Alignments for a candidate for hisD in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Stenotrophomonas chelatiphaga DSM 21508

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_057506748.1 ABB28_RS00530 histidinol dehydrogenase

Query= SwissProt::P06988
         (434 letters)



>NCBI__GCF_001431535.1:WP_057506748.1
          Length = 431

 Score =  404 bits (1038), Expect = e-117
 Identities = 222/429 (51%), Positives = 286/429 (66%), Gaps = 7/429 (1%)

Query: 7   IDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTAL 66
           ++W+      + + L RP  + +      V  ++  V+A GD ALRE +A+FD+  +  +
Sbjct: 4   LNWSELNELDRAEALQRPVQAVAAQTRHAVAALIAQVRADGDAALREITARFDRVQLDDI 63

Query: 67  KVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVAS 126
           +V+A E  AA + ++ +L+ AM  A   I  FH A       VET PGV C+++ RP+  
Sbjct: 64  EVTAAEFEAAEQAVAVDLRAAMEEAAARIRRFHEAGMSQGYAVETAPGVHCERMIRPIGR 123

Query: 127 VGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPI---ADE-ILYAAQLCGVQDVF 182
           VGLY+P GSAPL ST LML  PA++AGC +VVLC+PP     AD  +L AA+L GVQ VF
Sbjct: 124 VGLYVPAGSAPLPSTALMLGVPAALAGCPQVVLCTPPRADGSADPAVLVAARLTGVQRVF 183

Query: 183 NVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGA-AIDMPAGPSEVLV 241
            +GGAQAIAA+A GT SVP  DK+FGPGN+FVTEAK+QV+Q  DG+ AIDMPAGPSEVLV
Sbjct: 184 KLGGAQAIAAMAHGTASVPACDKLFGPGNSFVTEAKQQVAQ--DGSVAIDMPAGPSEVLV 241

Query: 242 IADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQA 301
           IAD+GA   FVA+DLLSQAEHGPDSQV+LLT  A +   V   VERQ+A LPR   AR+A
Sbjct: 242 IADAGANAAFVAADLLSQAEHGPDSQVLLLTDDAALLEAVEAEVERQVALLPRETIARRA 301

Query: 302 LNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDY 361
           L ASRLI+   L    EISN+Y PEHLI+  R  R  +  + +AGSVFLGD++PE+ GDY
Sbjct: 302 LGASRLILVDRLQDAFEISNRYAPEHLILALREPRAWLGQVQAAGSVFLGDYTPEALGDY 361

Query: 362 ASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKN 421
            SGTNHVLPT G     S + +A FQ  ++VQ  S EG  A+      LA+AE L AH+ 
Sbjct: 362 CSGTNHVLPTAGAARAWSGVSVASFQNTISVQSASAEGIVAIGGCARILASAEGLDAHER 421

Query: 422 AVTLRVNAL 430
           AV LR+ A+
Sbjct: 422 AVALRMEAV 430


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: 472
Number of extensions: 12
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: 434
Length of database: 431
Length adjustment: 32
Effective length of query: 402
Effective length of database: 399
Effective search space:   160398
Effective search space used:   160398
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_057506748.1 ABB28_RS00530 (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.3378.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-161  523.2   2.7   2.9e-161  523.0   2.7    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506748.1  ABB28_RS00530 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506748.1  ABB28_RS00530 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.0   2.7  2.9e-161  2.9e-161       1     393 []      33     426 ..      33     426 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.0 bits;  conditional E-value: 2.9e-161
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlp 69 
                                               v+++i++vr+ Gd+Al+e+t +fd+v+l++++v+++e+e+a++av  +l++a+e+aa++i++fhe+ ++
  lcl|NCBI__GCF_001431535.1:WP_057506748.1  33 VAALIAQVRADGDAALREITARFDRVQLDDIEVTAAEFEAAEQAVAVDLRAAMEEAAARIRRFHEAGMS 101
                                               6789***************************************************************** PP

                                 TIGR00069  70 esveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpav 138
                                               + ++vet++gv +++++rp+ rvglYvP+G+a++pSt+lm++vpA +Ag++++v++tPp+ dg+++pav
  lcl|NCBI__GCF_001431535.1:WP_057506748.1 102 QGYAVETAPGVHCERMIRPIGRVGLYVPAGSAPLPSTALMLGVPAALAGCPQVVLCTPPRADGSADPAV 170
                                               ********************************************************************* PP

                                 TIGR00069 139 laaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf..gevgidmiaGPsEv 205
                                               l+aa+l+gv++v+k+GGaqaiaa+a+Gt++vp++dk++GPGn++Vt+AK++v+  g+v+idm+aGPsEv
  lcl|NCBI__GCF_001431535.1:WP_057506748.1 171 LVAARLTGVQRVFKLGGAQAIAAMAHGTASVPACDKLFGPGNSFVTEAKQQVAqdGSVAIDMPAGPSEV 239
                                               *****************************************************777************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274
                                               lviad+ an+++vaaDllsqaEH++d+q++l+t++++l+e+ve+eve+q++ l+r++ia+++l   +++
  lcl|NCBI__GCF_001431535.1:WP_057506748.1 240 LVIADAGANAAFVAADLLSQAEHGPDSQVLLLTDDAALLEAVEAEVERQVALLPRETIARRALG-ASRL 307
                                               ****************************************************************.89** PP

                                 TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343
                                               ilvd l++a+e+sn+yApEHL+l+ ++p+++l ++++aGsvflG+ytpealgdy++G+nhvLPT+g+Ar
  lcl|NCBI__GCF_001431535.1:WP_057506748.1 308 ILVDRLQDAFEISNRYAPEHLILALREPRAWLGQVQAAGSVFLGDYTPEALGDYCSGTNHVLPTAGAAR 376
                                               ********************************************************************* PP

                                 TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               + sg+sv++F+++isvq++s e++ +++  ++ la+aEgL+aH++av+ R
  lcl|NCBI__GCF_001431535.1:WP_057506748.1 377 AWSGVSVASFQNTISVQSASAEGIVAIGGCARILASAEGLDAHERAVALR 426
                                               ***********************************************988 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.24
//
[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