GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisC in Burkholderia phytofirmans PsJN

Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate BPHYT_RS14905 BPHYT_RS14905 histidinol-phosphate aminotransferase

Query= curated2:Q46Y48
         (376 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS14905 BPHYT_RS14905
           histidinol-phosphate aminotransferase
          Length = 370

 Score =  563 bits (1452), Expect = e-165
 Identities = 279/363 (76%), Positives = 317/363 (87%)

Query: 13  FGPDYVRAISPYIAGKPISEVAREFGLDEAGIVKLASNENPLGMPESAKHAAAAAIAELG 72
           FGP YVRAI+PYIAGKPISEVAREFGLDEA IVKLASNENPLGMPESA+ A A A +ELG
Sbjct: 5   FGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELG 64

Query: 73  RYPDSNGFELKAALSTKLGVPQDWLTLGNGSNDILELAAHALVTPGQSIVYAEYSFAVYA 132
           RYPD+N FELKAALS + GVP DW+TLGNGSNDILE+AAHA V  GQSIVYA+YSFAVYA
Sbjct: 65  RYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYA 124

Query: 133 LATQEIGARAIVVKARDYGHDLDAMAAAITSDTRLVFIANPNNPTGTFVPAAALETFLAK 192
           LATQ +GARAIVV A  YGHDLDAM AA++ DTRL+F+ANPNNPTGTF+    LE FL K
Sbjct: 125 LATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDK 184

Query: 193 VPAEVVVVLDEAYNEYLDDDQQYDSVAWVRRYPNLLVSRTFSKAYGLAGLRIGYAVAQPE 252
           VP  VVVVLDEAY EYL  +++YDS+AWVRRYPNLLVSRTFSKA+GLAGLR+G+A+AQPE
Sbjct: 185 VPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPE 244

Query: 253 LTDLLNRIRQPFNVNSVAQAAAVAALGDTAFLQRSAELNRAGKAQLVEAFSRLGLEFVAS 312
           LTDLLNR+RQPFNVN++AQAAA+AAL D AFL++SA LN  G  +L EAF +LGLE+V S
Sbjct: 245 LTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPS 304

Query: 313 SGNFVLVRVGDDDDAGARVNVALLRQGVIVRPVGNYGMPRWLRVTIGLPDENAAFIAALE 372
            GNFVLVRVG+DD AG RVN+ LL+QGVIVRPVGNYG+P+WLR+TIGLP+EN AFIAALE
Sbjct: 305 DGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364

Query: 373 RAL 375
           R L
Sbjct: 365 RTL 367


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: 591
Number of extensions: 17
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: 376
Length of database: 370
Length adjustment: 30
Effective length of query: 346
Effective length of database: 340
Effective search space:   117640
Effective search space used:   117640
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: 50 (23.9 bits)

Align candidate BPHYT_RS14905 BPHYT_RS14905 (histidinol-phosphate aminotransferase)
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.16040.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   6.6e-113  363.1   0.0   7.4e-113  362.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS14905  BPHYT_RS14905 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS14905  BPHYT_RS14905 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.9   0.0  7.4e-113  7.4e-113       4     348 ..      10     365 ..       7     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 362.9 bits;  conditional E-value: 7.4e-113
                                TIGR01141   4 ikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeala 65 
                                              +++++pY +g      are+g +   +vkL+snEnP+g++e+++ a+ +++++l rYpd++a+elk+al+
  lcl|FitnessBrowser__BFirm:BPHYT_RS14905  10 VRAIAPYIAGkpisevAREFGLDeaTIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALS 79 
                                              8999*****************99999******************************************** PP

                                TIGR01141  66 kylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedlea 135
                                              +++gv ++ ++lgnGs++++e+ ++af+e+g++++++++++++Y++ ++  ga+ + vp+ + g +dl+a
  lcl|FitnessBrowser__BFirm:BPHYT_RS14905  80 ERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYG-HDLDA 148
                                              ***************************************************************6.9**** PP

                                TIGR01141 136 vleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypn 201
                                              +l+a++++++l+f+a+PnnPtG++++  ++e++l++v ++++VV+DeAY+e+ ++   ++ + ++++ypn
  lcl|FitnessBrowser__BFirm:BPHYT_RS14905 149 MLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVpRHVVVVLDEAYTEYLPQekrYDSIAWVRRYPN 218
                                              *************************************88**************9999999********** PP

                                TIGR01141 202 lvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkere 271
                                              l+v+rT+SKafgLAglRvG+aia++e+ + l++vr+p+nv++la++aa+aal+d++++ek+ + ++++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS14905 219 LLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYR 288
                                              ********************************************************************** PP

                                TIGR01141 272 rlleelkkleglevyeSkaNFvlikvke...daeelleallekgiivRdlksaeglleeclRitvGtree 338
                                              rl+e++ kl gle+++S++NFvl++v +   + +++  +ll++g+ivR ++++ gl +++lRit+G +ee
  lcl|FitnessBrowser__BFirm:BPHYT_RS14905 289 RLTEAFDKL-GLEYVPSDGNFVLVRVGNddaAGNRVNLELLKQGVIVRPVGNY-GL-PQWLRITIGLPEE 355
                                              *********.8***************998767788999***************.85.************* PP

                                TIGR01141 339 nerllealke 348
                                              ne++++al++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14905 356 NEAFIAALER 365
                                              *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (370 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: 00:00:00.01
# Mc/sec: 6.94
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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