Alignments for a candidate for hisD in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Phaeobacter inhibens BS107

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate GFF2510 PGA1_c25490 histidinol dehydrogenase HisD

Query= curated2:Q5SKC1
         (412 letters)



>FitnessBrowser__Phaeo:GFF2510
          Length = 421

 Score =  255 bits (651), Expect = 2e-72
 Identities = 155/406 (38%), Positives = 233/406 (57%), Gaps = 17/406 (4%)

Query: 20  DPTVEEIVRGILEAVREEGDEALDRFSRDLDGYPVEEV-----PKRAWREAYEDLDEDLR 74
           D  V +IV  +L+ +  EG+E + R+++ LDG+  + V      K A      +L ED++
Sbjct: 17  DNNVRDIVHVMLQTIEREGEEGVRRYAKKLDGWTGDIVLSDLDRKAACARVPVELKEDIQ 76

Query: 75  DALETARERIEAFYREEARGGFLRAE--GGGVLAQLVRPLERVGVYVPGGSAPLLSTLLM 132
            A    R   EA   ++A  G    E   G +  Q   P+   G YVPGG    +++ LM
Sbjct: 77  FAHANIRRFAEA---QKATMGECEIEVIPGLIAGQKQIPVSSAGCYVPGGRYSHVASALM 133

Query: 133 TVVPAKVAGVREVIVASPPKVHPGV----LAAAWVAGADRLFAMGGAQAIAALAYGTGRV 188
           TV  AKVAGV+ +   SP +   G+    + A  ++GAD +  +GG QAIAA+A G    
Sbjct: 134 TVTTAKVAGVQHITAVSPTRPETGIPDPIVYAMDLSGADLILNVGGVQAIAAMAQGLFGA 193

Query: 189 PRVDKIVGPGNRYVVAAKRLVYGTVGIDGLAGPTETMIIADGSASPRLLAADLLAQAEHG 248
              D +VGPGN YV  AKR+++G+VGID  AGPT++++IAD +A    +A DL++QAEHG
Sbjct: 194 KPADILVGPGNSYVAEAKRMLFGSVGIDMFAGPTDSLVIADNTAEVETVAWDLVSQAEHG 253

Query: 249 PDSEPWLLSPDRALLERVEAELSWQLQDL--PRAEVARQA-LEKGGLVLTKDLEEAFALA 305
            DS  WL++ D+ L + V       ++ L  P    ARQA  E+  ++L    EEA  ++
Sbjct: 254 ADSPVWLVTTDKDLAQGVMHRAQELIETLPEPNRSAARQAWAERAEVILAGSREEAAQVS 313

Query: 306 NLYAPEHLSLALSDPLPWLEKVQNAGGVFLGEGSPEALGDYIAGPSHVMPTSGTARFQGG 365
           + YAPEHL +   D   WL ++   G +FLG+ +  + GD  +GP+HV+PTSG AR+ GG
Sbjct: 314 DRYAPEHLQVQAEDLDWWLGRLSAYGSLFLGKETTVSFGDKTSGPNHVLPTSGAARYTGG 373

Query: 366 LAVRDFLKVIPVVGLSEGAARELAKKGALLARAEGLEGHARSLDLR 411
           L+V  F K +     +  A++ELA + A L+R EG+EGHA++ + R
Sbjct: 374 LSVHKFTKTVTWQHCNAAASKELALRTARLSRTEGMEGHAKAAEQR 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: 429
Number of extensions: 21
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: 421
Length adjustment: 31
Effective length of query: 381
Effective length of database: 390
Effective search space:   148590
Effective search space used:   148590
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: 50 (23.9 bits)

Align candidate GFF2510 PGA1_c25490 (histidinol dehydrogenase HisD)
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.9857.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.6e-132  428.4   0.2   1.9e-132  428.2   0.2    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2510  PGA1_c25490 histidinol dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2510  PGA1_c25490 histidinol dehydrogenase HisD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.2   0.2  1.9e-132  1.9e-132       1     393 []      24     419 ..      24     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 428.2 bits;  conditional E-value: 1.9e-132
                          TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes..vev 74 
                                        v+ +++ +++eG+e +++y++k+d+++  ++ +s+ + ++a ++v+ elke+++ a++ni++f+e+q+++   +e+
  lcl|FitnessBrowser__Phaeo:GFF2510  24 VHVMLQTIEREGEEGVRRYAKKLDGWT-GDIVLSDLDRKAACARVPVELKEDIQFAHANIRRFAEAQKATMgeCEI 98 
                                        5668999*******************5.88*************************************988656899 PP

                          TIGR00069  75 eteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdev 150
                                        e  +g ++gqk  p++++g+YvPgG++++++++lmt+ +AkvAgv++i++v+P++ +  + + +++a++l g+d +
  lcl|FitnessBrowser__Phaeo:GFF2510  99 EVIPGLIAGQKQIPVSSAGCYVPGGRYSHVASALMTVTTAKVAGVQHITAVSPTRPETGIPDPIVYAMDLSGADLI 174
                                        99****************************************************99999***************** PP

                          TIGR00069 151 ykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqa 226
                                        ++vGG+qaiaa+a G+   +++d++vGPGn+yV++AK+++fg+vgidm+aGP++ lviad++a+ e+va Dl+sqa
  lcl|FitnessBrowser__Phaeo:GFF2510 175 LNVGGVQAIAAMAQGLFGAKPADILVGPGNSYVAEAKRMLFGSVGIDMFAGPTDSLVIADNTAEVETVAWDLVSQA 250
                                        **************************************************************************** PP

                          TIGR00069 227 EHdedaqailvttseelaekveeeveeqleele..rkeiaekslekngaiilvddleealelsneyApEHLelqtk 300
                                        EH++d+ ++lvtt+++la+ v ++ +e +e+l+  +++ a++++++++++il+ + eea+++s++yApEHL++q++
  lcl|FitnessBrowser__Phaeo:GFF2510 251 EHGADSPVWLVTTDKDLAQGVMHRAQELIETLPepNRSAARQAWAERAEVILAGSREEAAQVSDRYAPEHLQVQAE 326
                                        ********************************866799************************************** PP

                          TIGR00069 301 dpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeavek 376
                                        d   +l +++++Gs+flG+ t++++gd+++GpnhvLPTsg+Ar+++glsv++F+k++++q+++ +a +ela  +++
  lcl|FitnessBrowser__Phaeo:GFF2510 327 DLDWWLGRLSAYGSLFLGKETTVSFGDKTSGPNHVLPTSGAARYTGGLSVHKFTKTVTWQHCNAAASKELALRTAR 402
                                        **************************************************************************** PP

                          TIGR00069 377 laeaEgLeaHaeavevR 393
                                        l+++Eg+e Ha+a+e+R
  lcl|FitnessBrowser__Phaeo:GFF2510 403 LSRTEGMEGHAKAAEQR 419
                                        *************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (421 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.46
//
[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