Alignments for a candidate for hisD in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Chlorobium phaeobacteroides BS1

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012475214.1 CPHAMN1_RS09080 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_000020545.1:WP_012475214.1
          Length = 430

 Score =  306 bits (784), Expect = 8e-88
 Identities = 167/401 (41%), Positives = 244/401 (60%), Gaps = 3/401 (0%)

Query: 29  DVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDAAPASTVEAL 88
           +V + V+E++  ++  GD AL  Y+R+F     +   I V+  EI  A++ A +  +  L
Sbjct: 27  EVRQVVQEVLSDIQERGDEALFGYTRKFQ--GFQPGEITVSLEEIREAYELADSDFIGIL 84

Query: 89  KLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASYPSSVLMNAMP 148
           + A   + + H  +  K   Y     V LG R T IE V LYVPGG A+YPSS+LMN  P
Sbjct: 85  EEAYRNVTEFHELETEKSFFYEKENRVILGQRVTPIERVMLYVPGGKAAYPSSLLMNVAP 144

Query: 149 AKVAGVDRIVMVVPAP-DGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPVA 207
           A+VAGV  I +  P   +G ++  +L AA +AGV  IY+ GGAQA+ A A+GT+++  V 
Sbjct: 145 ARVAGVPGIYLTTPCDAEGKVSRHILAAAHVAGVDTIYKFGGAQAVGAFAFGTQSVPKVD 204

Query: 208 KIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAAQ 267
           KI GPGN YVA AK+ VFG V ID +AGPSEV+++AD   +P++I  DL AQ+EHD  A 
Sbjct: 205 KITGPGNKYVAQAKKEVFGHVSIDSVAGPSEVVVIADDTADPEFIVLDLFAQSEHDPDAS 264

Query: 268 SILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAAE 327
           S+L+T+    A  V    +  + T+ R+E    +    GA++L +D +++  +++ IA E
Sbjct: 265 SVLITHSAELASEVSRLADEMVTTMERSEIIQHALTANGAIVLTRDLQESCEVSDMIAPE 324

Query: 328 HLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDY 387
           HLE+ V D+   +P +++AG+IF+GGY+ E +GDY  G NH LPT  +ARF S LSV D+
Sbjct: 325 HLELHVRDSWEILPDLKHAGAIFMGGYSCESVGDYFAGPNHTLPTNGTARFFSPLSVRDF 384

Query: 388 MKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428
           +K TS++    EQL   G      A  E L AHA++V  RL
Sbjct: 385 IKHTSIISYSKEQLALSGEKIARFADHEQLQAHAEAVRARL 425


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: 408
Number of extensions: 20
Number of successful extensions: 3
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: 430
Length adjustment: 32
Effective length of query: 398
Effective length of database: 398
Effective search space:   158404
Effective search space used:   158404
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_012475214.1 CPHAMN1_RS09080 (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.17183.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-162  524.8   0.1   9.7e-162  524.6   0.1    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012475214.1  CPHAMN1_RS09080 histidinol dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012475214.1  CPHAMN1_RS09080 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.6   0.1  9.7e-162  9.7e-162       1     393 []      32     424 ..      32     424 .. 1.00

  Alignments for each domain:
  == domain 1  score: 524.6 bits;  conditional E-value: 9.7e-162
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlp 69 
                                               v+e+++d++++GdeAl+ yt+kf+++++ +++vs ee++ea+e  d++++  le+a++n+++fhe +++
  lcl|NCBI__GCF_000020545.1:WP_012475214.1  32 VQEVLSDIQERGDEALFGYTRKFQGFQPGEITVSLEEIREAYELADSDFIGILEEAYRNVTEFHELETE 100
                                               899****************************************************************** PP

                                 TIGR00069  70 esveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpav 138
                                               +s+++e+e+ v+lgq+v+p+erv lYvPgGkaaypS++lm++ pA+vAgv+ i+++tP + +gkv++++
  lcl|NCBI__GCF_000020545.1:WP_012475214.1 101 KSFFYEKENRVILGQRVTPIERVMLYVPGGKAAYPSSLLMNVAPARVAGVPGIYLTTPCDAEGKVSRHI 169
                                               ********************************************************************* PP

                                 TIGR00069 139 laaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlv 207
                                               laaa+++gvd++yk GGaqa++a+a+Gt++vpkvdki+GPGn+yV++AKk+vfg+v+id++aGPsEv+v
  lcl|NCBI__GCF_000020545.1:WP_012475214.1 170 LAAAHVAGVDTIYKFGGAQAVGAFAFGTQSVPKVDKITGPGNKYVAQAKKEVFGHVSIDSVAGPSEVVV 238
                                               ********************************************************************* PP

                                 TIGR00069 208 iadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiil 276
                                               iad++a+pe++++Dl++q EHd+da+++l+t+s+ela++v++  +e+++++er+ei++++l+ ngai+l
  lcl|NCBI__GCF_000020545.1:WP_012475214.1 239 IADDTADPEFIVLDLFAQSEHDPDASSVLITHSAELASEVSRLADEMVTTMERSEIIQHALTANGAIVL 307
                                               ********************************************************************* PP

                                 TIGR00069 277 vddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfa 345
                                               ++dl+e +e+s+ +ApEHLel+++d++e+l+++k+aG++f+G y++e++gdy+aGpnh+LPT+gtArf 
  lcl|NCBI__GCF_000020545.1:WP_012475214.1 308 TRDLQESCEVSDMIAPEHLELHVRDSWEILPDLKHAGAIFMGGYSCESVGDYFAGPNHTLPTNGTARFF 376
                                               ********************************************************************* PP

                                 TIGR00069 346 sglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               s+lsv+dF+k++s++++ske+l+  +e+++++a+ E+L+aHaeav++R
  lcl|NCBI__GCF_000020545.1:WP_012475214.1 377 SPLSVRDFIKHTSIISYSKEQLALSGEKIARFADHEQLQAHAEAVRAR 424
                                               **********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (430 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: 7.63
//
[ok]

This GapMind analysis is from Apr 10 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