Alignments for a candidate for proA in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Pseudomonas simiae WCS417

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate GFF4838 PS417_24745 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__WCS417:GFF4838
          Length = 421

 Score =  377 bits (969), Expect = e-109
 Identities = 195/415 (46%), Positives = 279/415 (67%), Gaps = 3/415 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           + ++G AA+QAS  +A+ S+ +KNR L   AD L+A    +  AN QD+A+ RANGL  A
Sbjct: 9   MTRLGRAARQASRLIARASTAQKNRALLAAADALDASRSELTAANEQDLANGRANGLEPA 68

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           +LDRLALTPAR+  + + +RQV  L DP+G++ D   L SG+++ + RVPLGVIG+IYE+
Sbjct: 69  LLDRLALTPARIDDMIEGLRQVAKLPDPIGEIRDMRYLPSGIQVGKMRVPLGVIGIIYES 128

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

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A V  ++ M +++D+++PRGG  L +     + +PVI    GVCH+Y+D + +I +A+++
Sbjct: 189 AAVGALITMPEFVDVIVPRGGKSLIERVSRDAKVPVIKHLDGVCHVYIDIAADIDKAIRI 248

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
             NAKT R + CNT+ETLLV+  IAD  LP L+    + GV L       A L    A V
Sbjct: 249 ADNAKTHRYAPCNTMETLLVHVGIADRVLPPLAAIYRDKGVELRGCGRTRALL---GADV 305

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
           +     ++  E+ +  L++KIV DLD+AI HI  +G++H+DAI++    +A+RF+ EVDS
Sbjct: 306 IDATELDWYTEYTAPILSIKIVDDLDEAIEHINTYGSKHTDAIVSEHFSDARRFLTEVDS 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: 446
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 GFF4838 PS417_24745 (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.5447.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.7e-157  508.8   0.3   5.4e-157  508.6   0.3    1.0  1  lcl|FitnessBrowser__WCS417:GFF4838  PS417_24745 gamma-glutamyl phosp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4838  PS417_24745 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.6   0.3  5.4e-157  5.4e-157       1     398 []      16     410 ..      16     410 .. 0.99

  Alignments for each domain:
  == domain 1  score: 508.6 bits;  conditional E-value: 5.4e-157
                           TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdv 75 
                                         a++a+  +a  sta+kn+al + ad+L a  +++ aan++d+a++++nGl +alldrL+Lt +++ ++++++++v
  lcl|FitnessBrowser__WCS417:GFF4838  16 ARQASRLIARASTAQKNRALLAAADALDASRSELTAANEQDLANGRANGLEPALLDRLALTPARIDDMIEGLRQV 90 
                                         89************************************************************************* PP

                           TIGR00407  76 ieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalvev 150
                                         ++L+dP+G++ + r l +G+++ ++rvPlGv+g+iye+rP+v++d+asLclk+Gna iL+Gg+ea++sn+a+++ 
  lcl|FitnessBrowser__WCS417:GFF4838  91 AKLPDPIGEIRDMRYLPSGIQVGKMRVPLGVIGIIYESRPNVTIDAASLCLKSGNATILRGGSEAINSNRAIAAC 165
                                         *************************************************************************** PP

                           TIGR00407 151 iqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesa 225
                                         iq+ l+ + lp+e vq++e++dr+ v  l+++ e+vd+++PrGg++l++ + +++++Pv++h dGvCh+y+d  a
  lcl|FitnessBrowser__WCS417:GFF4838 166 IQQGLAVAELPAEVVQVVETTDRAAVGALITMPEFVDVIVPRGGKSLIERVSRDAKVPVIKHLDGVCHVYIDIAA 240
                                         *************************************************************************** PP

                           TIGR00407 226 dlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevsked 300
                                         d+ ka+++ ++akt+r + Cn++etLLv+  ia++ l+ L+    +kgvelr+   + +ll ++   ++++++ d
  lcl|FitnessBrowser__WCS417:GFF4838 241 DIDKAIRIADNAKTHRYAPCNTMETLLVHVGIADRVLPPLAAIYRDKGVELRGCGRTRALLGAD---VIDATELD 312
                                         *******************************************************999999776...8889999* PP

                           TIGR00407 301 fdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGae 375
                                         + +e+++++Ls+kiv+dl+eaiehi++yg+kh+dai++e+ + a++f++evdsa+v  nastrfadGf++G+Gae
  lcl|FitnessBrowser__WCS417:GFF4838 313 WYTEYTAPILSIKIVDDLDEAIEHINTYGSKHTDAIVSEHFSDARRFLTEVDSASVMINASTRFADGFEYGLGAE 387
                                         *************************************************************************** PP

                           TIGR00407 376 vgistqklharGPvGLeaLvsyk 398
                                         +gist+klharGPvGLe+L+s k
  lcl|FitnessBrowser__WCS417:GFF4838 388 IGISTDKLHARGPVGLEGLTSEK 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.63
//
[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