GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Novosphingobium barchaimii LL02

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate WP_059152892.1 V474_RS18660 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P07004
         (417 letters)



>NCBI__GCF_001046635.1:WP_059152892.1
          Length = 429

 Score =  344 bits (883), Expect = 3e-99
 Identities = 186/407 (45%), Positives = 256/407 (62%), Gaps = 6/407 (1%)

Query: 1   MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60
           ++EQ+    + A   LA++S  +K   L   A  L A    IL ANAQD+A   A GLS 
Sbjct: 19  LVEQLARDGRAAQRVLARISDADKAGALRAAAKALRAAESEILAANAQDIAAGEAKGLSA 78

Query: 61  AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120
           A+LDRL L   RL GIAD V QV  L DPVG+VI      +GL+L R RVP+G+IG+IYE
Sbjct: 79  ALLDRLRLDAGRLAGIADAVEQVAALPDPVGEVISADERPNGLKLSRVRVPIGLIGIIYE 138

Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180
           +RPNVT D A+LCL++GNAV+LRGG E   +N A  A +   L+S G+PA A+Q +   D
Sbjct: 139 SRPNVTADAAALCLRSGNAVMLRGGTEALHSNRAIRAALAAGLESVGIPAAAIQLVPTQD 198

Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240
           RA+V  ML     IDM++PRGG  L    +  + +PV+    G+CH YV  + +   A K
Sbjct: 199 RAVVGAMLTAAGLIDMIVPRGGKSLVARVQADARVPVLAHLDGICHTYVHAAADADMARK 258

Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300
           + VNAK +R   C  +ETLL++    +S   ++   + E+G  +  DA A    QA  ++
Sbjct: 259 LTVNAKLRRTGICGAMETLLLDTQFPES--ASVVGGLIEAGCEVRGDARA----QALDSR 312

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
           V+    E++D E+L   L+V +V  LD AI HI  H + H+DAI+T D   A+RF++EVD
Sbjct: 313 VLPASGEDWDTEYLDAVLSVAVVDGLDCAIEHIAAHSSHHTDAIVTDDAEAAERFLDEVD 372

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKW 407
           S+ V VNAS++F DGG+FGLGAE+ ++T +LHARGP+ LE LTTYKW
Sbjct: 373 SAIVMVNASSQFADGGEFGLGAEIGIATGRLHARGPVALEGLTTYKW 419


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: 447
Number of extensions: 25
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: 429
Length adjustment: 32
Effective length of query: 385
Effective length of database: 397
Effective search space:   152845
Effective search space used:   152845
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 WP_059152892.1 V474_RS18660 (glutamate-5-semialdehyde dehydrogenase)
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.2288663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-137  442.7   1.7   6.5e-137  442.5   1.7    1.0  1  NCBI__GCF_001046635.1:WP_059152892.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059152892.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.5   1.7  6.5e-137  6.5e-137       2     398 .]      28     418 ..      27     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: 442.5 bits;  conditional E-value: 6.5e-137
                             TIGR00407   2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkd 74 
                                           + a   la +s a+k  al + a++L+a+ ++ilaana+diaa++++Gl+ alldrL L+ ++l +iad+v++
  NCBI__GCF_001046635.1:WP_059152892.1  28 RAAQRVLARISDADKAGALRAAAKALRAAESEILAANAQDIAAGEAKGLSAALLDRLRLDAGRLAGIADAVEQ 100
                                           5678899****************************************************************** PP

                             TIGR00407  75 vieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkal 147
                                           v+ L+dPvG+vi+a e+ +GLkl rvrvP+G +g+iye+rP+v++d+a+Lcl++Gnav+L+Gg ea +sn+a+
  NCBI__GCF_001046635.1:WP_059152892.1 101 VAALPDPVGEVISADERPNGLKLSRVRVPIGLIGIIYESRPNVTADAAALCLRSGNAVMLRGGTEALHSNRAI 173
                                           ************************************************************************* PP

                             TIGR00407 148 veviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiy 220
                                            + +   le+ g+p+ a+ql+ ++dr+ v  +l+    +d+++PrGg++lv  ++ ++++Pvl h dG+Ch+y
  NCBI__GCF_001046635.1:WP_059152892.1 174 RAALAAGLESVGIPAAAIQLVPTQDRAVVGAMLTAAGLIDMIVPRGGKSLVARVQADARVPVLAHLDGICHTY 246
                                           ************************************************************************* PP

                             TIGR00407 221 ldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekate 293
                                           + + ad  +a+k++v+ak +r   C a+etLL++ ++ e+   +++  l e+g e+r+da +++l +      
  NCBI__GCF_001046635.1:WP_059152892.1 247 VHAAADADMARKLTVNAKLRRTGICGAMETLLLDTQFPES--ASVVGGLIEAGCEVRGDARAQALDSRV---- 313
                                           *************************************964..6788999************99987654.... PP

                             TIGR00407 294 aevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfad 366
                                             +s ed+d+e+l+ +Lsv +v+ l+ aiehi  ++++h+dai+t+d ++ae+f++evdsa v vnas +fad
  NCBI__GCF_001046635.1:WP_059152892.1 314 LPASGEDWDTEYLDAVLSVAVVDGLDCAIEHIAAHSSHHTDAIVTDDAEAAERFLDEVDSAIVMVNASSQFAD 386
                                           677889******************************************************************* PP

                             TIGR00407 367 GfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                           G++fG+Gae+gi+t +lharGPv Le+L++yk
  NCBI__GCF_001046635.1:WP_059152892.1 387 GGEFGLGAEIGIATGRLHARGPVALEGLTTYK 418
                                           *******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (429 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: 00:00:00.00
# Mc/sec: 23.85
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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