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)
to candidate BPHYT_RS02830 BPHYT_RS02830 aspartate aminotransferase

Query= reanno::Marino:GFF2483
         (350 letters)



>FitnessBrowser__BFirm:BPHYT_RS02830
          Length = 359

 Score =  435 bits (1118), Expect = e-126
 Identities = 213/353 (60%), Positives = 267/353 (75%), Gaps = 3/353 (0%)

Query: 1   MSKFWSPLVNDLVPYVPGEQPKMANLVKLNTNENPFGPSPKVIEAIQAELNDG---LRLY 57
           MS++WS +V+ L PYVPGEQP +A+ VKLNTNENP+ PSP+V+EAI+ EL D    LR Y
Sbjct: 1   MSRYWSDIVHRLTPYVPGEQPVVAHPVKLNTNENPYPPSPRVLEAIRQELGDAADSLRRY 60

Query: 58  PDPEGESLRETIAAYHKITPEQIFLGNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVY 117
           PDP  + LRET+AAYH I  EQ+F GNGSDEVLA  F  L +H +P+LFPDITYSFYP Y
Sbjct: 61  PDPTAQKLRETVAAYHGIRAEQVFAGNGSDEVLALTFQALLKHDKPLLFPDITYSFYPTY 120

Query: 118 CGLYNIESKKVPLTESFEINPEDFKQPNGGVIFPNPNAPTGRYLELQYVEEILAANPNRV 177
             L+ ++ + VPL +SF IN +D+K PNGG++FPNPNAPTGR L L  +E ++A+NP+ V
Sbjct: 121 ARLFEVDYRTVPLDDSFAINVDDYKSPNGGILFPNPNAPTGRPLPLADIERLVASNPDSV 180

Query: 178 VVVDEAYIDFGGESAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPDLIEALNRVKN 237
           VV+DEAY+DFG ESAI L+D+YPNLLV QT+SK+RSLAG+RVGFA G+ +LI ALNRVK+
Sbjct: 181 VVIDEAYVDFGAESAICLIDRYPNLLVVQTVSKSRSLAGMRVGFAFGNRELIGALNRVKD 240

Query: 238 SFNSYPLDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGLGFEVLPSKANFIFA 297
           SFNSYPLDRLA   A AAYED+AWFR  C  V++ RER+ A L  LGFEV+PS AN +FA
Sbjct: 241 SFNSYPLDRLAQVAAAAAYEDDAWFRDTCAKVMASRERLAAGLTALGFEVVPSAANLLFA 300

Query: 298 RHKEQPGEVLAKGLREQGIIVRHFNKPRISEFLRITIGTVEQNDALIARLESL 350
           RH+      L   LRE+ I VRHF  PRI + LRI++GT  + D L+  L  +
Sbjct: 301 RHEGYDAATLVLRLREKEIFVRHFKAPRIDQHLRISVGTDAECDVLLDALREI 353


Lambda     K      H
   0.319    0.139    0.410 

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: 463
Number of extensions: 16
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: 350
Length of database: 359
Length adjustment: 29
Effective length of query: 321
Effective length of database: 330
Effective search space:   105930
Effective search space used:   105930
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS02830 BPHYT_RS02830 (aspartate 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.17668.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    1.8e-93  299.1   0.0    2.1e-93  298.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS02830  BPHYT_RS02830 aspartate aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS02830  BPHYT_RS02830 aspartate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.9   0.0   2.1e-93   2.1e-93       4     349 .]       9     353 ..       6     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 298.9 bits;  conditional E-value: 2.1e-93
                                TIGR01141   4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk....klhrYpdpqalelkealakylg 69 
                                              ++ l+pY+pg++ +   + vkLn+nEnP++ps++v+ea+++el     +l+rYpdp a++l+e++a+y g
  lcl|FitnessBrowser__BFirm:BPHYT_RS02830   9 VHRLTPYVPGEQPVVA-HPVKLNTNENPYPPSPRVLEAIRQELGdaadSLRRYPDPTAQKLRETVAAYHG 77 
                                              7889*****9777776.6***********************99878889********************* PP

                                TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavlea 139
                                              + +e++++gnGsde++ l ++a+l+  +  l+++ tys Y+++a++ ++++++vpl++++  ++++ +  
  lcl|FitnessBrowser__BFirm:BPHYT_RS02830  78 IRAEQVFAGNGSDEVLALTFQALLKHDKPLLFPDITYSFYPTYARLFEVDYRTVPLDDSFAINVDDYK-- 145
                                              ***********************************************************977777777.. PP

                                TIGR01141 140 akekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlS 209
                                                +    + + +Pn+PtG  l  ++ie+++++  d +VV+DeAY++F  e s++ l+ +ypnl+v++T+S
  lcl|FitnessBrowser__BFirm:BPHYT_RS02830 146 --SPNGGILFPNPNAPTGRPLPLADIERLVASNPDSVVVIDEAYVDFGAE-SAICLIDRYPNLLVVQTVS 212
                                              ..444446679*********************77***************7.******************* PP

                                TIGR01141 210 KafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererllee 276
                                              K+ +LAg+RvG+a++n e+i al++v++++n   +++la+ aa aa++d++ +++t ++v ++rerl ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS02830 213 KSRSLAGMRVGFAFGNRELIGALNRVKDSFNsypLDRLAQVAAAAAYEDDAWFRDTCAKVMASRERLAAG 282
                                              ***************************87543339*********************************** PP

                                TIGR01141 277 lkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerllea 345
                                              l++l g+ev++S aN ++++ +  da+ l+ +l ek+i vR++k+  + ++++lRi+vGt+ e++ ll+a
  lcl|FitnessBrowser__BFirm:BPHYT_RS02830 283 LTAL-GFEVVPSAANLLFARHEGyDAATLVLRLREKEIFVRHFKA--PRIDQHLRISVGTDAECDVLLDA 349
                                              ****.8**************9999*******************94..468******************** PP

                                TIGR01141 346 lkei 349
                                              l+ei
  lcl|FitnessBrowser__BFirm:BPHYT_RS02830 350 LREI 353
                                              *996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (359 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: 8.79
//
[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