Alignments for a candidate for proA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Synechococcus elongatus PCC 7942

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; GSA dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; EC 1.2.1.41 (characterized)
to candidate Synpcc7942_2265 Synpcc7942_2265 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P54885
         (456 letters)



>FitnessBrowser__SynE:Synpcc7942_2265
          Length = 431

 Score =  352 bits (904), Expect = e-101
 Identities = 198/442 (44%), Positives = 278/442 (62%), Gaps = 24/442 (5%)

Query: 8   AKNARKAGNILKTISNEGRSDILYKIHDALKANAHAIEEANKIDLAVAKETGLADSLLKR 67
           A+  R A   L   S   R  +L  I   L+  A  I  AN+ D   A   G+A +L  R
Sbjct: 12  AQATRAAARQLAQWSGADRQRLLSAIATTLEQEAPRILAANQADCEAATTEGIAPALYAR 71

Query: 68  LDLFKGDKFEVMLQGIKDVAELEDPVGKVKMARELDDGLTLYQVTAPVGVLLVIFESRPE 127
           L L   DK    + G++D+A+L DP+G++++ RELD+GL L ++T PVGVL VIFE+RP+
Sbjct: 72  LKL-DADKLAAAIAGVRDLAQLPDPLGQIQIDRELDEGLILQRLTCPVGVLGVIFEARPD 130

Query: 128 VIANITALSIKSGNAAILKGGKESVNTFREMAKIVNDTIAQFQSETGVPVGSVQLIETRQ 187
            +  I +L+IKSGN AILKGG+E++ + + +       IAQ  +E   PV +++L+ +R+
Sbjct: 131 AVIQIASLAIKSGNGAILKGGREAICSCQAIVA----AIAQALAEQQAPVEAIRLLTSRE 186

Query: 188 DVSDLLDQDEYIDLVVPRGSNALVRKIKDTTKIPVLGHADGICSIYLDEDADLIKAKRIS 247
           +   LL  D Y+DL++PRGSN+ VR ++D T IPVLGHADGIC +Y+D+ A + K   I+
Sbjct: 187 ETLALLKLDRYVDLIIPRGSNSFVRFVQDNTHIPVLGHADGICHLYVDQAAAIEKTVTIT 246

Query: 248 LDAKTNYPAGCNAMETLLINPKFS-KWWEVLENLTLEGGVTIHATKDLKTAYFDKLNELG 306
           +DAKT YPA CNA+ETLLI+   + ++  V+     E GV++      +T          
Sbjct: 247 VDAKTQYPAACNAIETLLIHEAIAPQFLPVVAAALHEKGVSLRGDAAAQTIV-------- 298

Query: 307 KLTEAIQCKTVDADEEQDFDKEFLSLDLAAKFVTSTESAIQHINTHSSRHTDAIVTENKA 366
                     ++A  E+D+  E+  L LA + V S ++AI HIN + S HTDAI TE+ A
Sbjct: 299 ---------PMEAATEEDWRTEYSDLVLAVRLVPSLDAAIAHINEYGSGHTDAIATEDAA 349

Query: 367 NAEKFMKGVDSSGVYWNASTRFADGFRYGFGAEVGISTSKIHARGPVGLDGLVSYQYQIR 426
            A +F   VDS+GVY N STRFADGFRYGFGAEVGIST K+  RGPVGL+GLV+Y+Y + 
Sbjct: 350 AAAQFFSQVDSAGVYHNCSTRFADGFRYGFGAEVGISTQKLPPRGPVGLEGLVTYKYVLS 409

Query: 427 GDGQVASDYLGAGGNKAFVHKD 448
           GDGQ+A+ Y GA   K F+H+D
Sbjct: 410 GDGQIAATYSGAQA-KPFLHRD 430


Lambda     K      H
   0.315    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: 460
Number of extensions: 20
Number of successful extensions: 4
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: 456
Length of database: 431
Length adjustment: 32
Effective length of query: 424
Effective length of database: 399
Effective search space:   169176
Effective search space used:   169176
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate Synpcc7942_2265 Synpcc7942_2265 (glutamate-5-semialdehyde dehydrogenase)
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.17574.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-168  544.3   0.2   9.1e-168  544.1   0.2    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2265  Synpcc7942_2265 glutamate-5-semi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2265  Synpcc7942_2265 glutamate-5-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.1   0.2  9.1e-168  9.1e-168       2     398 .]      16     405 ..      15     405 .. 0.99

  Alignments for each domain:
  == domain 1  score: 544.1 bits;  conditional E-value: 9.1e-168
                                 TIGR00407   2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiad 70 
                                               + aa +laq s a+++++ls+ia  L++ea+ ilaan+ d++aa  +G+a+al+ rL+L+ +kl   ++
  lcl|FitnessBrowser__SynE:Synpcc7942_2265  16 RAAARQLAQWSGADRQRLLSAIATTLEQEAPRILAANQADCEAATTEGIAPALYARLKLDADKLAAAIA 84 
                                               789****************************************************************** PP

                                 TIGR00407  71 dvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgke 139
                                               +v+d+++L+dP+G+++  reldeGL l+r+++P+Gvlgvi+earP++++++asL++k+Gn +iLkGg+e
  lcl|FitnessBrowser__SynE:Synpcc7942_2265  85 GVRDLAQLPDPLGQIQIDRELDEGLILQRLTCPVGVLGVIFEARPDAVIQIASLAIKSGNGAILKGGRE 153
                                               ********************************************************************* PP

                                 TIGR00407 140 avrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiP 208
                                               a+ s++a+v+ i +al++   pvea++l++   ree   llkld+yvdl+iPrG+n++v+ ++++++iP
  lcl|FitnessBrowser__SynE:Synpcc7942_2265 154 AICSCQAIVAAIAQALAEQQAPVEAIRLLTS--REETLALLKLDRYVDLIIPRGSNSFVRFVQDNTHIP 220
                                               *****************************99..************************************ PP

                                 TIGR00407 209 vlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelr 277
                                               vl+hadG+Ch+y+d+ a ++k  +++vdaktq+P++CnaietLL+++aia +fl++++ +l+ekgv+lr
  lcl|FitnessBrowser__SynE:Synpcc7942_2265 221 VLGHADGICHLYVDQAAAIEKTVTITVDAKTQYPAACNAIETLLIHEAIAPQFLPVVAAALHEKGVSLR 289
                                               ********************************************************************* PP

                                 TIGR00407 278 adalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaek 346
                                               +da+++ ++++e ate     ed+++e+++l+L+v++v +l++ai+hi++yg+ h+dai ted ++a +
  lcl|FitnessBrowser__SynE:Synpcc7942_2265 290 GDAAAQTIVPMEAATE-----EDWRTEYSDLVLAVRLVPSLDAAIAHINEYGSGHTDAIATEDAAAAAQ 353
                                               ***********96665.....99********************************************** PP

                                 TIGR00407 347 fvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                               f  +vdsa+vy+n+strfadGfr+GfGaevgistqkl++rGPvGLe+Lv+yk
  lcl|FitnessBrowser__SynE:Synpcc7942_2265 354 FFSQVDSAGVYHNCSTRFADGFRYGFGAEVGISTQKLPPRGPVGLEGLVTYK 405
                                               ***************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (431 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: 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