Alignments for a candidate for hisD in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Hydrogenophaga taeniospiralis NBRC 102512

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_068174408.1 HTA01S_RS19435 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_001592305.1:WP_068174408.1
          Length = 447

 Score =  402 bits (1032), Expect = e-116
 Identities = 209/422 (49%), Positives = 289/422 (68%), Gaps = 4/422 (0%)

Query: 11  DFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT-GIAVT 69
           DFE +FAA L    E    +++ V +I+  V++ GD+A+L+Y+ RFD ++ +    + +T
Sbjct: 16  DFEARFAARLHWSAETDSAIEQRVADILADVQQRGDAAVLEYTARFDGLNADGVPALELT 75

Query: 70  EAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDR---YTDALGVELGSRWTAIEA 126
           +AE+ AAFD  PA+  +AL+ A  R+  +H  Q         Y D  G  LG + T ++ 
Sbjct: 76  QAELKAAFDGLPAAQRDALESAARRVRSYHEAQKRASGESWSYRDEDGTLLGQKVTPLDR 135

Query: 127 VGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYR 186
           VG+YVPGG A+YPSSVLMNA+PA VAGV  I+MVVP P G  NPLVL AA +AGV+  + 
Sbjct: 136 VGIYVPGGKAAYPSSVLMNAIPAHVAGVAEIIMVVPTPKGEKNPLVLAAAYVAGVTRAFT 195

Query: 187 VGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKD 246
           +GGAQA+AALAYGT T+  V KI GPGNAYVA+AK+ VFGTVGIDMIAGPSE+L++AD  
Sbjct: 196 IGGAQAVAALAYGTATVPKVDKITGPGNAYVASAKKRVFGTVGIDMIAGPSEILVLADGS 255

Query: 247 NNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFG 306
              DW+A DL +QAEHD  AQSIL+  D A+  AV+ A++R L T+ R    + S  D G
Sbjct: 256 TPADWVAMDLFSQAEHDELAQSILLCPDAAYIDAVQAAIDRLLPTMPRAAIIAKSLNDRG 315

Query: 307 AVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGC 366
           A+IL +D E+A  ++NRIA EHLE++ ++   + P +++AG+IF+G YT E +GDY  G 
Sbjct: 316 ALILTRDMEEACAISNRIAPEHLEVSSSEPHRWEPLLKHAGAIFLGAYTSESLGDYCAGP 375

Query: 367 NHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAI 426
           NHVLPT+ +ARFSS L V D+ KR+SL+++ +   + LG  A E+A  EGL AHA++  +
Sbjct: 376 NHVLPTSGTARFSSPLGVYDFQKRSSLIEVSAAGAQTLGIIAAELAYGEGLQAHARAAEL 435

Query: 427 RL 428
           RL
Sbjct: 436 RL 437


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: 481
Number of extensions: 19
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: 447
Length adjustment: 32
Effective length of query: 398
Effective length of database: 415
Effective search space:   165170
Effective search space used:   165170
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 WP_068174408.1 HTA01S_RS19435 (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.1655.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-160  518.6   0.3   7.1e-160  518.4   0.3    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068174408.1  HTA01S_RS19435 histidinol dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068174408.1  HTA01S_RS19435 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.4   0.3  7.1e-160  7.1e-160       1     393 []      39     436 ..      39     436 .. 0.98

  Alignments for each domain:
  == domain 1  score: 518.4 bits;  conditional E-value: 7.1e-160
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkle...slrvseeeleealeavdeelkealelaaeniekfhek 66 
                                               v++i++dv+++Gd+A+leyt +fd+++++   +l+++++el++a + ++++ ++ale aa++++++he+
  lcl|NCBI__GCF_001592305.1:WP_068174408.1  39 VADILADVQQRGDAAVLEYTARFDGLNADgvpALELTQAELKAAFDGLPAAQRDALESAARRVRSYHEA 107
                                               789***********************66534489*********************************** PP

                                 TIGR00069  67 qlpes...veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdg 132
                                               q+++s   +++++e+g+llgqkv+pl+rvg+YvPgGkaaypS+vlm+a+pA+vAgv ei++v P+  +g
  lcl|NCBI__GCF_001592305.1:WP_068174408.1 108 QKRASgesWSYRDEDGTLLGQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPAHVAGVAEIIMVVPTP-KG 175
                                               *9876667*********************************************************6.9* PP

                                 TIGR00069 133 kvnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaG 201
                                               + np vlaaa ++gv++ +++GGaqa+aalayGt+tvpkvdki+GPGn+yV+ AKk vfg+vgidmiaG
  lcl|NCBI__GCF_001592305.1:WP_068174408.1 176 EKNPLVLAAAYVAGVTRAFTIGGAQAVAALAYGTATVPKVDKITGPGNAYVASAKKRVFGTVGIDMIAG 244
                                               ********************************************************************* PP

                                 TIGR00069 202 PsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslek 270
                                               PsE+lv+ad s+ +++va+Dl+sqaEHde aq+il++++++ +++v++++++ l +++r+ i+ ksl++
  lcl|NCBI__GCF_001592305.1:WP_068174408.1 245 PSEILVLADGSTPADWVAMDLFSQAEHDELAQSILLCPDAAYIDAVQAAIDRLLPTMPRAAIIAKSLND 313
                                               ********************************************************************* PP

                                 TIGR00069 271 ngaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTs 339
                                               +ga+il++d+eea+++sn++ApEHLe+  ++p+++ + +k+aG++flG+yt+e+lgdy+aGpnhvLPTs
  lcl|NCBI__GCF_001592305.1:WP_068174408.1 314 RGALILTRDMEEACAISNRIAPEHLEVSSSEPHRWEPLLKHAGAIFLGAYTSESLGDYCAGPNHVLPTS 382
                                               ********************************************************************* PP

                                 TIGR00069 340 gtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               gtArf+s+l+v+dF+kr+s++e+s +++++l+  +++la  EgL+aHa+a+e R
  lcl|NCBI__GCF_001592305.1:WP_068174408.1 383 GTARFSSPLGVYDFQKRSSLIEVSAAGAQTLGIIAAELAYGEGLQAHARAAELR 436
                                               **************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (447 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: 10.42
//
[ok]

This GapMind analysis is from Apr 10 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