Alignments for a candidate for hisD in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Dinoroseobacter shibae DFL-12

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate 3608641 Dshi_2034 Histidinol dehydrogenase (RefSeq)

Query= curated2:Q5SKC1
         (412 letters)



>FitnessBrowser__Dino:3608641
          Length = 435

 Score =  268 bits (685), Expect = 2e-76
 Identities = 147/399 (36%), Positives = 235/399 (58%), Gaps = 11/399 (2%)

Query: 24  EEIVRGILEAVREEGDEALDRFSRDLDGYPVEEVPKR-AWREAYEDLDEDLRDALETARE 82
           ++IVR IL+ +   GD+A   ++R  D Y  E +  + A   A   + E L+  ++ A  
Sbjct: 21  KKIVRAILDEIEAGGDDAALAYARKFDNYEGEILLSQDAIDAAIAQVPEKLKHDIDFAHA 80

Query: 83  RIEAF---YREEARGGFLRAEGGGVLAQLVRPLERVGVYVPGGSAPLLSTLLMTVVPAKV 139
            ++ F    R+      +    G +  Q   P+   G YVPGG    +++ +MTV  AKV
Sbjct: 81  NVKRFAEAQRDTVANFEIEVVPGLIAGQKAIPVHAAGCYVPGGRYSHIASAIMTVTTAKV 140

Query: 140 AGVREVIVASPPK----VHPGVLAAAWVAGADRLFAMGGAQAIAALAYGTGRVPRVDKIV 195
           AG + ++  SPP+    + P ++ AA V GAD++ AMGG Q +AA+ +G   +P+ + +V
Sbjct: 141 AGCKHIVACSPPRPDVGIAPAIVYAAHVCGADKIMAMGGVQGVAAMTFGLFGLPKANILV 200

Query: 196 GPGNRYVVAAKRLVYGTVGIDGLAGPTETMIIADGSASPRLLAADLLAQAEHGPDSEPWL 255
           GPGN++V  AKR+++G VGID +AGPT+++I+AD SA P ++A DL+ QAEHG +S  WL
Sbjct: 201 GPGNQFVAEAKRMLFGRVGIDMIAGPTDSLILADASADPMVVAVDLVGQAEHGYNSPVWL 260

Query: 256 LSPDRALLERVEAELSWQLQDLP---RAEVARQALEKGGLVLTKDLEEAFALANLYAPEH 312
           ++ DRAL E+V   +   + DLP   R        +   +++  D EE  A ++ YAPEH
Sbjct: 261 VTDDRALAEKVMELVPGLIDDLPDVNRENATAAWRDYAEVIVCADREEMAATSDEYAPEH 320

Query: 313 LSLALSDPLPWLEKVQNAGGVFLGEGSPEALGDYIAGPSHVMPTSGTARFQGGLAVRDFL 372
           L++   D   WLE++   G +FLGE +  A GD  +G +HV+PTSG A + GGL+V  ++
Sbjct: 321 LTVQAEDLDWWLERLSCYGSLFLGEETTVAFGDKASGTNHVLPTSGAANYTGGLSVHKYM 380

Query: 373 KVIPVVGLSEGAARELAKKGALLARAEGLEGHARSLDLR 411
           K++     +   ++ +A   A ++R EG+EGHAR+ D+R
Sbjct: 381 KIVTWQRSTREGSKPVALATARISRLEGMEGHARTADIR 419


Lambda     K      H
   0.318    0.137    0.396 

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: 425
Number of extensions: 27
Number of successful extensions: 4
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: 412
Length of database: 435
Length adjustment: 32
Effective length of query: 380
Effective length of database: 403
Effective search space:   153140
Effective search space used:   153140
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 3608641 Dshi_2034 (Histidinol dehydrogenase (RefSeq))
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.7759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   7.9e-138  445.9   0.3   9.2e-138  445.6   0.3    1.0  1  lcl|FitnessBrowser__Dino:3608641  Dshi_2034 Histidinol dehydrogena


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608641  Dshi_2034 Histidinol dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.6   0.3  9.2e-138  9.2e-138       1     393 []      24     419 ..      24     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 445.6 bits;  conditional E-value: 9.2e-138
                         TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes..veve 75 
                                       v++i++++++ Gd+A l+y++kfd+++  ++ +s++ +++a ++v+e+lk++++ a++n+++f+e+q+++   +e+e
  lcl|FitnessBrowser__Dino:3608641  24 VRAILDEIEAGGDDAALAYARKFDNYE-GEILLSQDAIDAAIAQVPEKLKHDIDFAHANVKRFAEAQRDTVanFEIE 99 
                                       789***********************6.889************************************9775459999 PP

                         TIGR00069  76 teegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevyk 152
                                         +g ++gqk+ p++++g+YvPgG+++++++++mt+ +AkvAg+k+iv+++Pp+ d  ++pa+++aa+++g+d++++
  lcl|FitnessBrowser__Dino:3608641 100 VVPGLIAGQKAIPVHAAGCYVPGGRYSHIASAIMTVTTAKVAGCKHIVACSPPRPDVGIAPAIVYAAHVCGADKIMA 176
                                       ******************************************************9********************** PP

                         TIGR00069 153 vGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHd 229
                                       +GG+q++aa+++G+  +pk++++vGPGn++V++AK+++fg+vgidmiaGP++ l++ad+sa+p +va+Dl+ qaEH+
  lcl|FitnessBrowser__Dino:3608641 177 MGGVQGVAAMTFGLFGLPKANILVGPGNQFVAEAKRMLFGRVGIDMIAGPTDSLILADASADPMVVAVDLVGQAEHG 253
                                       ***************************************************************************** PP

                         TIGR00069 230 edaqailvttseelaekveeeveeqleele..rkeiaekslekngaiilvddleealelsneyApEHLelqtkdpee 304
                                        ++ ++lvt++++laekv e v   +++l+  ++e a++++++++++i+++d ee++++s+eyApEHL++q++d   
  lcl|FitnessBrowser__Dino:3608641 254 YNSPVWLVTDDRALAEKVMELVPGLIDDLPdvNRENATAAWRDYAEVIVCADREEMAATSDEYAPEHLTVQAEDLDW 330
                                       *****************************977799****************************************** PP

                         TIGR00069 305 llkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaE 381
                                       +l++++ +Gs+flGe t++a+gd+++G+nhvLPTsg+A++++glsv++++k +++q+ ++e+ + +a a+++++++E
  lcl|FitnessBrowser__Dino:3608641 331 WLERLSCYGSLFLGEETTVAFGDKASGTNHVLPTSGAANYTGGLSVHKYMKIVTWQRSTREGSKPVALATARISRLE 407
                                       ***************************************************************************** PP

                         TIGR00069 382 gLeaHaeavevR 393
                                       g+e Ha+++++R
  lcl|FitnessBrowser__Dino:3608641 408 GMEGHARTADIR 419
                                       *******99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (435 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: 9.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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