GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proA in Klebsiella michiganensis M5al

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate BWI76_RS05835 BWI76_RS05835 gamma-glutamyl-phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS05835 BWI76_RS05835
           gamma-glutamyl-phosphate reductase
          Length = 417

 Score =  694 bits (1791), Expect = 0.0
 Identities = 351/417 (84%), Positives = 386/417 (92%)

Query: 1   MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60
           MLEQMGIAAK ASYKLAQLSSREKN+VLEKIAD LEAQ++ IL ANA+D+A+ARANGLSE
Sbjct: 1   MLEQMGIAAKAASYKLAQLSSREKNQVLEKIADYLEAQTDAILRANAEDLAEARANGLSE 60

Query: 61  AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120
           A+LDRLAL PARL GIA+DVRQVC+LADPVGQVIDGG+LDSGLR+ERRRVPLGV+GVIYE
Sbjct: 61  ALLDRLALNPARLSGIANDVRQVCSLADPVGQVIDGGLLDSGLRIERRRVPLGVVGVIYE 120

Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180
           ARPNVTVDVASLCLKTGNA ILRGGKET RTNAATV VIQ AL+ CGLPA  VQAI++PD
Sbjct: 121 ARPNVTVDVASLCLKTGNAAILRGGKETWRTNAATVKVIQQALQECGLPAATVQAIESPD 180

Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240
           RALV EML+MDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIY+D S ++AEALK
Sbjct: 181 RALVGEMLKMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYIDHSADVAEALK 240

Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300
           VIVNAK QRPS CN+VETLLV+++IA+ FLPALSKQMAESGV+LHADAA+L  LQ GPA 
Sbjct: 241 VIVNAKVQRPSACNSVETLLVHQDIAERFLPALSKQMAESGVSLHADAASLPALQNGPAS 300

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
           V  VKAE+YD+E+LSLDLNVK+V+D D+A+AHIREHGTQHSDAILTR + NA RF+NEVD
Sbjct: 301 VEPVKAEQYDNEYLSLDLNVKVVADQDEAVAHIREHGTQHSDAILTRTLGNANRFINEVD 360

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIRA 417
           SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIG GD TIRA
Sbjct: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGFGDDTIRA 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: 627
Number of extensions: 15
Number of successful extensions: 1
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: 417
Length adjustment: 31
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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 BWI76_RS05835 BWI76_RS05835 (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.10246.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   9.4e-194  629.6   1.8   1.1e-193  629.4   1.8    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS05835  BWI76_RS05835 gamma-glutamyl-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS05835  BWI76_RS05835 gamma-glutamyl-phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.4   1.8  1.1e-193  1.1e-193       1     398 []       9     406 ..       9     406 .. 1.00

  Alignments for each domain:
  == domain 1  score: 629.4 bits;  conditional E-value: 1.1e-193
                               TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiadd 71 
                                             ak a++klaqls++ekn++l+kiad L+a++++il ana+d+a+a++nGl++alldrL+L+ ++l +ia+d
  lcl|FitnessBrowser__Koxy:BWI76_RS05835   9 AKAASYKLAQLSSREKNQVLEKIADYLEAQTDAILRANAEDLAEARANGLSEALLDRLALNPARLSGIAND 79 
                                             899******************************************************************** PP

                               TIGR00407  72 vkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavr 142
                                             v++v++LadPvG+vi+++ ld+GL++er+rvPlGv+gviyearP+v+vdvasLclktGna+iL+Ggke+ r
  lcl|FitnessBrowser__Koxy:BWI76_RS05835  80 VRQVCSLADPVGQVIDGGLLDSGLRIERRRVPLGVVGVIYEARPNVTVDVASLCLKTGNAAILRGGKETWR 150
                                             *********************************************************************** PP

                               TIGR00407 143 snkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvleha 213
                                             +n+a+v+viq+al+++glp+ +vq+ie pdr+ v e+lk+d+y+d+liPrGg++l+kl++e+stiPv++++
  lcl|FitnessBrowser__Koxy:BWI76_RS05835 151 TNAATVKVIQQALQECGLPAATVQAIESPDRALVGEMLKMDKYIDMLIPRGGAGLHKLCREQSTIPVITGG 221
                                             *********************************************************************** PP

                               TIGR00407 214 dGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlk 284
                                             +GvChiy+d+sad+a+a kviv+ak qrPs+Cn++etLLv+++iae+fl++L+kq++e+gv+l+ada+ l 
  lcl|FitnessBrowser__Koxy:BWI76_RS05835 222 IGVCHIYIDHSADVAEALKVIVNAKVQRPSACNSVETLLVHQDIAERFLPALSKQMAESGVSLHADAASLP 292
                                             *********************************************************************** PP

                               TIGR00407 285 llelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaa 355
                                              l+ ++a++  v++e++d+e+lsldL+vk+v d +ea++hir++gt+hsdailt+   na++f++evds+a
  lcl|FitnessBrowser__Koxy:BWI76_RS05835 293 ALQNGPASVEPVKAEQYDNEYLSLDLNVKVVADQDEAVAHIREHGTQHSDAILTRTLGNANRFINEVDSSA 363
                                             *********************************************************************** PP

                               TIGR00407 356 vyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                             vyvnastrf+dG++fG+Gaev++stqklharGP+GLeaL++yk
  lcl|FitnessBrowser__Koxy:BWI76_RS05835 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYK 406
                                             ******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (417 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.07
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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