Alignments for a candidate for proA in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Clostridium acetobutylicum ATCC 824

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate NP_349848.1 CA_C3254 gamma-glutamyl phosphate reductase

Query= BRENDA::A7Y114
         (420 letters)



>NCBI__GCF_000008765.1:NP_349848.1
          Length = 418

 Score =  398 bits (1022), Expect = e-115
 Identities = 204/407 (50%), Positives = 275/407 (67%)

Query: 14  AIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDR 73
           A  +K A+K L       KN AL  ++  L  + + IL+ N+ D+ N  + G ++A +DR
Sbjct: 11  AKNSKLAAKKLSYADTNTKNKALIEMSKALLENKDYILSQNKIDIENAEKIGTSKALIDR 70

Query: 74  LSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNV 133
           L+L+ +RI D A+ L   + L+DP G+ +  W   + LQ+ ++ VPLGVIG+IYEARPNV
Sbjct: 71  LTLNDKRITDMAEALIKTSSLQDPIGEVIKMWKTPDELQIGQMRVPLGVIGIIYEARPNV 130

Query: 134 TVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATN 193
           TVDA  L +KSGN+++L+GG  AINSN AI ++I  A+    +P  S++FI  TDR   N
Sbjct: 131 TVDAAALCIKSGNSVILRGGKEAINSNTAIAKIIKNAVVTAGLPDGSIEFIDITDRETVN 190

Query: 194 QLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNA 253
            +  +   +DVLIPRGG  LI++VVEN++VPV+ETG GNCH+Y+DK AD +KA  I++NA
Sbjct: 191 VMMRLNGLIDVLIPRGGAGLIKSVVENSSVPVIETGTGNCHVYVDKYADFDKAERIIINA 250

Query: 254 KTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGEDDW 313
           K  RPAVCNA E+L+VHKD   +    + S LK+  + + G      I+ D VPA ++D+
Sbjct: 251 KLQRPAVCNAMESLLVHKDVAHEFLPRISSKLKELKVQIRGCAATQKIVKDIVPATDEDF 310

Query: 314 KNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHNAS 373
             E+L   ++VK VD L +AI HI  Y TKHSEAI+TEN   A +FL  VDAAA+Y NAS
Sbjct: 311 GKEFLDLILSVKVVDSLEEAIDHIFKYSTKHSEAIITENYTNAQRFLKEVDAAAVYVNAS 370

Query: 374 TRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
           TRFTDG   GFG EIGISTQKLHARGPMGL  LTT K+++ G GQIR
Sbjct: 371 TRFTDGEQFGFGGEIGISTQKLHARGPMGLEQLTTTKYVIYGDGQIR 417


Lambda     K      H
   0.315    0.131    0.365 

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: 473
Number of extensions: 21
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: 420
Length of database: 418
Length adjustment: 32
Effective length of query: 388
Effective length of database: 386
Effective search space:   149768
Effective search space used:   149768
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: 50 (23.9 bits)

Align candidate NP_349848.1 CA_C3254 (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.27616.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   9.8e-159  514.3   5.5   1.2e-158  514.1   5.5    1.0  1  lcl|NCBI__GCF_000008765.1:NP_349848.1  CA_C3254 gamma-glutamyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_349848.1  CA_C3254 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.1   5.5  1.2e-158  1.2e-158       2     398 .]      15     407 ..      14     407 .. 0.99

  Alignments for each domain:
  == domain 1  score: 514.1 bits;  conditional E-value: 1.2e-158
                              TIGR00407   2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 
                                            k aa kl    t+ kn+al  + ++L ++ + il +n++di++a++ G ++al+drL+L+++++ ++a+++ 
  lcl|NCBI__GCF_000008765.1:NP_349848.1  15 KLAAKKLSYADTNTKNKALIEMSKALLENKDYILSQNKIDIENAEKIGTSKALIDRLTLNDKRITDMAEALI 86 
                                            6799******************************************************************** PP

                              TIGR00407  74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnk 145
                                            +  +L+dP+G+vi+  +  + L++ ++rvPlGv+g+iyearP+v+vd+a+Lc+k+Gn+viL+Ggkea++sn 
  lcl|NCBI__GCF_000008765.1:NP_349848.1  87 KTSSLQDPIGEVIKMWKTPDELQIGQMRVPLGVIGIIYEARPNVTVDAAALCIKSGNSVILRGGKEAINSNT 158
                                            ************************************************************************ PP

                              TIGR00407 146 alveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvC 217
                                            a++++i++a+  +glp ++++ i+ +dre+v+ +++l+  +d+liPrGg++l+k + e+s +Pv+e+++G+C
  lcl|NCBI__GCF_000008765.1:NP_349848.1 159 AIAKIIKNAVVTAGLPDGSIEFIDITDRETVNVMMRLNGLIDVLIPRGGAGLIKSVVENSSVPVIETGTGNC 230
                                            ************************************************************************ PP

                              TIGR00407 218 hiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllele 289
                                            h+y+d+ ad  ka+++i++ak qrP++Cna+e+LLv+k++a+efl++++++l+e  v++r+ a+++k+++  
  lcl|NCBI__GCF_000008765.1:NP_349848.1 231 HVYVDKYADFDKAERIIINAKLQRPAVCNAMESLLVHKDVAHEFLPRISSKLKELKVQIRGCAATQKIVKDI 302
                                            *******************************************************************99876 PP

                              TIGR00407 290 kateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnas 361
                                                + +++edf kefl+l+Lsvk+v++leeai+hi +y+tkhs+ai+te+ +na++f+kevd+aavyvnas
  lcl|NCBI__GCF_000008765.1:NP_349848.1 303 ----VPATDEDFGKEFLDLILSVKVVDSLEEAIDHIFKYSTKHSEAIITENYTNAQRFLKEVDAAAVYVNAS 370
                                            ....677889************************************************************** PP

                              TIGR00407 362 trfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                            trf+dG +fGfG e+gistqklharGP+GLe L+++k
  lcl|NCBI__GCF_000008765.1:NP_349848.1 371 TRFTDGEQFGFGGEIGISTQKLHARGPMGLEQLTTTK 407
                                            **********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (418 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.75
//
[ok]

This GapMind analysis is from Apr 10 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