GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Shewanella loihica PV-4

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 5210406 Shew_2847 gamma-glutamyl phosphate reductase (RefSeq)

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__PV4:5210406
          Length = 429

 Score =  469 bits (1208), Expect = e-137
 Identities = 241/416 (57%), Positives = 309/416 (74%), Gaps = 2/416 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           L  +G  AK ASY +A L++ +K  +L  IA +L  +   I+ AN QDVA AR NGL++A
Sbjct: 14  LNTLGEQAKAASYAMASLTASQKRDLLRAIAAKLTDKRAQIVAANQQDVAKARENGLNDA 73

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           M+DRL L  +RL G+  D+  V  LADP+G  ++  +LD+GLRL RRRVPLGV+GVIYEA
Sbjct: 74  MIDRLLLDESRLSGVIADIENVVALADPIGSELESQLLDNGLRLSRRRVPLGVLGVIYEA 133

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVTVD+A L LKTGNAVILRGGKET  +N A    I++A+   GLP+ AVQ I +PDR
Sbjct: 134 RPNVTVDIAVLALKTGNAVILRGGKETLASNLALSEAIREAISEQGLPSDAVQLIQDPDR 193

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           ALVS +L++DKY+DM++PRGG  L +LC EQ+TIPVI GGIG+CH+YVD  V+  +A++V
Sbjct: 194 ALVSGLLKLDKYVDMIVPRGGQNLQRLCAEQATIPVILGGIGICHLYVDSEVDQLKAIEV 253

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHA-DAAALAQLQAGPAK 300
           I NAK QRP+ CN ++T+LV+++IA +FLP L   ++  GV+ HA D A      AG   
Sbjct: 254 IANAKVQRPTVCNALDTVLVHQSIAQTFLPKLYAHLSALGVSFHACDQAEAIGKDAGTVT 313

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
             A   E +  E+LSL+L V++V D+D AIAHIR   + HS+ IL+ ++    RF+NEVD
Sbjct: 314 HQA-SDETFGTEWLSLNLGVRVVDDMDMAIAHIRRFSSGHSEGILSDNIHATARFINEVD 372

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           ++AVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIG+GDYT R
Sbjct: 373 AAAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGVGDYTAR 428


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: 499
Number of extensions: 15
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 5210406 Shew_2847 (gamma-glutamyl phosphate reductase (RefSeq))
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.30982.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.2e-167  543.7   3.1   1.3e-167  543.5   3.1    1.0  1  lcl|FitnessBrowser__PV4:5210406  Shew_2847 gamma-glutamyl phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210406  Shew_2847 gamma-glutamyl phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.5   3.1  1.3e-167  1.3e-167       1     398 []      21     418 ..      21     418 .. 0.99

  Alignments for each domain:
  == domain 1  score: 543.5 bits;  conditional E-value: 1.3e-167
                        TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieL 78 
                                      ak a++ +a+l++ +k ++l +ia +L+ +   i+aan++d+a+a+enGl da++drLlL+e++l ++++d+++v+ L
  lcl|FitnessBrowser__PV4:5210406  21 AKAASYAMASLTASQKRDLLRAIAAKLTDKRAQIVAANQQDVAKARENGLNDAMIDRLLLDESRLSGVIADIENVVAL 98 
                                      899*************************************************************************** PP

                        TIGR00407  79 adPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdale 156
                                      adP+G  +e++ ld+GL+l r+rvPlGvlgviyearP+v+vd+a L+lktGnaviL+Ggke+  sn al e i++a+ 
  lcl|FitnessBrowser__PV4:5210406  99 ADPIGSELESQLLDNGLRLSRRRVPLGVLGVIYEARPNVTVDIAVLALKTGNAVILRGGKETLASNLALSEAIREAIS 176
                                      ****************************************************************************** PP

                        TIGR00407 157 qtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakakkvi 234
                                      + glp  avqli+dpdr+ v+ llkld+yvd+++PrGg++l +l+ e++tiPv+ +++G+Ch+y+d ++d+ ka++vi
  lcl|FitnessBrowser__PV4:5210406 177 EQGLPSDAVQLIQDPDRALVSGLLKLDKYVDMIVPRGGQNLQRLCAEQATIPVILGGIGICHLYVDSEVDQLKAIEVI 254
                                      ****************************************************************************** PP

                        TIGR00407 235 vdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsldLsv 312
                                       +ak qrP++Cna++t+Lv+++ia+ fl++L  +l++ gv+++a ++++++ + ++    ++s+e f +e+lsl L v
  lcl|FitnessBrowser__PV4:5210406 255 ANAKVQRPTVCNALDTVLVHQSIAQTFLPKLYAHLSALGVSFHACDQAEAIGKDAGTVTHQASDETFGTEWLSLNLGV 332
                                      ********************************************999999998888888899999************* PP

                        TIGR00407 313 kivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvG 390
                                      ++v+d++ ai+hir++++ hs++il+++ ++  +f++evd+aavyvnastrf+dG++fG+Gaev++stqklharGP+G
  lcl|FitnessBrowser__PV4:5210406 333 RVVDDMDMAIAHIRRFSSGHSEGILSDNIHATARFINEVDAAAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMG 410
                                      ****************************************************************************** PP

                        TIGR00407 391 LeaLvsyk 398
                                      LeaL++yk
  lcl|FitnessBrowser__PV4:5210406 411 LEALTTYK 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: 00:00:00.01
# Mc/sec: 10.97
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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