GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Stenotrophomonas chelatiphaga DSM 21508

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate WP_057687245.1 ABB28_RS15340 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P07004
         (417 letters)



>NCBI__GCF_001431535.1:WP_057687245.1
          Length = 418

 Score =  354 bits (908), Expect = e-102
 Identities = 189/415 (45%), Positives = 270/415 (65%), Gaps = 4/415 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           +E    A + A+  +A L + ++  +L+ +A  LE+ +  IL ANA+D+A AR  G+  A
Sbjct: 4   IEGQARACRAAATVVAGLDTVQRTALLQSMAAALESHAGQILAANARDLAAARDKGIGSA 63

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           MLDRL L P RL  +A  +R V  L DPVGQV    V  +G+R+++ RVPLGVI +IYEA
Sbjct: 64  MLDRLMLDPPRLFAMAQALRDVAGLPDPVGQVTRDDVRPNGIRVQKVRVPLGVIAMIYEA 123

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT + A+LCLK GN VILRGG E   +N A  A +  AL + G+P  AV  + +  R
Sbjct: 124 RPNVTAEAAALCLKAGNGVILRGGSEAIHSNTAIAAALGSALPAHGVPEAAVTVLTDLRR 183

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
             + E+L++   ID+ IPRGG GL +   E + +PVI    GVCH++VD S +I +A+ +
Sbjct: 184 EAMLELLQLHDLIDLAIPRGGEGLIRFVAEHARVPVIKHYKGVCHLFVDASADIDQAIDL 243

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
           +V+ K  RPS CN++ETLLV++++A  FLP   + +A  GV L ADA +L  L    A  
Sbjct: 244 LVDGKCSRPSACNSLETLLVHRDVAAEFLPRAGQALAARGVELRADALSLPLL----AGS 299

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
            A   E+Y  EFL L + VK+V DL+ AI HIR + + H++ I TRD  +A+RF++ + S
Sbjct: 300 TAATDEDYAAEFLDLVIAVKVVDDLEAAITHIRRYTSDHTEVIATRDADHAERFIHALQS 359

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           + V VNAS+RF+DGGQ GLG+E+ +ST +LHA GPMGLEALT  +++  G+  +R
Sbjct: 360 AVVMVNASSRFSDGGQLGLGSEIGISTTRLHAYGPMGLEALTVERFVVRGEGQVR 414


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: 437
Number of extensions: 18
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: 418
Length adjustment: 32
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
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 WP_057687245.1 ABB28_RS15340 (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.2689281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-140  453.7   0.5   3.1e-140  453.4   0.5    1.0  1  NCBI__GCF_001431535.1:WP_057687245.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001431535.1:WP_057687245.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.4   0.5  3.1e-140  3.1e-140       2     396 ..      12     402 ..      11     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 453.4 bits;  conditional E-value: 3.1e-140
                             TIGR00407   2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkd 74 
                                           + aa+ +a l t ++  +l+ +a +L+ +a  ilaana+d+aaa+++G+  a+ldrL L+  +l  +a++++d
  NCBI__GCF_001431535.1:WP_057687245.1  12 RAAATVVAGLDTVQRTALLQSMAAALESHAGQILAANARDLAAARDKGIGSAMLDRLMLDPPRLFAMAQALRD 84 
                                           7899999****************************************************************** PP

                             TIGR00407  75 vieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkal 147
                                           v+ L+dPvG+v+    + +G+++++vrvPlGv+ +iyearP+v++++a+Lclk+Gn viL+Gg+ea++sn a+
  NCBI__GCF_001431535.1:WP_057687245.1  85 VAGLPDPVGQVTRDDVRPNGIRVQKVRVPLGVIAMIYEARPNVTAEAAALCLKAGNGVILRGGSEAIHSNTAI 157
                                           ************************************************************************* PP

                             TIGR00407 148 veviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiy 220
                                           ++ + +al   g+p  av +++d  re + ell+l + +dl iPrGg++l++ + e++++Pv++h +GvCh++
  NCBI__GCF_001431535.1:WP_057687245.1 158 AAALGSALPAHGVPEAAVTVLTDLRREAMLELLQLHDLIDLAIPRGGEGLIRFVAEHARVPVIKHYKGVCHLF 230
                                           ************************************************************************* PP

                             TIGR00407 221 ldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekate 293
                                           +d+sad+ +a+ + vd k  rPs+Cn++etLLv++++a+efl++  ++l++ gvelradal l ll  +    
  NCBI__GCF_001431535.1:WP_057687245.1 231 VDASADIDQAIDLLVDGKCSRPSACNSLETLLVHRDVAAEFLPRAGQALAARGVELRADALSLPLLAGS---- 299
                                           ***************************************************************999887.... PP

                             TIGR00407 294 aevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfad 366
                                           +++++ed+  efl+l+++vk+v+dle+ai hir+y++ h++ i t+d   ae+f+++  sa v vnas rf+d
  NCBI__GCF_001431535.1:WP_057687245.1 300 TAATDEDYAAEFLDLVIAVKVVDDLEAAITHIRRYTSDHTEVIATRDADHAERFIHALQSAVVMVNASSRFSD 372
                                           456789******************************************************************* PP

                             TIGR00407 367 GfrfGfGaevgistqklharGPvGLeaLvs 396
                                           G++ G+G+e+gist +lha GP+GLeaL+ 
  NCBI__GCF_001431535.1:WP_057687245.1 373 GGQLGLGSEIGISTTRLHAYGPMGLEALTV 402
                                           ****************************95 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.55
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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