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 1; HDH 1; EC 1.1.1.23 (uncharacterized)
to candidate GFF2695 PGA1_c27370 histidinol dehydrogenase HisD

Query= curated2:Q8YSM8
         (431 letters)



>FitnessBrowser__Phaeo:GFF2695
          Length = 442

 Score =  293 bits (750), Expect = 7e-84
 Identities = 168/410 (40%), Positives = 237/410 (57%), Gaps = 3/410 (0%)

Query: 20  SDRREATVDVSGTVRDILAHVKARGDAAVQEYTSRFDHYRPHSHHLSAAFIAEQAAKCSD 79
           +DR E     +  V   L  ++ARGDAAV+E   +FD+Y   S+ LS A I    AK S 
Sbjct: 13  ADRAEDDAKTASVVASTLKDIEARGDAAVRELACKFDNYDRDSYRLSEAEIEAIIAKVSP 72

Query: 80  EVKAALELAAERISSFHQKQLPQ--DIGYTDTAGVKLGLNWVALSQVGIYVPGGRASYPS 137
              A ++ A ++++ F Q Q     DI      GV LG   + +  VG YVPGG+    +
Sbjct: 73  REMADIQFAQDQVTKFAQAQRDSMLDIEVEPMPGVILGHKNIPVQSVGCYVPGGKFPMVA 132

Query: 138 SVLMNALPAKIAGVERIVMTVPMPHGEINPAVLAAAQVAGVTEIYSIGGAQAVGALAYGT 197
           S  M+   AK+AGV RIV   P  +GE NPAV+AA  + G  EIY +GG QAVGA+A GT
Sbjct: 133 SAHMSVATAKVAGVPRIVACTPPFNGEPNPAVIAAMHLGGAHEIYVLGGIQAVGAMAIGT 192

Query: 198 ETITPVDKIVGPGNAYVAEAKRQVFGTVGIDSIAGPSEILVVADRQNNPEWIAWDLLSQA 257
           E+I PV  +VGPGNA+VAEAKRQ+FG VGID  AGP+E +V+AD   + E  A DLL QA
Sbjct: 193 ESIAPVHLLVGPGNAFVAEAKRQLFGRVGIDLFAGPTETMVIADDTVDAELCATDLLGQA 252

Query: 258 EHDPSAQSILITDSESFAQQVIAAVEQILTTLPSQKVASSSWQNHGAVIIVRDLAESIPL 317
           EH  ++ ++L+T+S + A+  +  +++ILT LP+   A  SW+++G VI+     E + +
Sbjct: 253 EHGYNSPAVLVTNSRTLAEDTLKEIDRILTILPTAGTARVSWEDYGEVILCDSYDEMLAV 312

Query: 318 LNQLAPEHVELCVDNPQLLASQIKCAGSLFLGRYTPEAIGDYLGGPNHVLPTSRSARFAS 377
            + +A EHV++  D        + C G+LFLG  T  A GD + G NH LPT ++ R+  
Sbjct: 313 ADDIASEHVQVMTDRDDWFLDNMTCYGALFLGPRTNVANGDKVIGTNHTLPTKKAGRYTG 372

Query: 378 GLSVYDFLKRITYLE-CNQAALQKIGQSAVTLAETEGLPAHAGSVAVRLQ 426
           GL V  FLK  +Y +  +  A   IG+    L   EG   HA    +R++
Sbjct: 373 GLWVGKFLKTHSYQKVTSDEAATLIGEYGSRLCMLEGFVGHAEQCNIRVR 422


Lambda     K      H
   0.316    0.131    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: 441
Number of extensions: 16
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: 431
Length of database: 442
Length adjustment: 32
Effective length of query: 399
Effective length of database: 410
Effective search space:   163590
Effective search space used:   163590
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate GFF2695 PGA1_c27370 (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.10688.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.8e-132  427.1   0.0   4.6e-132  426.9   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2695  PGA1_c27370 histidinol dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2695  PGA1_c27370 histidinol dehydrogenase HisD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.9   0.0  4.6e-132  4.6e-132       1     393 []      26     420 ..      26     420 .. 0.98

  Alignments for each domain:
  == domain 1  score: 426.9 bits;  conditional E-value: 4.6e-132
                          TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes..vev 74 
                                        v++ ++d++++Gd+A++e++ kfd+++ +s r+se+e+e+  ++v+++  ++++ a+++++kf+++q+++   +ev
  lcl|FitnessBrowser__Phaeo:GFF2695  26 VASTLKDIEARGDAAVRELACKFDNYDRDSYRLSEAEIEAIIAKVSPREMADIQFAQDQVTKFAQAQRDSMldIEV 101
                                        567799**************************************************************99766899 PP

                          TIGR00069  75 eteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdev 150
                                        e ++gv+lg+k  p+++vg+YvPgGk ++++++ m + +AkvAgv++iv++tPp  +g+ npav+aa++l g++e+
  lcl|FitnessBrowser__Phaeo:GFF2695 102 EPMPGVILGHKNIPVQSVGCYVPGGKFPMVASAHMSVATAKVAGVPRIVACTPPF-NGEPNPAVIAAMHLGGAHEI 176
                                        9*****************************************************6.9******************* PP

                          TIGR00069 151 ykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqa 226
                                        y +GG qa++a+a Gte++ +v  +vGPGn++V++AK+++fg+vgid++aGP+E +viad++ ++el+a+Dll qa
  lcl|FitnessBrowser__Phaeo:GFF2695 177 YVLGGIQAVGAMAIGTESIAPVHLLVGPGNAFVAEAKRQLFGRVGIDLFAGPTETMVIADDTVDAELCATDLLGQA 252
                                        **************************************************************************** PP

                          TIGR00069 227 EHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdp 302
                                        EH+ ++ a+lvt+s++lae++ +e+++ l+ l+++ +a+ s+e++g++il+d+++e+l++++++A EH++++t+  
  lcl|FitnessBrowser__Phaeo:GFF2695 253 EHGYNSPAVLVTNSRTLAEDTLKEIDRILTILPTAGTARVSWEDYGEVILCDSYDEMLAVADDIASEHVQVMTDRD 328
                                        **************************************************************************** PP

                          TIGR00069 303 eellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealee.laeavekl 377
                                          +l++++ +G++flG+ t +a gd+v G+nh+LPT+++ r+++gl+v +Flk+ s+q+++++++++ ++e  ++l
  lcl|FitnessBrowser__Phaeo:GFF2695 329 DWFLDNMTCYGALFLGPRTNVANGDKVIGTNHTLPTKKAGRYTGGLWVGKFLKTHSYQKVTSDEAATlIGEYGSRL 404
                                        ************************************************************98877762577889** PP

                          TIGR00069 378 aeaEgLeaHaeavevR 393
                                        + +Eg+  Hae  ++R
  lcl|FitnessBrowser__Phaeo:GFF2695 405 CMLEGFVGHAEQCNIR 420
                                        ***********99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (442 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: 00:00:00.02
# Mc/sec: 7.59
//
[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