Alignments for a candidate for proA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Pseudomonas stutzeri RCH2

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate GFF503 Psest_0508 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__psRCH2:GFF503
          Length = 421

 Score =  375 bits (964), Expect = e-108
 Identities = 190/415 (45%), Positives = 279/415 (67%), Gaps = 3/415 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           + ++G AA++AS  LA+ S+ +KNR L+  A  L+A  + ++ AN  D+A  RANGL  A
Sbjct: 9   MTRLGRAAREASRVLARASTAQKNRALQAAAAALDAARDELVRANELDLAGGRANGLDAA 68

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           MLDRLALTP  + G+ + +RQV  L DP+G + D   + SG+++ + RVPLGV+G+IYE+
Sbjct: 69  MLDRLALTPKVIDGMIEGLRQVATLPDPIGAIRDMRYMPSGIQVGKMRVPLGVVGIIYES 128

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

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A V  ++ M +++D+++PRGG GL +     + +PVI    G+CH+Y+D + ++ +A+++
Sbjct: 189 AAVGALISMPEFVDVIVPRGGKGLIERISRDARVPVIKHLDGICHVYIDVAADVDKAIRI 248

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
             NAKTQR + CNT+ETLLV+  IA+  LP L+    E  V L       A L    + V
Sbjct: 249 ADNAKTQRFAPCNTMETLLVHPGIAEQVLPPLAAIYREKSVELRGCPRTRALL---GSDV 305

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
           +    E++  E+ +  L++++V  LD AI HI  +G+QH+DAI+T +  +A+RF+ EVDS
Sbjct: 306 LEASEEDWSTEYNAPILSIRLVDSLDAAIEHINRYGSQHTDAIVTENFTDARRFLTEVDS 365

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           ++V +NASTRF DG ++GLGAE+ +ST KLHARGP+GLE LT+ K++  GD  +R
Sbjct: 366 ASVMINASTRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTSEKYVVFGDGHVR 420


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: 434
Number of extensions: 20
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: 421
Length adjustment: 32
Effective length of query: 385
Effective length of database: 389
Effective search space:   149765
Effective search space used:   149765
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 GFF503 Psest_0508 (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.31634.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.1e-156  505.7   0.1   4.7e-156  505.5   0.1    1.0  1  lcl|FitnessBrowser__psRCH2:GFF503  Psest_0508 gamma-glutamyl phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF503  Psest_0508 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.5   0.1  4.7e-156  4.7e-156       1     398 []      16     410 ..      16     410 .. 0.99

  Alignments for each domain:
  == domain 1  score: 505.5 bits;  conditional E-value: 4.7e-156
                          TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvi 76 
                                        a+ea+  la  sta+kn+al++ a +L a+ ++++ an+ d+a +++nGl  a+ldrL+Lt + + ++++++++v+
  lcl|FitnessBrowser__psRCH2:GFF503  16 AREASRVLARASTAQKNRALQAAAAALDAARDELVRANELDLAGGRANGLDAAMLDRLALTPKVIDGMIEGLRQVA 91 
                                        89************************************************************************** PP

                          TIGR00407  77 eLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviq 152
                                         L+dP+G + + r + +G+++ ++rvPlGv+g+iye+rP+v++d+asLclk+Gna iL+Gg+ea++sn+a+++ iq
  lcl|FitnessBrowser__psRCH2:GFF503  92 TLPDPIGAIRDMRYMPSGIQVGKMRVPLGVVGIIYESRPNVTIDAASLCLKSGNATILRGGSEAIHSNQAIARCIQ 167
                                        **************************************************************************** PP

                          TIGR00407 153 daleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadla 228
                                          l+++glp+ avq++e++dr+ v  l+++ e+vd+++PrGg++l++ i +++++Pv++h dG+Ch+y+d  ad+ 
  lcl|FitnessBrowser__psRCH2:GFF503 168 LGLAEAGLPAAAVQVVETTDRAAVGALISMPEFVDVIVPRGGKGLIERISRDARVPVIKHLDGICHVYIDVAADVD 243
                                        **************************************************************************** PP

                          TIGR00407 229 kakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdke 304
                                        ka+++ ++aktqr + Cn++etLLv++ iae+ l+ L+    ek+velr+   + +ll ++   + e+s+ed+ +e
  lcl|FitnessBrowser__psRCH2:GFF503 244 KAIRIADNAKTQRFAPCNTMETLLVHPGIAEQVLPPLAAIYREKSVELRGCPRTRALLGSD---VLEASEEDWSTE 316
                                        *********************************************************9988...677899****** PP

                          TIGR00407 305 flsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgist 380
                                        + +++Ls+++v++l++aiehi++yg++h+dai+te+ + a++f++evdsa+v  nastrfadGf++G+Gae+gist
  lcl|FitnessBrowser__psRCH2:GFF503 317 YNAPILSIRLVDSLDAAIEHINRYGSQHTDAIVTENFTDARRFLTEVDSASVMINASTRFADGFEYGLGAEIGIST 392
                                        **************************************************************************** PP

                          TIGR00407 381 qklharGPvGLeaLvsyk 398
                                        +klharGPvGLe+L+s k
  lcl|FitnessBrowser__psRCH2:GFF503 393 DKLHARGPVGLEGLTSEK 410
                                        ***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (421 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: 7.36
//
[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