Alignments for a candidate for proA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Dyella japonica UNC79MFTsu3.2

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate N515DRAFT_3773 N515DRAFT_3773 glutamate-5-semialdehyde dehydrogenase

Query= BRENDA::A7Y114
         (420 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3773
          Length = 420

 Score =  346 bits (887), Expect = e-100
 Identities = 180/411 (43%), Positives = 256/411 (62%)

Query: 10  VEAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEA 69
           +  QA+  + A++ L  L+ + K   L  +AD L      +L AN +D+   RE+G   A
Sbjct: 4   MRTQALACRDAAQVLAELTTEAKRALLQALADALHAGTGVVLEANARDMAAAREKGVQGA 63

Query: 70  FMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEA 129
            +DRL L + R+      LR+VA L DP G      T  NGL+VE+V VPLGVI MIYEA
Sbjct: 64  MLDRLRLDEARVAGIVAALREVAALPDPVGVVTRRETRPNGLEVERVRVPLGVIAMIYEA 123

Query: 130 RPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDR 189
           RPNVT DA  L L +GN ++L+GGS A++SN AI  V+ +ALA   +P+ ++  ++   R
Sbjct: 124 RPNVTADAAALCLMAGNGVILRGGSEAVHSNTAIAGVLRQALAAQGVPEAALTLVSDLRR 183

Query: 190 AATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISI 249
               +L  + + VD+ IPRGG  LI+ V E+A VPV++   G CH+Y+D+ AD   A+ +
Sbjct: 184 ETMVELLQLSDIVDLAIPRGGEGLIRFVAEHARVPVIKHYKGVCHLYVDRAADQALALDL 243

Query: 250 LVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAG 309
           LV+ KT RP VCNA ETL+VH+D  A+       AL +  + + G E    ++P   PA 
Sbjct: 244 LVDGKTSRPGVCNALETLLVHRDIAAEFLPRAADALGRRKVELRGCERSRALVPAMKPAD 303

Query: 310 EDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIY 369
           E D+  EYL   +AV+ VDDL  A+AHI  Y + H+E I T +++AA +F+  + +A + 
Sbjct: 304 ETDYAAEYLDLILAVRIVDDLEAALAHIHRYSSDHTEVIATRDEDAARRFVRGIRSAVVM 363

Query: 370 HNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
            NAS+RF+DGG LG GAEIGIST +LHA GPMG  ALT  +F+++G GQ+R
Sbjct: 364 VNASSRFSDGGELGLGAEIGISTTRLHAYGPMGAEALTVERFVVRGDGQVR 414


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: 449
Number of extensions: 22
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: 420
Length adjustment: 32
Effective length of query: 388
Effective length of database: 388
Effective search space:   150544
Effective search space used:   150544
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 N515DRAFT_3773 N515DRAFT_3773 (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.19351.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.1e-141  456.3   0.8   4.7e-141  456.1   0.8    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3773  N515DRAFT_3773 glutamate-5-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3773  N515DRAFT_3773 glutamate-5-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.1   0.8  4.7e-141  4.7e-141       2     396 ..      12     402 ..      11     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 456.1 bits;  conditional E-value: 4.7e-141
                                    TIGR00407   2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklks 67 
                                                  ++aa+ la+l+t+ k  +l+++ad+L+a + ++l+ana+d+aaa+e+G+  a+ldrL L+e+++ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3773  12 RDAAQVLAELTTEAKRALLQALADALHAGTGVVLEANARDMAAAREKGVQGAMLDRLRLDEARVAG 77 
                                                  89**************************************************************** PP

                                    TIGR00407  68 iaddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnavi 133
                                                  i++++++v+ L+dPvG v+  +++ +GL +ervrvPlGv+ +iyearP+v++d+a+Lcl +Gn vi
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3773  78 IVAALREVAALPDPVGVVTRRETRPNGLEVERVRVPLGVIAMIYEARPNVTADAAALCLMAGNGVI 143
                                                  ****************************************************************** PP

                                    TIGR00407 134 LkGgkeavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvk 199
                                                  L+Gg+eav+sn a++ v+++al+  g+p  a+ l+ d  re++ ell+l + vdl iPrGg++l++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3773 144 LRGGSEAVHSNTAIAGVLRQALAAQGVPEAALTLVSDLRRETMVELLQLSDIVDLAIPRGGEGLIR 209
                                                  ****************************************************************** PP

                                    TIGR00407 200 likeestiPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeL 265
                                                   + e++++Pv++h +GvCh+y+d+ ad+a a  + vd kt rP +Cna+etLLv+++ia+efl++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3773 210 FVAEHARVPVIKHYKGVCHLYVDRAADQALALDLLVDGKTSRPGVCNALETLLVHRDIAAEFLPRA 275
                                                  ****************************************************************** PP

                                    TIGR00407 266 ekqleekgvelradalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtk 331
                                                  +++l    velr+ +   +l+++ k     + ++d+  e+l+l+L+v+iv+dle+a++hi++y++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3773 276 ADALGRRKVELRGCERSRALVPAMKP----ADETDYAAEYLDLILAVRIVDDLEAALAHIHRYSSD 337
                                                  *****************999998743....3468******************************** PP

                                    TIGR00407 332 hsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvs 396
                                                  h++ i t+d+ +a++fv+ + sa v vnas rf+dG++ G+Gae+gist +lha GP+G eaL+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3773 338 HTEVIATRDEDAARRFVRGIRSAVVMVNASSRFSDGGELGLGAEIGISTTRLHAYGPMGAEALTV 402
                                                  ***************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (420 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: 7.66
//
[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