHa+++e R
  lcl|FitnessBrowser__HerbieS:HSERO_RS20345 377 VLPTSRTARFSSPLGVYDFQKRSSIIRVSEEGAQTLGKIAAELAYGEGLQAHARSAELR 435
                                                *******************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (438 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: 11.39
//
[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