Alignments for a candidate for hisC in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Burkholderia phytofirmans PsJN

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate BPHYT_RS17705 BPHYT_RS17705 histidinol-phosphate aminotransferase

Query= uniprot:A0A2R7PAQ8
         (373 letters)



>FitnessBrowser__BFirm:BPHYT_RS17705
          Length = 356

 Score =  365 bits (937), Expect = e-105
 Identities = 196/373 (52%), Positives = 260/373 (69%), Gaps = 18/373 (4%)

Query: 1   MTTPASSPLQALARIRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGSV 60
           MTTP          IR DV AM SY V  +TG +K+DAMENPF LP  L A LG+ L  V
Sbjct: 1   MTTPQDI-------IRRDVLAMTSYPVPDATGYIKLDAMENPFTLPPVLAAHLGEHLAGV 53

Query: 61  ALNRYPGDRIADLKAALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLAP 120
           ALNRYP  R   L   + +   +P G  ++LGNGSDE+I+++++ACAQPG    A +LAP
Sbjct: 54  ALNRYPAPRPDALIEKIKRVMQVPAGCDVLLGNGSDEIISMVSVACAQPG----AKVLAP 109

Query: 121 MPGFVMYPLSAQLQGLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLWD 180
           +PGFVMY +SA+L  L+F+GVPL  DF LD  AMLAAI +H+PAI Y+AYPNNPT TL+D
Sbjct: 110 VPGFVMYQMSAKLANLEFIGVPLKADFTLDTEAMLAAIAEHQPAIIYLAYPNNPTGTLYD 169

Query: 181 EGAVQRIIDAAGAQGGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAGV 240
           +  ++RII  A A   +VV+DEAYQPFA ++W+ R  A      +V++MRT+SK GLAG+
Sbjct: 170 DADMERII--AAANKSLVVIDEAYQPFAQQSWLPRADAFD----NVVVMRTVSKLGLAGI 223

Query: 241 RLGYLIGPSAFVSEIDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAAL 300
           RLGYL+G   +++E DKVRPPYN +VL   AA F L+H +V  +QAA++R ER  L  A+
Sbjct: 224 RLGYLVGKPGWLTEFDKVRPPYNTNVLTQAAADFLLDHVDVLDSQAAQLREERTKLARAV 283

Query: 301 RQMPGVEKCWDSEANMVLIRVADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNAE 360
            Q+PG E  + S  N +L+RV D++  +E +   +VL+KNVS MHPLLANC+RLTVG+ E
Sbjct: 284 SQLPGAE-VFPSAGNFLLVRVPDASVLFETLLTARVLIKNVSKMHPLLANCVRLTVGSPE 342

Query: 361 DNAQMLAALQASL 373
           +NAQ+LA L+  L
Sbjct: 343 ENAQLLAGLKLVL 355


Lambda     K      H
   0.321    0.134    0.392 

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: 392
Number of extensions: 16
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: 373
Length of database: 356
Length adjustment: 29
Effective length of query: 344
Effective length of database: 327
Effective search space:   112488
Effective search space used:   112488
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS17705 BPHYT_RS17705 (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.18587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    2.9e-97  311.6   0.0    3.2e-97  311.5   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS17705  BPHYT_RS17705 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS17705  BPHYT_RS17705 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.5   0.0   3.2e-97   3.2e-97       2     347 ..      10     352 ..       9     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 311.5 bits;  conditional E-value: 3.2e-97
                                TIGR01141   2 ekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealakylg 69 
                                              +++ +++ Y  +      ++ +kL+++EnPf  ++ + ++l e+l+   l+rYp p + +l e++ ++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS17705  10 RDVLAMTSYPVP----DATGYIKLDAMENPFTLPPVLAAHLGEHLAgvALNRYPAPRPDALIEKIKRVMQ 75 
                                              566666777663....22378*************************999********************* PP

                                TIGR01141  70 vee.enillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavle 138
                                              v +  ++llgnGsde+i+++  a+++pg++vl++ p + mY++sak+a+ e + vplk+d++ d+ea+l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS17705  76 VPAgCDVLLGNGSDEIISMVSVACAQPGAKVLAPVPGFVMYQMSAKLANLEFIGVPLKADFTLDTEAMLA 145
                                              765269*******************************************************9*****999 PP

                                TIGR01141 139 .aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrT 207
                                               +a++++ +++la+PnnPtG+l + +++e++++++++ lVV+DeAY  F+++ s+l+ +  ++n+vv+rT
  lcl|FitnessBrowser__BFirm:BPHYT_RS17705 146 aIAEHQPAIIYLAYPNNPTGTLYDDADMERIIAAANKSLVVIDEAYQPFAQQ-SWLPRADAFDNVVVMRT 214
                                              67899******************************9***************7.***************** PP

                                TIGR01141 208 lSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleel 277
                                              +SK+  LAg+R+Gy+++++ +  +++kvr+pyn+++l+++aa   l++ d + ++ +++++er+ l  ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS17705 215 VSKLG-LAGIRLGYLVGKPGWLTEFDKVRPPYNTNVLTQAAADFLLDHVDVLDSQAAQLREERTKLARAV 283
                                              ***86.**************************************************************** PP

                                TIGR01141 278 kkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                              ++l+g ev++S +NF+l++v+ da+ l+e+ll +++++++++++++ll +c+R+tvG++een +ll+ lk
  lcl|FitnessBrowser__BFirm:BPHYT_RS17705 284 SQLPGAEVFPSAGNFLLVRVP-DASVLFETLLTARVLIKNVSKMHPLLANCVRLTVGSPEENAQLLAGLK 352
                                              *********************.*******************************************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (356 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: 00:00:00.01
# Mc/sec: 10.28
//
[ok]

This GapMind analysis is from Apr 09 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