Alignments for a candidate for proA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Shewanella loihica PV-4

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 5210406 Shew_2847 gamma-glutamyl phosphate reductase (RefSeq)

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__PV4:5210406
          Length = 429

 Score =  469 bits (1208), Expect = e-137
 Identities = 241/416 (57%), Positives = 309/416 (74%), Gaps = 2/416 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           L  +G  AK ASY +A L++ +K  +L  IA +L  +   I+ AN QDVA AR NGL++A
Sbjct: 14  LNTLGEQAKAASYAMASLTASQKRDLLRAIAAKLTDKRAQIVAANQQDVAKARENGLNDA 73

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           M+DRL L  +RL G+  D+  V  LADP+G  ++  +LD+GLRL RRRVPLGV+GVIYEA
Sbjct: 74  MIDRLLLDESRLSGVIADIENVVALADPIGSELESQLLDNGLRLSRRRVPLGVLGVIYEA 133

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVTVD+A L LKTGNAVILRGGKET  +N A    I++A+   GLP+ AVQ I +PDR
Sbjct: 134 RPNVTVDIAVLALKTGNAVILRGGKETLASNLALSEAIREAISEQGLPSDAVQLIQDPDR 193

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           ALVS +L++DKY+DM++PRGG  L +LC EQ+TIPVI GGIG+CH+YVD  V+  +A++V
Sbjct: 194 ALVSGLLKLDKYVDMIVPRGGQNLQRLCAEQATIPVILGGIGICHLYVDSEVDQLKAIEV 253

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHA-DAAALAQLQAGPAK 300
           I NAK QRP+ CN ++T+LV+++IA +FLP L   ++  GV+ HA D A      AG   
Sbjct: 254 IANAKVQRPTVCNALDTVLVHQSIAQTFLPKLYAHLSALGVSFHACDQAEAIGKDAGTVT 313

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
             A   E +  E+LSL+L V++V D+D AIAHIR   + HS+ IL+ ++    RF+NEVD
Sbjct: 314 HQA-SDETFGTEWLSLNLGVRVVDDMDMAIAHIRRFSSGHSEGILSDNIHATARFINEVD 372

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           ++AVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIG+GDYT R
Sbjct: 373 AAAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGVGDYTAR 428


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: 499
Number of extensions: 15
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: 429
Length adjustment: 32
Effective length of query: 385
Effective length of database: 397
Effective search space:   152845
Effective search space used:   152845
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 5210406 Shew_2847 (gamma-glutamyl phosphate reductase (RefSeq))
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.12841.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.2e-167  543.7   3.1   1.3e-167  543.5   3.1    1.0  1  lcl|FitnessBrowser__PV4:5210406  Shew_2847 gamma-glutamyl phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210406  Shew_2847 gamma-glutamyl phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.5   3.1  1.3e-167  1.3e-167       1     398 []      21     418 ..      21     418 .. 0.99

  Alignments for each domain:
  == domain 1  score: 543.5 bits;  conditional E-value: 1.3e-167
                        TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieL 78 
                                      ak a++ +a+l++ +k ++l +ia +L+ +   i+aan++d+a+a+enGl da++drLlL+e++l ++++d+++v+ L
  lcl|FitnessBrowser__PV4:5210406  21 AKAASYAMASLTASQKRDLLRAIAAKLTDKRAQIVAANQQDVAKARENGLNDAMIDRLLLDESRLSGVIADIENVVAL 98 
                                      899*************************************************************************** PP

                        TIGR00407  79 adPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdale 156
                                      adP+G  +e++ ld+GL+l r+rvPlGvlgviyearP+v+vd+a L+lktGnaviL+Ggke+  sn al e i++a+ 
  lcl|FitnessBrowser__PV4:5210406  99 ADPIGSELESQLLDNGLRLSRRRVPLGVLGVIYEARPNVTVDIAVLALKTGNAVILRGGKETLASNLALSEAIREAIS 176
                                      ****************************************************************************** PP

                        TIGR00407 157 qtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakakkvi 234
                                      + glp  avqli+dpdr+ v+ llkld+yvd+++PrGg++l +l+ e++tiPv+ +++G+Ch+y+d ++d+ ka++vi
  lcl|FitnessBrowser__PV4:5210406 177 EQGLPSDAVQLIQDPDRALVSGLLKLDKYVDMIVPRGGQNLQRLCAEQATIPVILGGIGICHLYVDSEVDQLKAIEVI 254
                                      ****************************************************************************** PP

                        TIGR00407 235 vdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsldLsv 312
                                       +ak qrP++Cna++t+Lv+++ia+ fl++L  +l++ gv+++a ++++++ + ++    ++s+e f +e+lsl L v
  lcl|FitnessBrowser__PV4:5210406 255 ANAKVQRPTVCNALDTVLVHQSIAQTFLPKLYAHLSALGVSFHACDQAEAIGKDAGTVTHQASDETFGTEWLSLNLGV 332
                                      ********************************************999999998888888899999************* PP

                        TIGR00407 313 kivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvG 390
                                      ++v+d++ ai+hir++++ hs++il+++ ++  +f++evd+aavyvnastrf+dG++fG+Gaev++stqklharGP+G
  lcl|FitnessBrowser__PV4:5210406 333 RVVDDMDMAIAHIRRFSSGHSEGILSDNIHATARFINEVDAAAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMG 410
                                      ****************************************************************************** PP

                        TIGR00407 391 LeaLvsyk 398
                                      LeaL++yk
  lcl|FitnessBrowser__PV4:5210406 411 LEALTTYK 418
                                      *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (429 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: 13.01
//
[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