GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Nocardiopsis lucentensis DSM 44048

Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate WP_017599139.1 D471_RS0113730 histidinol-phosphate transaminase

Query= curated2:Q46Y48
         (376 letters)



>NCBI__GCF_000341125.1:WP_017599139.1
          Length = 360

 Score =  233 bits (594), Expect = 6e-66
 Identities = 138/326 (42%), Positives = 183/326 (56%), Gaps = 9/326 (2%)

Query: 45  VKLASNENPLGMPESAKHAAAAAIAELGRYPDSNGFELKAALSTKLGVPQDWLTLGNGSN 104
           +KL+SNE+P G   S + A A A AEL RYPD     L   L+  LGVP++ + LG GS 
Sbjct: 34  IKLSSNESPFGPLPSVREAVAQASAELNRYPDPGATALVTELARHLGVPEEHVALGAGSV 93

Query: 105 DILELAAHALVTPGQSIVYAEYSFAVYALATQEIGARAIVVKARDYGHDLDAMAAAITSD 164
            +L+    A+  PG  +VYA  SF  Y L  +  G  ++ V  RD  HDLDA+A AIT  
Sbjct: 94  GLLQQLLEAVGEPGAEVVYAWRSFEAYPLLAELAGVTSVRVPLRDETHDLDAIADAITES 153

Query: 165 TRLVFIANPNNPTGTFVPAAALETFLAKVPAEVVVVLDEAYNEYLDDDQQYDSVAWVRRY 224
           TR+V + NPNNPTGT VP   L  FL +VP  V+V+LDEAY+EY+ D +  D V   R  
Sbjct: 154 TRMVLVCNPNNPTGTTVPKGELLAFLDRVPEHVLVILDEAYHEYVRDPRVPDGVELYRDR 213

Query: 225 PNLLVSRTFSKAYGLAGLRIGYAVAQPELTDLLNRIRQPFNVNSVAQAAAVAALGDTAFL 284
           PN+ V RTFSKAYGLA +R+GY VA P +     +   PF VN +AQAA +A+L     L
Sbjct: 214 PNVAVLRTFSKAYGLAAVRLGYLVAHPHVAAAARKTLVPFAVNHLAQAAGIASLAARDEL 273

Query: 285 QRSAELNRAGKAQLVEAFSRLGLEFVASSGNFVLVRVGDDD-DAGARVNVALLRQGVIVR 343
               E     + ++ +A    G     +  NFV +RVG+D  D  A       + GV VR
Sbjct: 274 MERVEATVGERTRVRDALIASGWTVPPTEANFVWLRVGEDTLDFAAE----CAKVGVSVR 329

Query: 344 PVGNYGMPRWLRVTIGLPDENAAFIA 369
           P    G     RV++G P+EN  F++
Sbjct: 330 PFEGEG----ARVSLGTPEENDVFLS 351


Lambda     K      H
   0.318    0.134    0.382 

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: 336
Number of extensions: 9
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: 376
Length of database: 360
Length adjustment: 30
Effective length of query: 346
Effective length of database: 330
Effective search space:   114180
Effective search space used:   114180
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: 49 (23.5 bits)

Align candidate WP_017599139.1 D471_RS0113730 (histidinol-phosphate transaminase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.16166.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.6e-91  292.1   0.0    2.9e-91  291.9   0.0    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017599139.1  D471_RS0113730 histidinol-phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017599139.1  D471_RS0113730 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.9   0.0   2.9e-91   2.9e-91       2     345 ..      12     352 ..      11     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 291.9 bits;  conditional E-value: 2.9e-91
                                 TIGR01141   2 ekikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                                 ++++ +Y+pg + +g +   +kL+snE+Pfgp ++v+ea+ ++ ++l+rYpdp a++l ++la++lg
  lcl|NCBI__GCF_000341125.1:WP_017599139.1  12 SVLESIPAYKPGRKVVGPDgRSIKLSSNESPFGPLPSVREAVAQASAELNRYPDPGATALVTELARHLG 80 
                                               5688999*****888888899************************99********************** PP

                                 TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavle 138
                                               v ee ++lg+Gs +l++ l++a+ epg++v+++  +++ Y++ a++ag+  + vpl+++ ++dl+a+++
  lcl|NCBI__GCF_000341125.1:WP_017599139.1  81 VPEEHVALGAGSVGLLQQLLEAVGEPGAEVVYAWRSFEAYPLLAELAGVTSVRVPLRDE-THDLDAIAD 148
                                               **********************************************************9.6******** PP

                                 TIGR01141 139 aakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlv 203
                                               a++e++++v +++PnnPtG+ + + e+ ++l++v e++lV++DeAY e+ ++   ++ +el +++pn++
  lcl|NCBI__GCF_000341125.1:WP_017599139.1 149 AITESTRMVLVCNPNNPTGTTVPKGELLAFLDRVpEHVLVILDEAYHEYVRDprvPDGVELYRDRPNVA 217
                                               **********************************99****************9999************* PP

                                 TIGR01141 204 vlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkerer 272
                                               vlrT+SKa+gLA++R+Gy++a+++++ a +k   p+ v+ la++a++a+l  +d+++++ve+   er+r
  lcl|NCBI__GCF_000341125.1:WP_017599139.1 218 VLRTFSKAYGLAAVRLGYLVAHPHVAAAARKTLVPFAVNHLAQAAGIASLAARDELMERVEATVGERTR 286
                                               ********************************************************************* PP

                                 TIGR01141 273 lleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreener 341
                                               + ++l +  g  v + +aNFv ++v ed  +++ +  + g+ vR ++   g      R++ Gt+een+ 
  lcl|NCBI__GCF_000341125.1:WP_017599139.1 287 VRDALIAS-GWTVPPTEANFVWLRVGEDTLDFAAECAKVGVSVRPFEGE-G-----ARVSLGTPEENDV 348
                                               ******98.89***********************************966.6.....5************ PP

                                 TIGR01141 342 llea 345
                                               +l +
  lcl|NCBI__GCF_000341125.1:WP_017599139.1 349 FLSV 352
                                               *987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (360 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: 9.79
//
[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:

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:

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:

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:

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