Alignments for a candidate for hisD in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Bradyrhizobium sp. BTAi1

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012041205.1 BBTA_RS04225 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000015165.1:WP_012041205.1
          Length = 431

 Score =  575 bits (1483), Expect = e-169
 Identities = 293/430 (68%), Positives = 343/430 (79%)

Query: 1   MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60
           M   L +   DF+ +F  FL+ KRE S DV+ A R IVD V + GD+ALL+ +R+FDR++
Sbjct: 1   MPIRLSRAHADFDAQFRQFLAAKRETSADVEAAARAIVDDVAKRGDAALLEATRKFDRLE 60

Query: 61  LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
           L    + VT  EI+AA  A  A+T++ALK ARDRIE  H +QLP+D R+TDA GVELG R
Sbjct: 61  LTAASLRVTADEIEAAVTACDAATLDALKFARDRIEAFHLKQLPQDQRFTDAAGVELGWR 120

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
           W+AIE+ GLYVPGGTA+YPSSVLMNA+PAKVAGV R+VMVVPAPDG LNPLVL AA L G
Sbjct: 121 WSAIESAGLYVPGGTAAYPSSVLMNAIPAKVAGVSRLVMVVPAPDGKLNPLVLAAAHLGG 180

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           VSEIYRVGGAQA+AALA+GT TI PV KIVGPGNAYVAAAKR+VFG VGIDMIAGPSEVL
Sbjct: 181 VSEIYRVGGAQAVAALAHGTATIAPVVKIVGPGNAYVAAAKRLVFGKVGIDMIAGPSEVL 240

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           ++AD   N DWIAADLLAQAEHD +AQSIL+T+    A  V  AVE QL TL R + A A
Sbjct: 241 VIADDSGNADWIAADLLAQAEHDASAQSILITDSRRLADDVARAVEGQLKTLPRAQIAGA 300

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           SW DFGA+I V+D + A+PLA+ IAAEHLEI   D +AF  R+RNAG+IF+G +TPE IG
Sbjct: 301 SWADFGAIIEVEDLDQAVPLADAIAAEHLEIMTRDPDAFAARVRNAGAIFLGAHTPEAIG 360

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DYVGG NHVLPTARSARFSSGL VLD+MKRTSLLK G EQLRALGPAA+ + +AEGLDAH
Sbjct: 361 DYVGGSNHVLPTARSARFSSGLGVLDFMKRTSLLKCGPEQLRALGPAAMTLGKAEGLDAH 420

Query: 421 AQSVAIRLNL 430
           ++SV IRLNL
Sbjct: 421 SRSVGIRLNL 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: 551
Number of extensions: 17
Number of successful extensions: 1
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: 431
Length adjustment: 32
Effective length of query: 398
Effective length of database: 399
Effective search space:   158802
Effective search space used:   158802
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_012041205.1 BBTA_RS04225 (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.28396.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-162  525.2   0.7   7.3e-162  525.0   0.7    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012041205.1  BBTA_RS04225 histidinol dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012041205.1  BBTA_RS04225 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.0   0.7  7.3e-162  7.3e-162       2     393 .]      35     427 ..      34     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 525.0 bits;  conditional E-value: 7.3e-162
                                 TIGR00069   2 keiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekql 68 
                                               ++i++dv k+Gd+Alle t+kfd++  +++slrv+++e+e+a++a+d+++ +al+ a ++ie+fh kql
  lcl|NCBI__GCF_000015165.1:WP_012041205.1  35 RAIVDDVAKRGDAALLEATRKFDRLelTAASLRVTADEIEAAVTACDAATLDALKFARDRIEAFHLKQL 103
                                               68*********************9977888*************************************** PP

                                 TIGR00069  69 pesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpa 137
                                               p++   ++++gv lg ++ ++e++glYvPgG+aaypS+vlm+a+pAkvAgv+++v+v P   dgk+np 
  lcl|NCBI__GCF_000015165.1:WP_012041205.1 104 PQDQRFTDAAGVELGWRWSAIESAGLYVPGGTAAYPSSVLMNAIPAKVAGVSRLVMVVPAP-DGKLNPL 171
                                               ************************************************************6.******* PP

                                 TIGR00069 138 vlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvl 206
                                               vlaaa+l gv+e+y+vGGaqa+aala+Gt+t+ +v kivGPGn+yV+aAK+lvfg+vgidmiaGPsEvl
  lcl|NCBI__GCF_000015165.1:WP_012041205.1 172 VLAAAHLGGVSEIYRVGGAQAVAALAHGTATIAPVVKIVGPGNAYVAAAKRLVFGKVGIDMIAGPSEVL 240
                                               ********************************************************************* PP

                                 TIGR00069 207 viadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaii 275
                                               viad+s n++++aaDll+qaEHd++aq+il+t+s++la++v ++ve ql++l+r++ia +s+++ gaii
  lcl|NCBI__GCF_000015165.1:WP_012041205.1 241 VIADDSGNADWIAADLLAQAEHDASAQSILITDSRRLADDVARAVEGQLKTLPRAQIAGASWADFGAII 309
                                               ********************************************************************* PP

                                 TIGR00069 276 lvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArf 344
                                                v+dl++a+ l++++A+EHLe++t+dp +++ +++naG++flG++tpea+gdyv G+nhvLPT+++Arf
  lcl|NCBI__GCF_000015165.1:WP_012041205.1 310 EVEDLDQAVPLADAIAAEHLEIMTRDPDAFAARVRNAGAIFLGAHTPEAIGDYVGGSNHVLPTARSARF 378
                                               ********************************************************************* PP

                                 TIGR00069 345 asglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               +sgl+v dF+kr+s+ ++  e+l++l++a+++l +aEgL+aH ++v +R
  lcl|NCBI__GCF_000015165.1:WP_012041205.1 379 SSGLGVLDFMKRTSLLKCGPEQLRALGPAAMTLGKAEGLDAHSRSVGIR 427
                                               **********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (431 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: 9.12
//
[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