Alignments for a candidate for hisD in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Malonomonas rubra DSM 5091

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_072907092.1 BUB13_RS06015 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_900142125.1:WP_072907092.1
          Length = 429

 Score =  399 bits (1024), Expect = e-115
 Identities = 205/424 (48%), Positives = 293/424 (69%)

Query: 5   LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64
           L+ +D DF+ +F        EV   ++  V+ I+  VR+ GD AL + + +FD+++L+  
Sbjct: 4   LKFSDSDFDTEFRRIEQRAEEVPAGIEETVKNIIADVRKRGDVALFELTAKFDKLELDVD 63

Query: 65  GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAI 124
            + VTE EI+AA     A ++ AL+LA +RI  +HA+Q  +    TD   V +G     +
Sbjct: 64  SLEVTEEEIEAAMAQISAESLSALQLAAERIADYHAKQKQETWISTDESDVLVGQMVRPL 123

Query: 125 EAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEI 184
           + VG+YVPGG A+YPSSVLMNA+PAKVAGV+ ++MVVP P+G +NP VL AA+++GV  I
Sbjct: 124 DRVGIYVPGGKATYPSSVLMNAVPAKVAGVEEVIMVVPMPNGEVNPHVLAAAKISGVDRI 183

Query: 185 YRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVAD 244
           +++GGAQA+AALAYGT+++  V KI GPGN YVA AK++VFG V IDMIAGPSE+L++ D
Sbjct: 184 FKLGGAQAVAALAYGTDSVPRVDKITGPGNIYVATAKQLVFGQVDIDMIAGPSEILVIND 243

Query: 245 KDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRD 304
              N   IAADLL+QAEHD  A S+L+T+ E  A AV+  VE+QL  L+R   A  S  D
Sbjct: 244 GSGNAAHIAADLLSQAEHDELASSVLVTSCEKMAAAVQAEVEKQLSELSREGIARKSIDD 303

Query: 305 FGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVG 364
           +GA+IL ++ ++AI  +NRIA EHLE+AV      +P+I++AG++F+G +TPE  GDY+ 
Sbjct: 304 YGAIILAQNLDEAIAFSNRIAPEHLELAVDSPFDILPQIKHAGAVFMGHHTPEAAGDYLA 363

Query: 365 GCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSV 424
           G NH LPT  +ARF S LS+ D++K++S++      L+ LG   + IA  EGL+AHA+SV
Sbjct: 364 GPNHTLPTGGTARFFSPLSLDDFVKKSSIVSFSQAGLQRLGNEIVHIAELEGLEAHAKSV 423

Query: 425 AIRL 428
           +IRL
Sbjct: 424 SIRL 427


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: 449
Number of extensions: 23
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: 429
Length adjustment: 32
Effective length of query: 398
Effective length of database: 397
Effective search space:   158006
Effective search space used:   158006
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_072907092.1 BUB13_RS06015 (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.13045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-172  560.0   4.8   1.9e-172  559.8   4.8    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072907092.1  BUB13_RS06015 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072907092.1  BUB13_RS06015 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.8   4.8  1.9e-172  1.9e-172       1     393 []      33     426 ..      33     426 .. 0.99

  Alignments for each domain:
  == domain 1  score: 559.8 bits;  conditional E-value: 1.9e-172
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                               vk+ii+dvrk+Gd Al+e+t kfdk+  +++sl+v+eee+e+a++++++e  +al+laae+i+++h+kq
  lcl|NCBI__GCF_900142125.1:WP_072907092.1  33 VKNIIADVRKRGDVALFELTAKFDKLelDVDSLEVTEEEIEAAMAQISAESLSALQLAAERIADYHAKQ 101
                                               89***********************977889************************************** PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136
                                               ++e++ +++e++vl+gq+vrpl+rvg+YvPgGka+ypS+vlm+avpAkvAgv+e+++v P+  +g+vnp
  lcl|NCBI__GCF_900142125.1:WP_072907092.1 102 KQETWISTDESDVLVGQMVRPLDRVGIYVPGGKATYPSSVLMNAVPAKVAGVEEVIMVVPMP-NGEVNP 169
                                               *************************************************************6.****** PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                               +vlaaak+ gvd+++k+GGaqa+aalayGt++vp+vdki+GPGniyV++AK+lvfg+v+idmiaGPsE+
  lcl|NCBI__GCF_900142125.1:WP_072907092.1 170 HVLAAAKISGVDRIFKLGGAQAVAALAYGTDSVPRVDKITGPGNIYVATAKQLVFGQVDIDMIAGPSEI 238
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               lvi d s n++++aaDllsqaEHde a+++lvt+ e++a++v++eve+ql+el+r+ ia+ks++++gai
  lcl|NCBI__GCF_900142125.1:WP_072907092.1 239 LVINDGSGNAAHIAADLLSQAEHDELASSVLVTSCEKMAAAVQAEVEKQLSELSREGIARKSIDDYGAI 307
                                               ********************************************************************* PP

                                 TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                               il+++l+ea+++sn++ApEHLel++++p ++l++ik+aG+vf+G++tpea+gdy+aGpnh+LPT+gtAr
  lcl|NCBI__GCF_900142125.1:WP_072907092.1 308 ILAQNLDEAIAFSNRIAPEHLELAVDSPFDILPQIKHAGAVFMGHHTPEAAGDYLAGPNHTLPTGGTAR 376
                                               ********************************************************************* PP

                                 TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               f s+ls++dF+k++s++++s+++l++l+++++++ae+EgLeaHa++v++R
  lcl|NCBI__GCF_900142125.1:WP_072907092.1 377 FFSPLSLDDFVKKSSIVSFSQAGLQRLGNEIVHIAELEGLEAHAKSVSIR 426
                                               ************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (429 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 8.32
//
[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