Alignments for a candidate for hisD in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Steroidobacter denitrificans DSM 18526

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_210399219.1 ACG33_RS07645 histidinol dehydrogenase

Query= SwissProt::P06988
         (434 letters)



>NCBI__GCF_001579945.1:WP_210399219.1
          Length = 463

 Score =  404 bits (1038), Expect = e-117
 Identities = 207/423 (48%), Positives = 284/423 (67%), Gaps = 4/423 (0%)

Query: 9   WNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKV 68
           W+S +A+++   L RPA   ++++   V +I+  V++RGD AL +Y+ +FD   +T L+V
Sbjct: 14  WSSLSAQERYTALRRPAQRNTQALHEQVREIIQEVRSRGDHALVDYARRFDGVELTTLEV 73

Query: 69  SAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVG 128
           +  E AAA   L    +QA+  A+ N+  FH AQ+  P+ +E  PGV C++  RP+ +VG
Sbjct: 74  TPAEFAAAQTSLDAVQRQALERAIANVRRFHEAQRAEPIRLEISPGVTCEREFRPIDAVG 133

Query: 129 LYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPP---IADE-ILYAAQLCGVQDVFNV 184
           LY+P G APL ST +MLA PA IAGC   ++C+PP     AD  +L  A+LCG++ VF +
Sbjct: 134 LYVPAGVAPLPSTAIMLAVPALIAGCPTRIICTPPRKDGSADPAVLTVARLCGIERVFKL 193

Query: 185 GGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIAD 244
           GGAQAIAA+A+GT SVPKVDK++GPGNA+VT AK  V+   DGAA+D+PAGPSEVLVIAD
Sbjct: 194 GGAQAIAAMAYGTASVPKVDKVYGPGNAWVTAAKLLVANDPDGAALDLPAGPSEVLVIAD 253

Query: 245 SGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNA 304
             A P+FVA+DLL+Q EH  D+Q +L+T +  +A+   E +  Q+  L R  T R+A+  
Sbjct: 254 EQAHPEFVAADLLAQTEHSADAQSVLVTTSMALAQATLEQLAAQMPRLERERTLREAIQN 313

Query: 305 SRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASG 364
           +RL +   L    ++SN Y PEHLIIQ   AR  V  + +AGSVFLG W+PE+ GDY SG
Sbjct: 314 TRLFLVDSLQDAFDLSNTYAPEHLIIQIAAARAWVPQVRNAGSVFLGAWTPETMGDYCSG 373

Query: 365 TNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVT 424
           TNHVLPTYG+    S LGL DF KR+T+QEL+ +G   L  T  T+A  E L AH NAV 
Sbjct: 374 TNHVLPTYGFARAYSGLGLGDFLKRITIQELTADGLRDLGPTALTIAHMEGLGAHANAVQ 433

Query: 425 LRV 427
           +R+
Sbjct: 434 VRL 436


Lambda     K      H
   0.315    0.128    0.356 

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: 500
Number of extensions: 17
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: 434
Length of database: 463
Length adjustment: 33
Effective length of query: 401
Effective length of database: 430
Effective search space:   172430
Effective search space used:   172430
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_210399219.1 ACG33_RS07645 (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.742203.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-161  524.5   0.0   1.2e-161  524.3   0.0    1.0  1  NCBI__GCF_001579945.1:WP_210399219.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001579945.1:WP_210399219.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.3   0.0  1.2e-161  1.2e-161       1     393 []      41     435 ..      41     435 .. 0.99

  Alignments for each domain:
  == domain 1  score: 524.3 bits;  conditional E-value: 1.2e-161
                             TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 
                                           v+eii++vr++Gd+Al++y+++fd+v+l++l+v+ +e+++a++++d+  ++ale+a++n+++fhe+q++e + 
  NCBI__GCF_001579945.1:WP_210399219.1  41 VREIIQEVRSRGDHALVDYARRFDGVELTTLEVTPAEFAAAQTSLDAVQRQALERAIANVRRFHEAQRAEPIR 113
                                           89*********************************************************************** PP

                             TIGR00069  74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllg 146
                                           +e+++gv++++ +rp+++vglYvP+G a++pSt++m+avpA +Ag+++ +++tPp+kdg+++pavl++a+l+g
  NCBI__GCF_001579945.1:WP_210399219.1 114 LEISPGVTCEREFRPIDAVGLYVPAGVAPLPSTAIMLAVPALIAGCPTRIICTPPRKDGSADPAVLTVARLCG 186
                                           ************************************************************************* PP

                             TIGR00069 147 vdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf...gevgidmiaGPsEvlviadesanpe 216
                                           +++v+k+GGaqaiaa+ayGt++vpkvdk+ GPGn++VtaAK lv+   +  ++d++aGPsEvlviade+a+pe
  NCBI__GCF_001579945.1:WP_210399219.1 187 IERVFKLGGAQAIAAMAYGTASVPKVDKVYGPGNAWVTAAKLLVAndpDGAALDLPAGPSEVLVIADEQAHPE 259
                                           *********************************************6555899********************* PP

                             TIGR00069 217 lvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289
                                           +vaaDll+q EH +daq++lvtts +la+++ e++++q+ +ler+++ +++++ n++++lvd+l++a++lsn+
  NCBI__GCF_001579945.1:WP_210399219.1 260 FVAADLLAQTEHSADAQSVLVTTSMALAQATLEQLAAQMPRLERERTLREAIQ-NTRLFLVDSLQDAFDLSNT 331
                                           *****************************************************.89***************** PP

                             TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362
                                           yApEHL++q++ +++++++++naGsvflG++tpe++gdy++G+nhvLPT+g+Ar++sgl++ dFlkri++qel
  NCBI__GCF_001579945.1:WP_210399219.1 332 YAPEHLIIQIAAARAWVPQVRNAGSVFLGAWTPETMGDYCSGTNHVLPTYGFARAYSGLGLGDFLKRITIQEL 404
                                           ************************************************************************* PP

                             TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393
                                           + ++l++l++++ ++a++EgL aHa+av+vR
  NCBI__GCF_001579945.1:WP_210399219.1 405 TADGLRDLGPTALTIAHMEGLGAHANAVQVR 435
                                           *****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (463 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: 00:00:00.00
# Mc/sec: 18.33
//
[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