Alignments for a candidate for proA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Cupriavidus basilensis 4G11

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate RR42_RS17530 RR42_RS17530 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Cup4G11:RR42_RS17530
          Length = 426

 Score =  344 bits (882), Expect = 3e-99
 Identities = 179/416 (43%), Positives = 269/416 (64%), Gaps = 1/416 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           ++++G  A+ AS  +A+ S+ +KNR L  IA  +   +  +   NA DV  ARANG   A
Sbjct: 10  MDRVGQQARAASRAMARASTADKNRALLTIAAAIRRDAAHLKAVNAGDVERARANGQDAA 69

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
            +DRL L+   +  +A  + Q+  LADP+G++ +     +G+++ + RVPLGVIG+IYE+
Sbjct: 70  FIDRLTLSDKAIDTMAAGLEQIAALADPIGEISNMKFRPTGIQVGQMRVPLGVIGIIYES 129

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT+D A+LCLK+GNA ILRGG E   +N A  A++ + L + GLP  AVQ I   DR
Sbjct: 130 RPNVTIDAAALCLKSGNATILRGGSEAIDSNTALAALVAEGLAAAGLPPEAVQVISTTDR 189

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           A V  ++ M +Y+D+++PRGG  L      ++ +P+I    G+CH+Y+D   ++ +A++V
Sbjct: 190 AAVGRLVTMTEYVDVIVPRGGKSLIARLMAEARVPMIKHLDGICHVYIDVDADLDKAVRV 249

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQ-AGPAK 300
             NAKTQR + CNT+ETLLV + +A + LP L +   E GV L   AA  A L+ AG   
Sbjct: 250 ADNAKTQRYAPCNTMETLLVARAVAAAALPPLCRIYQEKGVELRVCAATRATLEAAGFTG 309

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
           +V    E++  E+L+  L ++ V+ LD+AI HI  +G+ H+D+I+T +     RF+ EVD
Sbjct: 310 LVDATEEDWRLEYLAPVLAIRTVAGLDEAIEHINTYGSAHTDSIITENYTTGMRFLREVD 369

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           S++V +NASTRF DG ++GLGAE+ +S  KLHARGP+GLE LT+ K++  G   IR
Sbjct: 370 SASVMINASTRFADGFEYGLGAEIGISNDKLHARGPVGLEGLTSLKYVVFGHGEIR 425


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: 12
Number of successful extensions: 3
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: 426
Length adjustment: 32
Effective length of query: 385
Effective length of database: 394
Effective search space:   151690
Effective search space used:   151690
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 RR42_RS17530 RR42_RS17530 (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.8508.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-148  479.1   1.9   5.5e-148  478.9   1.9    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS17530  RR42_RS17530 gamma-glutamyl phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS17530  RR42_RS17530 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.9   1.9  5.5e-148  5.5e-148       1     398 []      17     415 ..      17     415 .. 0.98

  Alignments for each domain:
  == domain 1  score: 478.9 bits;  conditional E-value: 5.5e-148
                                 TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 
                                               a+ a+  +a  sta+kn+al +ia +++++a  + a na d++ a++nG   a++drL+L+++ + ++a
  lcl|FitnessBrowser__Cup4G11:RR42_RS17530  17 ARAASRAMARASTADKNRALLTIAAAIRRDAAHLKAVNAGDVERARANGQDAAFIDRLTLSDKAIDTMA 85 
                                               899****************************************************************** PP

                                 TIGR00407  70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138
                                               +++++++ LadP+G++ + + +  G+++ ++rvPlGv+g+iye+rP+v++d+a+Lclk+Gna iL+Gg+
  lcl|FitnessBrowser__Cup4G11:RR42_RS17530  86 AGLEQIAALADPIGEISNMKFRPTGIQVGQMRVPLGVIGIIYESRPNVTIDAAALCLKSGNATILRGGS 154
                                               ********************************************************************* PP

                                 TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207
                                               ea+ sn al++++ + l+ +glp eavq+i ++dr+ v  l+++ eyvd+++PrGg++l+  +  e+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS17530 155 EAIDSNTALAALVAEGLAAAGLPPEAVQVISTTDRAAVGRLVTMTEYVDVIVPRGGKSLIARLMAEARV 223
                                               ********************************************************************* PP

                                 TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276
                                               P+++h dG+Ch+y+d +adl ka +v ++aktqr + Cn++etLLv +a+a+  l+ L +  +ekgvel
  lcl|FitnessBrowser__Cup4G11:RR42_RS17530 224 PMIKHLDGICHVYIDVDADLDKAVRVADNAKTQRYAPCNTMETLLVARAVAAAALPPLCRIYQEKGVEL 292
                                               ********************************************************************* PP

                                 TIGR00407 277 radalvlkllelekat.eaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkkna 344
                                               r  a++ + le+++ t  +++++ed++ e+l+++L++++v  l+eaiehi++yg+ h+d+i+te+ ++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS17530 293 RVCAATRATLEAAGFTgLVDATEEDWRLEYLAPVLAIRTVAGLDEAIEHINTYGSAHTDSIITENYTTG 361
                                               **9988888887776626899************************************************ PP

                                 TIGR00407 345 ekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                                +f++evdsa+v  nastrfadGf++G+Gae+gis +klharGPvGLe+L+s k
  lcl|FitnessBrowser__Cup4G11:RR42_RS17530 362 MRFLREVDSASVMINASTRFADGFEYGLGAEIGISNDKLHARGPVGLEGLTSLK 415
                                               ***************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (426 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: 11.15
//
[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