Alignments for a candidate for hisD in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Thermodesulforhabdus norvegica DSM 9990

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_093394626.1 BM091_RS07235 histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>NCBI__GCF_900114975.1:WP_093394626.1
          Length = 438

 Score =  331 bits (849), Expect = 2e-95
 Identities = 183/409 (44%), Positives = 264/409 (64%), Gaps = 7/409 (1%)

Query: 26  VSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDAAPA--- 82
           V E ++  V+ I++ VR++GD A+++Y+R FD  D EK  IAV++ EI+ A++       
Sbjct: 26  VDETIEARVKGILEEVRKKGDRAIVEYTRAFDCPDFEKAMIAVSDDEIEKAYEEISGFDR 85

Query: 83  STVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASYP--- 139
              + ++ A D + + H  Q  +    T   GV LG     +E+VG Y+PGG        
Sbjct: 86  DFTDIIRRAADNVREFHEAQKERSWFMTRDDGVFLGQMVRPVESVGAYIPGGAEGATPLI 145

Query: 140 SSVLMNAMPAKVAGVDRIVMVVPA-PDGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAY 198
           S+V+M  +PA+VAGV  I +  P   DG L+P +LV A+  G   IYR+G A A+AA A+
Sbjct: 146 STVIMTVIPARVAGVKEIAIASPPRKDGTLHPGLLVTAKECGAQRIYRMGSAWAVAAFAW 205

Query: 199 GTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLA 258
           GTET++PV  IVGPGN YV  AKR++ G VG+D+IAGPSEVLI+AD+  NP ++AADLL+
Sbjct: 206 GTETVKPVNIIVGPGNIYVTTAKRLLMGIVGVDIIAGPSEVLIIADETANPVFVAADLLS 265

Query: 259 QAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFEDAI 318
           QAEHDT A  +L+T ++  A  V E V+RQ+ +L R + A  +  ++GA  LV++ + A 
Sbjct: 266 QAEHDTYASPVLITWNKELAEGVIEEVKRQVRSLPRRDVALEALTNYGACFLVENEDVAA 325

Query: 319 PLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARF 378
            LANRIA EHLE+ V     ++ +I NAG++FIG YTPE +GDY  G NHVLPT+++ARF
Sbjct: 326 ELANRIAPEHLELHVKTPWDWLGKITNAGALFIGHYTPEPLGDYFAGPNHVLPTSQTARF 385

Query: 379 SSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427
           +S L V ++++R SLL    E       A   +AR EGL+AHA+S++IR
Sbjct: 386 ASALGVQNFLRRISLLHYPEEAFFRDASAVERMARWEGLEAHARSISIR 434


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: 415
Number of extensions: 18
Number of successful extensions: 5
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: 438
Length adjustment: 32
Effective length of query: 398
Effective length of database: 406
Effective search space:   161588
Effective search space used:   161588
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_093394626.1 BM091_RS07235 (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.130397.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-158  512.4   0.0   5.7e-158  512.2   0.0    1.0  1  NCBI__GCF_900114975.1:WP_093394626.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900114975.1:WP_093394626.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.2   0.0  5.7e-158  5.7e-158       1     393 []      34     434 ..      34     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 512.2 bits;  conditional E-value: 5.7e-158
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeav...deelkealelaaeniekfhekql 68 
                                           vk i+e+vrk+Gd+A++eyt+ fd    +++ ++vs++e+e+a+e++   d+++ + +++aa+n+++fhe+q+
  NCBI__GCF_900114975.1:WP_093394626.1  34 VKGILEEVRKKGDRAIVEYTRAFDCPdfEKAMIAVSDDEIEKAYEEIsgfDRDFTDIIRRAADNVREFHEAQK 106
                                           789*********************985577889***********997444689******************** PP

                             TIGR00069  69 pesveveteegvllgqkvrplervglYvPgGk...aaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpav 138
                                           ++s+++++ +gv+lgq+vrp+e+vg+Y+PgG    ++++Stv+mt++pA+vAgvkei++++Pp+kdg+++p +
  NCBI__GCF_900114975.1:WP_093394626.1 107 ERSWFMTRDDGVFLGQMVRPVESVGAYIPGGAegaTPLISTVIMTVIPARVAGVKEIAIASPPRKDGTLHPGL 179
                                           ******************************8655589************************************ PP

                             TIGR00069 139 laaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviade 211
                                           l++ak +g++++y++G a a+aa+a+Gtetv++v++ivGPGniyVt+AK+l++g vg+d+iaGPsEvl+iade
  NCBI__GCF_900114975.1:WP_093394626.1 180 LVTAKECGAQRIYRMGSAWAVAAFAWGTETVKPVNIIVGPGNIYVTTAKRLLMGIVGVDIIAGPSEVLIIADE 252
                                           ************************************************************************* PP

                             TIGR00069 212 sanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleeal 284
                                           +anp +vaaDllsqaEHd+ a+ +l+t ++elae v eev++q+++l+r+++a ++l+++ga++lv++ + a+
  NCBI__GCF_900114975.1:WP_093394626.1 253 TANPVFVAADLLSQAEHDTYASPVLITWNKELAEGVIEEVKRQVRSLPRRDVALEALTNYGACFLVENEDVAA 325
                                           ************************************************************************* PP

                             TIGR00069 285 elsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkri 357
                                           el+n++ApEHLel++k p+++l ki+naG++f+G+ytpe+lgdy+aGpnhvLPTs+tArfas+l+v++Fl+ri
  NCBI__GCF_900114975.1:WP_093394626.1 326 ELANRIAPEHLELHVKTPWDWLGKITNAGALFIGHYTPEPLGDYFAGPNHVLPTSQTARFASALGVQNFLRRI 398
                                           ************************************************************************* PP

                             TIGR00069 358 svqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                           s+ ++ +ea+ + a+ave++a++EgLeaHa+++++R
  NCBI__GCF_900114975.1:WP_093394626.1 399 SLLHYPEEAFFRDASAVERMARWEGLEAHARSISIR 434
                                           **********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (438 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: 15.89
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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