Alignments for a candidate for proA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Burkholderia phytofirmans PsJN

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate BPHYT_RS16770 BPHYT_RS16770 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__BFirm:BPHYT_RS16770
          Length = 423

 Score =  368 bits (945), Expect = e-106
 Identities = 192/411 (46%), Positives = 271/411 (65%), Gaps = 1/411 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           +  +G  A+QAS  +A+ S+  KN  L  +A  +E  + ++  ANA+DVA AR  G   A
Sbjct: 7   MTDLGRRARQASRAMARASTAAKNAALAAVAQGIERDAALLKEANARDVARAREKGHDAA 66

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
            +DRL L+   LK + + +RQV  LADP+G++ +     SG+++ + RVPLGVIG+IYE+
Sbjct: 67  FIDRLTLSDKALKTMVEGLRQVAALADPIGEISNLKYRPSGIQVGQMRVPLGVIGIIYES 126

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT+D A+LCLK+GNA ILRGG E    NAA   +I + L+  GLP  AVQ +   DR
Sbjct: 127 RPNVTIDAAALCLKSGNATILRGGSEALECNAALAKLIGEGLEKAGLPQEAVQVVATSDR 186

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A V +++ M +Y+D+++PRGG  L +    ++ +P+I    G+CH+YVD+  ++A+AL V
Sbjct: 187 AAVGKLITMTEYVDVIVPRGGKSLIERLMNEARVPMIKHLDGICHVYVDDRADLAKALTV 246

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQL-QAGPAK 300
             NAKT R  TCNT+ETLLV + IA   LP L K   +  V L  DAAA A L  AG   
Sbjct: 247 CDNAKTHRYGTCNTMETLLVARGIAAEVLPPLGKLYRDKQVELRVDAAARAVLADAGVGP 306

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
           +V    E++  E+L+  L +K+V +LD AI HI  + +QH+DAI+T D   A RF+ EVD
Sbjct: 307 LVDATEEDWRTEYLAPVLAIKVVENLDAAIDHINTYSSQHTDAIVTEDHDRAMRFLREVD 366

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIG 411
           S++V VNASTRF DG +FGLGAE+ +S  KLHARGP+GLE LT+ K++ +G
Sbjct: 367 SASVMVNASTRFADGFEFGLGAEIGISNDKLHARGPVGLEGLTSLKYVVLG 417


Lambda     K      H
   0.317    0.133    0.369 

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: 421
Number of extensions: 18
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: 417
Length of database: 423
Length adjustment: 32
Effective length of query: 385
Effective length of database: 391
Effective search space:   150535
Effective search space used:   150535
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_RS16770 BPHYT_RS16770 (gamma-glutamyl phosphate reductase)
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))

# 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/TIGR00407.hmm
# target sequence database:        /tmp/gapView.6768.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00407  [M=398]
Accession:   TIGR00407
Description: proA: glutamate-5-semialdehyde 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     9e-155  501.3   2.6     1e-154  501.1   2.6    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16770  BPHYT_RS16770 gamma-glutamyl pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16770  BPHYT_RS16770 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.1   2.6    1e-154    1e-154       1     398 []      14     412 ..      14     412 .. 0.98

  Alignments for each domain:
  == domain 1  score: 501.1 bits;  conditional E-value: 1e-154
                                TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiad 70 
                                              a++a+  +a  sta kn al+++a++++++a l+ +ana+d+a a+e+G   a++drL+L+++ lk++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16770  14 ARQASRAMARASTAAKNAALAAVAQGIERDAALLKEANARDVARAREKGHDAAFIDRLTLSDKALKTMVE 83 
                                              89******************************************************************** PP

                                TIGR00407  71 dvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkea 140
                                              ++++v+ LadP+G++ + + + +G+++ ++rvPlGv+g+iye+rP+v++d+a+Lclk+Gna iL+Gg+ea
  lcl|FitnessBrowser__BFirm:BPHYT_RS16770  84 GLRQVAALADPIGEISNLKYRPSGIQVGQMRVPLGVIGIIYESRPNVTIDAAALCLKSGNATILRGGSEA 153
                                              ********************************************************************** PP

                                TIGR00407 141 vrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvl 210
                                               + n+al+++i + le++glp+eavq++ ++dr+ v +l+++ eyvd+++PrGg++l++ + +e+++P++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16770 154 LECNAALAKLIGEGLEKAGLPQEAVQVVATSDRAAVGKLITMTEYVDVIVPRGGKSLIERLMNEARVPMI 223
                                              ********************************************************************** PP

                                TIGR00407 211 ehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelrada 280
                                              +h dG+Ch+y+d+ adlaka +v ++akt+r  tCn++etLLv + ia+e l+ L k   +k velr da
  lcl|FitnessBrowser__BFirm:BPHYT_RS16770 224 KHLDGICHVYVDDRADLAKALTVCDNAKTHRYGTCNTMETLLVARGIAAEVLPPLGKLYRDKQVELRVDA 293
                                              *********************************************************************9 PP

                                TIGR00407 281 lvlkll.elekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvk 349
                                              ++ ++l +++    +++++ed+++e+l+++L++k+ve+l++ai+hi++y+++h+dai+ted+  a +f++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16770 294 AARAVLaDAGVGPLVDATEEDWRTEYLAPVLAIKVVENLDAAIDHINTYSSQHTDAIVTEDHDRAMRFLR 363
                                              9988761555567899****************************************************** PP

                                TIGR00407 350 evdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                              evdsa+v vnastrfadGf+fG+Gae+gis +klharGPvGLe+L+s k
  lcl|FitnessBrowser__BFirm:BPHYT_RS16770 364 EVDSASVMVNASTRFADGFEFGLGAEIGISNDKLHARGPVGLEGLTSLK 412
                                              **********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (423 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.51
//
[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