Alignments for a candidate for proA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Pseudomonas putida KT2440

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate PP_4811 PP_4811 Gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Putida:PP_4811
          Length = 423

 Score =  356 bits (913), Expect = e-103
 Identities = 181/415 (43%), Positives = 266/415 (64%), Gaps = 5/415 (1%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           + ++G AA++AS  + + S+ +KNR L+  AD L+A    +  AN  D+A  RA+GL  A
Sbjct: 9   MTRLGRAAREASRVIGRASTAQKNRALQAAADALDAARAELTAANELDLAAGRASGLEPA 68

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           +LDRLALTPAR+ G+   +RQV +L DPVG + D     SG+++ + R PLGVIG+IYE+
Sbjct: 69  LLDRLALTPARIDGMITGLRQVASLPDPVGAIRDMSYRPSGIQVGKMRTPLGVIGIIYES 128

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT+D ASLCLK+GNA ILRGG E   +N A    IQ  L   GLPA  VQ ++  DR
Sbjct: 129 RPNVTIDAASLCLKSGNATILRGGSEAIHSNRAIATCIQRGLAEAGLPAAVVQVVETTDR 188

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
             V  ++ M +++D+++PRGG GL +     + +PVI    G+CHIYV +  ++ +A  V
Sbjct: 189 EAVGALISMPEFVDVIVPRGGRGLIERISRDARVPVIKHLDGICHIYVSQHADLDKAWNV 248

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
             NAKT R   C  +ETLLV++ +A+ FLP ++++  E GV L       A + A PA  
Sbjct: 249 AFNAKTYRYGICGAMETLLVDQQVAERFLPEMARRFVEKGVELRGCERTQAIISAKPA-- 306

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
                 ++  E+L   L++++V  L+ AI HI  +G+ H+D+I++     A++F+ EVDS
Sbjct: 307 ---TEADWHTEYLDAILSIRVVDGLNQAIEHINHYGSHHTDSIISEHQGEARQFMAEVDS 363

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           ++V +N  T F DG ++GLGAE+ +ST KLHARGP+GLE LT  K++ IGD  +R
Sbjct: 364 ASVMLNTPTCFADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYVVIGDGQLR 418


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: 423
Number of extensions: 19
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: 423
Length adjustment: 32
Effective length of query: 385
Effective length of database: 391
Effective search space:   150535
Effective search space used:   150535
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 PP_4811 PP_4811 (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.8074.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.1e-150  486.9   0.0   2.4e-150  486.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4811  PP_4811 Gamma-glutamyl phosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4811  PP_4811 Gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.7   0.0  2.4e-150  2.4e-150       1     397 [.      16     407 ..      16     408 .. 0.99

  Alignments for each domain:
  == domain 1  score: 486.7 bits;  conditional E-value: 2.4e-150
                           TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdv 75 
                                         a+ea+  +   sta+kn+al++ ad+L a+  ++ aan+ d+aa+++ Gl +alldrL+Lt +++ +++ ++++v
  lcl|FitnessBrowser__Putida:PP_4811  16 AREASRVIGRASTAQKNRALQAAADALDAARAELTAANELDLAAGRASGLEPALLDRLALTPARIDGMITGLRQV 90 
                                         89************************************************************************* PP

                           TIGR00407  76 ieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalvev 150
                                         ++L+dPvG + +   + +G+++ ++r+PlGv+g+iye+rP+v++d+asLclk+Gna iL+Gg+ea++sn+a++  
  lcl|FitnessBrowser__Putida:PP_4811  91 ASLPDPVGAIRDMSYRPSGIQVGKMRTPLGVIGIIYESRPNVTIDAASLCLKSGNATILRGGSEAIHSNRAIATC 165
                                         *************************************************************************** PP

                           TIGR00407 151 iqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesa 225
                                         iq+ l+++glp+  vq++e++dre v  l+++ e+vd+++PrGg++l++ i +++++Pv++h dG+Chiy+ ++a
  lcl|FitnessBrowser__Putida:PP_4811 166 IQRGLAEAGLPAAVVQVVETTDREAVGALISMPEFVDVIVPRGGRGLIERISRDARVPVIKHLDGICHIYVSQHA 240
                                         *************************************************************************** PP

                           TIGR00407 226 dlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevsked 300
                                         dl ka +v  +akt r   C a+etLLv++++ae+fl+e++++  ekgvelr+ + +++++++++ate      d
  lcl|FitnessBrowser__Putida:PP_4811 241 DLDKAWNVAFNAKTYRYGICGAMETLLVDQQVAERFLPEMARRFVEKGVELRGCERTQAIISAKPATE-----AD 310
                                         ****************************************************************9999.....46 PP

                           TIGR00407 301 fdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGae 375
                                         +++e+l+ +Ls+++v+ l++aiehi++yg++h+d+i++e++ +a++f+ evdsa+v  n+ t fadGf++G+Gae
  lcl|FitnessBrowser__Putida:PP_4811 311 WHTEYLDAILSIRVVDGLNQAIEHINHYGSHHTDSIISEHQGEARQFMAEVDSASVMLNTPTCFADGFEYGLGAE 385
                                         779************************************************************************ PP

                           TIGR00407 376 vgistqklharGPvGLeaLvsy 397
                                         +gist+klharGPvGLe+L+  
  lcl|FitnessBrowser__Putida:PP_4811 386 IGISTDKLHARGPVGLEGLTCE 407
                                         *******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (423 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 8.03
//
[ok]

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

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis