Alignments for a candidate for hisD in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Rhodomicrobium vannielii ATCC 17100

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_013418233.1 RVAN_RS02720 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000166055.1:WP_013418233.1
          Length = 433

 Score =  521 bits (1342), Expect = e-152
 Identities = 263/430 (61%), Positives = 324/430 (75%), Gaps = 1/430 (0%)

Query: 1   MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60
           M   LR T+PDF+Q+F A + G+R+   DV  AVR ++  VR  GD+AL++++ RFD +D
Sbjct: 1   MTLYLRSTEPDFQQRFDALVHGRRDQPHDVQDAVRSMIAAVRERGDAALIEFTERFDHVD 60

Query: 61  LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
           L +TG+A+   E++AA++        AL+ A +RIEKHH RQ+P DDRY DA+G ELG R
Sbjct: 61  LAETGLAIAPEELEAAWNGLAPDLKAALQTAYERIEKHHRRQIPADDRYADAIGAELGHR 120

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
           WT +++VGLYVPGG ASYPSSVLMNA+PAKVAGV R+VMVVP P G +NP VL AA LAG
Sbjct: 121 WTPLDSVGLYVPGGKASYPSSVLMNAVPAKVAGVPRLVMVVPTPKGEVNPAVLAAAHLAG 180

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           + E+YR+GGAQA+AALAYGTETI+PV KIVGPGNA+VA AKR VFG VGIDMIAGPSEV+
Sbjct: 181 IREVYRIGGAQAVAALAYGTETIKPVVKIVGPGNAWVAEAKRQVFGVVGIDMIAGPSEVV 240

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
            VAD   +P W+AADLLAQAEHD AAQSIL+T+  A A A  +AV+ QL  + R   A+ 
Sbjct: 241 AVADARADPVWLAADLLAQAEHDEAAQSILITDSPALAEATAKAVDAQLAIMPRGAIAAK 300

Query: 301 SWRDFGAVILVKDF-EDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVI 359
           SW D GAV+LV D  ++A  L N +A EHLE+A  +AEA +P IRNAG+IFIG +TPE +
Sbjct: 301 SWADHGAVLLVSDLAKEAPALVNALAPEHLELACDEAEAMLPAIRNAGAIFIGHFTPEAV 360

Query: 360 GDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDA 419
           GDYVGG NHVLPT+R+ARFSSGL VLDYMKRTSLLKL    L  L    + +A AEGL  
Sbjct: 361 GDYVGGSNHVLPTSRAARFSSGLGVLDYMKRTSLLKLSRASLAVLAAPTMTLAEAEGLFG 420

Query: 420 HAQSVAIRLN 429
           H QSVA+R N
Sbjct: 421 HRQSVAVRTN 430


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: 505
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: 430
Length of database: 433
Length adjustment: 32
Effective length of query: 398
Effective length of database: 401
Effective search space:   159598
Effective search space used:   159598
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_013418233.1 RVAN_RS02720 (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.11469.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-158  514.1   3.1   1.7e-158  513.9   3.1    1.0  1  lcl|NCBI__GCF_000166055.1:WP_013418233.1  RVAN_RS02720 histidinol dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013418233.1  RVAN_RS02720 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.9   3.1  1.7e-158  1.7e-158       1     393 []      34     428 ..      34     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 513.9 bits;  conditional E-value: 1.7e-158
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                               v+++i++vr++Gd+Al+e+te+fd+v    + l++  eele+a++ + ++lk+al++a+e+iek h++q
  lcl|NCBI__GCF_000166055.1:WP_013418233.1  34 VRSMIAAVRERGDAALIEFTERFDHVdlAETGLAIAPEELEAAWNGLAPDLKAALQTAYERIEKHHRRQ 102
                                               7899**********************55556799*********************************** PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                               +p++  + ++ g  lg++++pl++vglYvPgGka+ypS+vlm+avpAkvAgv+++v+v P+  +g+vnp
  lcl|NCBI__GCF_000166055.1:WP_013418233.1 103 IPADDRYADAIGAELGHRWTPLDSVGLYVPGGKASYPSSVLMNAVPAKVAGVPRLVMVVPTP-KGEVNP 170
                                               *************************************************************6.9***** PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                               avlaaa+l+g++evy++GGaqa+aalayGtet+++v kivGPGn++V++AK++vfg vgidmiaGPsEv
  lcl|NCBI__GCF_000166055.1:WP_013418233.1 171 AVLAAAHLAGIREVYRIGGAQAVAALAYGTETIKPVVKIVGPGNAWVAEAKRQVFGVVGIDMIAGPSEV 239
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               + +ad++a+p ++aaDll+qaEHde aq+il+t+s +lae++ ++v++ql+ ++r  ia ks++++ga+
  lcl|NCBI__GCF_000166055.1:WP_013418233.1 240 VAVADARADPVWLAADLLAQAEHDEAAQSILITDSPALAEATAKAVDAQLAIMPRGAIAAKSWADHGAV 308
                                               ********************************************************************* PP

                                 TIGR00069 275 ilvddl.eealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342
                                               +lv+dl +ea +l+n++ApEHLel+++++e++l+ i+naG++f+G+ tpea+gdyv G+nhvLPTs++A
  lcl|NCBI__GCF_000166055.1:WP_013418233.1 309 LLVSDLaKEAPALVNALAPEHLELACDEAEAMLPAIRNAGAIFIGHFTPEAVGDYVGGSNHVLPTSRAA 377
                                               ***998358899********************************************************* PP

                                 TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               rf+sgl+v d++kr+s+ +ls+++l+ la  +++laeaEgL  H+++v+vR
  lcl|NCBI__GCF_000166055.1:WP_013418233.1 378 RFSSGLGVLDYMKRTSLLKLSRASLAVLAAPTMTLAEAEGLFGHRQSVAVR 428
                                               ************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (433 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: 10.11
//
[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