GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proA in Pseudomonas fluorescens GW456-L13

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate PfGW456L13_1356 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)

Query= SwissProt::P07004
         (417 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356
           Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
          Length = 415

 Score =  368 bits (944), Expect = e-106
 Identities = 189/415 (45%), Positives = 269/415 (64%), Gaps = 5/415 (1%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           + ++G AA++AS  + + S+ +KNR L+  A+ L+A    +  AN QD+A  RANGL  A
Sbjct: 1   MTRLGRAAREASRVIGRASTAQKNRALQAAANALDAARAELTAANEQDLAAGRANGLEPA 60

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           +L+RLALTPAR+ G+   +RQV  L DPVG + D     SG+++ + RVPLGVIG+IYE+
Sbjct: 61  LLERLALTPARIDGMIVGLRQVAALPDPVGAIRDMSFRPSGIQVGKMRVPLGVIGIIYES 120

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT+D ASLCLK+GNA ILRGG E   +N A  A IQ  L    LPA  VQ ++  DR
Sbjct: 121 RPNVTIDAASLCLKSGNATILRGGSEAIHSNRAIAACIQRGLAEADLPAAVVQVVETTDR 180

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A V  ++ M +Y+D+++PRGG GL +     + +PVI    G+CH+YV E  ++A+A ++
Sbjct: 181 AAVGALITMPEYVDVIVPRGGRGLIERVSRDARVPVIKHLDGICHVYVSEHADLAKAQRI 240

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
             NAKT R   C  +ETLLV+  +A  FLPA++ Q  E GV L       A + A     
Sbjct: 241 AFNAKTYRYGICGAMETLLVDHTVAKDFLPAMAAQFREKGVELRGCERTRAIIDA----- 295

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
           VA   E++  E+L+  L++++V  L  AI HI  +G+ H+D+I++    + +RFV EVDS
Sbjct: 296 VAATEEDWSTEYLAAILSIRVVDGLGQAIEHINHYGSHHTDSIVSEHQGDTRRFVAEVDS 355

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           S+V +N  T F DG ++GLGAE+ +ST KLHARGP+GLE LT  K+I +GD  +R
Sbjct: 356 SSVMINTPTCFADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYIVVGDGQLR 410


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: 408
Number of extensions: 17
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: 415
Length adjustment: 31
Effective length of query: 386
Effective length of database: 384
Effective search space:   148224
Effective search space used:   148224
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 PfGW456L13_1356 (Gamma-glutamyl phosphate reductase (EC 1.2.1.41))
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.25696.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   7.1e-149  481.9   0.2   8.2e-149  481.7   0.2    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356  Gamma-glutamyl phosphate reducta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356  Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.7   0.2  8.2e-149  8.2e-149       1     397 [.       8     399 ..       8     400 .. 0.99

  Alignments for each domain:
  == domain 1  score: 481.7 bits;  conditional E-value: 8.2e-149
                                               TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladall 55 
                                                             a+ea+  +   sta+kn+al++ a++L a+  ++ aan++d+aa+++nGl +all
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356   8 AREASRVIGRASTAQKNRALQAAANALDAARAELTAANEQDLAAGRANGLEPALL 62 
                                                             89***************************************************** PP

                                               TIGR00407  56 drLlLteeklksiaddvkdvieLadPvGkvieareldeGLklervrvPlGvlgvi 110
                                                             +rL+Lt +++ +++ ++++v+ L+dPvG + +   + +G+++ ++rvPlGv+g+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356  63 ERLALTPARIDGMIVGLRQVAALPDPVGAIRDMSFRPSGIQVGKMRVPLGVIGII 117
                                                             ******************************************************* PP

                                               TIGR00407 111 yearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdaleqtglpveav 165
                                                             ye+rP+v++d+asLclk+Gna iL+Gg+ea++sn+a+++ iq+ l+++ lp+  v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356 118 YESRPNVTIDAASLCLKSGNATILRGGSEAIHSNRAIAACIQRGLAEADLPAAVV 172
                                                             ******************************************************* PP

                                               TIGR00407 166 qliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiy 220
                                                             q++e++dr+ v  l+++ eyvd+++PrGg++l++ + +++++Pv++h dG+Ch+y
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356 173 QVVETTDRAAVGALITMPEYVDVIVPRGGRGLIERVSRDARVPVIKHLDGICHVY 227
                                                             ******************************************************* PP

                                               TIGR00407 221 ldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgve 275
                                                             + e+adlaka+++  +akt r   C a+etLLv++++a++fl++++ q  ekgve
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356 228 VSEHADLAKAQRIAFNAKTYRYGICGAMETLLVDHTVAKDFLPAMAAQFREKGVE 282
                                                             ******************************************************* PP

                                               TIGR00407 276 lradalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygt 330
                                                             lr+ + + +++++  at     +ed+ +e+l+ +Ls+++v+ l +aiehi++yg+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356 283 LRGCERTRAIIDAVAAT-----EEDWSTEYLAAILSIRVVDGLGQAIEHINHYGS 332
                                                             **********9988555.....599****************************** PP

                                               TIGR00407 331 khsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklha 385
                                                             +h+d+i++e++   ++fv evds++v  n+ t fadGf++G+Gae+gist+klha
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356 333 HHTDSIVSEHQGDTRRFVAEVDSSSVMINTPTCFADGFEYGLGAEIGISTDKLHA 387
                                                             ******************************************************* PP

                                               TIGR00407 386 rGPvGLeaLvsy 397
                                                             rGPvGLe+L+  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1356 388 RGPVGLEGLTCE 399
                                                             *********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (415 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.01
//
[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