GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Marinobacter adhaerens HP15

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate GFF618 HP15_601 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Marino:GFF618
          Length = 418

 Score =  365 bits (936), Expect = e-105
 Identities = 189/415 (45%), Positives = 270/415 (65%), Gaps = 4/415 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           + ++G  A+ A+  +A+ ++  +N+ L   A+ L+A  E +  AN +D+   R NGL  A
Sbjct: 7   MAEVGQQARAAATGVARSTTAVRNQALLATAEALDAAREELALANGKDLQMGRENGLDAA 66

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           MLDRL LTP R+  + + +RQV +L DP+G + D     SG+++ + RVPLGVIG+IYE+
Sbjct: 67  MLDRLELTPQRIDTMIEGLRQVASLPDPIGAITDMNYRPSGIQVGKMRVPLGVIGIIYES 126

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVTV+ ASLCLK+GNA ILRGG E+  +N A    +   L   GLP  AVQ I   DR
Sbjct: 127 RPNVTVEAASLCLKSGNATILRGGSESIHSNQAIARCLSAGLAKAGLPENAVQVIKTTDR 186

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A V E++ M  Y+D+++PRGG GL +     + +PVI    GVCH+Y+D   +  +ALKV
Sbjct: 187 AAVGELITMPDYVDVIVPRGGKGLIERISRDARVPVIKHLDGVCHVYIDSHADPEKALKV 246

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
            +NAKT R  TCNT+ETLLV+  IA+  LP L++   E GV L       A ++     V
Sbjct: 247 AINAKTHRYGTCNTMETLLVDAEIAEDILPLLAQAFVEKGVELRGCERTRAIVEG----V 302

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
           V     +++ E+L+  L V++V  L+ AIAHI  + +QH+D+I+T +   A+RF+ EVDS
Sbjct: 303 VEATEADWEAEYLAPVLAVRVVDGLEGAIAHINRYSSQHTDSIITENYTRARRFITEVDS 362

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           S+V VNASTRF DG ++GLGAE+ +ST K+HARGP+GLE LT+ K++  GD  IR
Sbjct: 363 SSVMVNASTRFADGFEYGLGAEIGISTDKIHARGPVGLEGLTSQKYVVFGDGHIR 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: 415
Number of extensions: 10
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: 418
Length adjustment: 32
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
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 GFF618 HP15_601 (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.19843.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.3e-156  507.4   0.7   1.5e-156  507.2   0.7    1.0  1  lcl|FitnessBrowser__Marino:GFF618  HP15_601 gamma-glutamyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF618  HP15_601 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.2   0.7  1.5e-156  1.5e-156       1     398 []      14     407 ..      14     407 .. 0.99

  Alignments for each domain:
  == domain 1  score: 507.2 bits;  conditional E-value: 1.5e-156
                          TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvi 76 
                                        a+ aa+ +a  +ta +n+al + a++L a+ e++  an kd++ ++enGl  a+ldrL+Lt +++ ++++++++v+
  lcl|FitnessBrowser__Marino:GFF618  14 ARAAATGVARSTTAVRNQALLATAEALDAAREELALANGKDLQMGRENGLDAAMLDRLELTPQRIDTMIEGLRQVA 89 
                                        799************************************************************************* PP

                          TIGR00407  77 eLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviq 152
                                        +L+dP+G +++ + + +G+++ ++rvPlGv+g+iye+rP+v+v++asLclk+Gna iL+Gg+e+++sn+a+++ + 
  lcl|FitnessBrowser__Marino:GFF618  90 SLPDPIGAITDMNYRPSGIQVGKMRVPLGVIGIIYESRPNVTVEAASLCLKSGNATILRGGSESIHSNQAIARCLS 165
                                        **************************************************************************** PP

                          TIGR00407 153 daleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadla 228
                                          l+++glp +avq+i+++dr+ v el+++ +yvd+++PrGg++l++ i +++++Pv++h dGvCh+y+d +ad +
  lcl|FitnessBrowser__Marino:GFF618 166 AGLAKAGLPENAVQVIKTTDRAAVGELITMPDYVDVIVPRGGKGLIERISRDARVPVIKHLDGVCHVYIDSHADPE 241
                                        **************************************************************************** PP

                          TIGR00407 229 kakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdke 304
                                        ka kv ++akt+r  tCn++etLLv+ +iae+ l+ L+++  ekgvelr+ + + +++e      +e+++ d++ e
  lcl|FitnessBrowser__Marino:GFF618 242 KALKVAINAKTHRYGTCNTMETLLVDAEIAEDILPLLAQAFVEKGVELRGCERTRAIVEGV----VEATEADWEAE 313
                                        *****************************************************99998865....788999***** PP

                          TIGR00407 305 flsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgist 380
                                        +l+++L+v++v+ le ai+hi++y+++h+d+i+te+ + a++f++evds++v vnastrfadGf++G+Gae+gist
  lcl|FitnessBrowser__Marino:GFF618 314 YLAPVLAVRVVDGLEGAIAHINRYSSQHTDSIITENYTRARRFITEVDSSSVMVNASTRFADGFEYGLGAEIGIST 389
                                        **************************************************************************** PP

                          TIGR00407 381 qklharGPvGLeaLvsyk 398
                                        +k+harGPvGLe+L+s k
  lcl|FitnessBrowser__Marino:GFF618 390 DKIHARGPVGLEGLTSQK 407
                                        ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (418 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: 8.42
//
[ok]

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

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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