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 5210587 Shew_3015 gamma-glutamyl phosphate reductase (RefSeq)

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__PV4:5210587
          Length = 415

 Score =  341 bits (875), Expect = 2e-98
 Identities = 183/417 (43%), Positives = 259/417 (62%), Gaps = 4/417 (0%)

Query: 1   MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60
           ++E +   A QA+  LAQ+ ++ KN +L  +A  L   S  I +AN  D+A A   GLS 
Sbjct: 3   IIETLSRDAAQAAKTLAQVDTQTKNTILLDMARSLRDNSFEIRSANLIDLASAEQAGLSH 62

Query: 61  AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120
           AM+DRL L   R++ +A  +  +  L DP+G   D     +GL + + RVPLGV+ +IYE
Sbjct: 63  AMIDRLTLDGDRIEAMAHGIEIIATLPDPIGVQRDLSTRPNGLAISKMRVPLGVVCMIYE 122

Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180
           ARPNVT D  +LC K+GNAVILRGGKE   T+    +V+Q  LK  GLPA  +  + +PD
Sbjct: 123 ARPNVTADAGALCFKSGNAVILRGGKEALHTSKVIASVLQKVLKQYGLPASLIAVVPDPD 182

Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240
           RAL+ E+++    ID++IPRGG GL     E S +PVI    GVCH+YVD+  ++ +AL 
Sbjct: 183 RALLMELMQQRDTIDVIIPRGGEGLINFVTEHSKVPVIQHFKGVCHLYVDKDADLDKALA 242

Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300
           +++N KTQR   CN +E LLV+  +A  FL   +  +A+  V ++      A  Q   A 
Sbjct: 243 LLLNGKTQRTGVCNALEGLLVHSEVAPKFLAMAATALAKHQVKIN----CCANTQQYFAA 298

Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360
              +  EE+  E+L L+L V+ V D D A+AHI   G++H++ I T +   A+RF   VD
Sbjct: 299 AQVLSDEEFGQEYLDLELAVRQVKDFDQAVAHIHRFGSRHTEVICTENELTAKRFQRTVD 358

Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIRA 417
           +S V VNAS+RF+DGG+ GLGAE+ ++T KLHA GPMGLE+LTT K++  GD  IRA
Sbjct: 359 ASVVMVNASSRFSDGGELGLGAEIGIATTKLHAYGPMGLESLTTEKYLVNGDGQIRA 415


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: 405
Number of extensions: 17
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: 415
Length adjustment: 31
Effective length of query: 386
Effective length of database: 384
Effective search space:   148224
Effective search space used:   148224
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 5210587 Shew_3015 (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.26262.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
     5e-140  452.7   1.7   5.8e-140  452.5   1.7    1.0  1  lcl|FitnessBrowser__PV4:5210587  Shew_3015 gamma-glutamyl phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210587  Shew_3015 gamma-glutamyl phosphate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.5   1.7  5.8e-140  5.8e-140       1     398 []      11     404 ..      11     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 452.5 bits;  conditional E-value: 5.8e-140
                        TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieL 78 
                                      a +aa +laq+ t+ kn++l  +a +L+ ++ +i  an +d+a+a++ Gl++a++drL+L+ ++++ +a++++ ++ L
  lcl|FitnessBrowser__PV4:5210587  11 AAQAAKTLAQVDTQTKNTILLDMARSLRDNSFEIRSANLIDLASAEQAGLSHAMIDRLTLDGDRIEAMAHGIEIIATL 88 
                                      679*************************************************************************** PP

                        TIGR00407  79 adPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdale 156
                                      +dP+G   +  ++ +GL + ++rvPlGv+ +iyearP+v++d+ +Lc+k+GnaviL+Ggkea ++ k++++v+q+ l+
  lcl|FitnessBrowser__PV4:5210587  89 PDPIGVQRDLSTRPNGLAISKMRVPLGVVCMIYEARPNVTADAGALCFKSGNAVILRGGKEALHTSKVIASVLQKVLK 166
                                      ****************************************************************************** PP

                        TIGR00407 157 qtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakakkvi 234
                                      q glp+  + ++ dpdr+ ++el+++ + +d++iPrGg++l++ + e+s++Pv++h +GvCh+y+d++adl ka  + 
  lcl|FitnessBrowser__PV4:5210587 167 QYGLPASLIAVVPDPDRALLMELMQQRDTIDVIIPRGGEGLINFVTEHSKVPVIQHFKGVCHLYVDKDADLDKALALL 244
                                      ****************************************************************************** PP

                        TIGR00407 235 vdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsldLsv 312
                                      ++ ktqr  +Cna+e LLv+ ++a +fl   + +l+++ v+++  a +++   ++  +    s+e+f +e+l+l L+v
  lcl|FitnessBrowser__PV4:5210587 245 LNGKTQRTGVCNALEGLLVHSEVAPKFLAMAATALAKHQVKINCCANTQQYFAAA--Q--VLSDEEFGQEYLDLELAV 318
                                      *******************************************999998887776..3..366899************ PP

                        TIGR00407 313 kivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvG 390
                                      + v+d ++a++hi+++g++h++ i te++ +a++f+++vd++ v vnas rf+dG++ G+Gae+gi+t klha GP+G
  lcl|FitnessBrowser__PV4:5210587 319 RQVKDFDQAVAHIHRFGSRHTEVICTENELTAKRFQRTVDASVVMVNASSRFSDGGELGLGAEIGIATTKLHAYGPMG 396
                                      ****************************************************************************** PP

                        TIGR00407 391 LeaLvsyk 398
                                      Le+L++ k
  lcl|FitnessBrowser__PV4:5210587 397 LESLTTEK 404
                                      *****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (415 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: 00:00:00.02
# Mc/sec: 7.56
//
[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