Alignments for a candidate for proA in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Shewanella sp. ANA-3

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 7023725 Shewana3_0955 gamma-glutamyl phosphate reductase (RefSeq)

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__ANA3:7023725
          Length = 425

 Score =  477 bits (1228), Expect = e-139
 Identities = 245/416 (58%), Positives = 310/416 (74%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           L+Q+G  AKQASY LA LS+ +K  +LE IA+ L   ++ IL ANA+DVA A+A GL++A
Sbjct: 10  LQQLGSQAKQASYALANLSAVQKADLLEAIAEALTQNTQAILAANAKDVAAAKAEGLNDA 69

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           M+DRL L  +RL GI  D+  V  LADPVG+     VLD+GLRL RRRVPLGVIGVIYEA
Sbjct: 70  MIDRLLLNESRLAGIIGDIGDVVRLADPVGEEFGSRVLDNGLRLTRRRVPLGVIGVIYEA 129

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVTVD+A L LKTGNAVILRGGKET  +N     VI+ A+ S GLP  AVQ ID+PDR
Sbjct: 130 RPNVTVDIAVLALKTGNAVILRGGKETLESNKLISEVIRGAIASQGLPVDAVQLIDSPDR 189

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           ALV+ +L++D+Y+DM++PRGG  L +LC EQ+TIPVI GGIG+CH+YVD+  ++  AL+V
Sbjct: 190 ALVTGLLKLDQYVDMIVPRGGQALQRLCAEQATIPVILGGIGICHLYVDKHADLERALEV 249

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
           I NAK QRP+ CN ++TLLV+  +A+ F+P +++ +   GV       + A L      +
Sbjct: 250 IANAKVQRPTVCNALDTLLVDTAVAERFVPQIAEYLHRLGVRFSVCEQSYALLDGLGFDI 309

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
                + +  E+LSL L +K+VSD+D AIAHIR + + HS+AILT D+  A  F+NEV+S
Sbjct: 310 SPATEQSFATEWLSLTLGIKVVSDIDTAIAHIRTYSSGHSEAILTDDIHVATHFMNEVNS 369

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIRA 417
           +AVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKW+  GDYT RA
Sbjct: 370 AAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWLAWGDYTSRA 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: 511
Number of extensions: 15
Number of successful extensions: 1
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: 425
Length adjustment: 32
Effective length of query: 385
Effective length of database: 393
Effective search space:   151305
Effective search space used:   151305
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 7023725 Shewana3_0955 (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.31824.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.3e-169  547.9   1.8   7.1e-169  547.7   1.8    1.0  1  lcl|FitnessBrowser__ANA3:7023725  Shewana3_0955 gamma-glutamyl pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023725  Shewana3_0955 gamma-glutamyl phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  547.7   1.8  7.1e-169  7.1e-169       1     398 []      17     414 ..      17     414 .. 1.00

  Alignments for each domain:
  == domain 1  score: 547.7 bits;  conditional E-value: 7.1e-169
                         TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvie 77 
                                       ak+a++ la+ls+ +k ++l++ia++L++++++ilaanakd+aaak++Gl da++drLlL+e++l +i+ d+ dv+ 
  lcl|FitnessBrowser__ANA3:7023725  17 AKQASYALANLSAVQKADLLEAIAEALTQNTQAILAANAKDVAAAKAEGLNDAMIDRLLLNESRLAGIIGDIGDVVR 93 
                                       8**************************************************************************** PP

                         TIGR00407  78 LadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqda 154
                                       LadPvG+   +r ld+GL+l r+rvPlGv+gviyearP+v+vd+a L+lktGnaviL+Ggke+ +snk + evi+ a
  lcl|FitnessBrowser__ANA3:7023725  94 LADPVGEEFGSRVLDNGLRLTRRRVPLGVIGVIYEARPNVTVDIAVLALKTGNAVILRGGKETLESNKLISEVIRGA 170
                                       ***************************************************************************** PP

                         TIGR00407 155 leqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakak 231
                                       +++ glpv avqli+ pdr+ v+ llkld+yvd+++PrGg++l +l+ e++tiPv+ +++G+Ch+y+d++adl++a 
  lcl|FitnessBrowser__ANA3:7023725 171 IASQGLPVDAVQLIDSPDRALVTGLLKLDQYVDMIVPRGGQALQRLCAEQATIPVILGGIGICHLYVDKHADLERAL 247
                                       ***************************************************************************** PP

                         TIGR00407 232 kvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsl 308
                                       +vi +ak qrP++Cna++tLLv+ a+ae+f++++++ l+  gv++   ++  +ll+  + + + ++++ f +e+lsl
  lcl|FitnessBrowser__ANA3:7023725 248 EVIANAKVQRPTVCNALDTLLVDTAVAERFVPQIAEYLHRLGVRFSVCEQSYALLDGLGFDISPATEQSFATEWLSL 324
                                       *********************************************************99****************** PP

                         TIGR00407 309 dLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklha 385
                                        L +k+v+d++ ai+hir+y++ hs+ailt+d + a++f++ev+saavyvnastrf+dG++fG+Gaev++stqklha
  lcl|FitnessBrowser__ANA3:7023725 325 TLGIKVVSDIDTAIAHIRTYSSGHSEAILTDDIHVATHFMNEVNSAAVYVNASTRFTDGGQFGLGAEVAVSTQKLHA 401
                                       ***************************************************************************** PP

                         TIGR00407 386 rGPvGLeaLvsyk 398
                                       rGP+GLeaL++yk
  lcl|FitnessBrowser__ANA3:7023725 402 RGPMGLEALTTYK 414
                                       ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (425 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.29
//
[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