GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Xenophilus azovorans DSM 13620

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_038203754.1 Q392_RS07075 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P07004
         (417 letters)



>NCBI__GCF_000745855.1:WP_038203754.1
          Length = 427

 Score =  360 bits (923), Expect = e-104
 Identities = 189/418 (45%), Positives = 271/418 (64%), Gaps = 2/418 (0%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           ++ +G+ AK AS ++A+  +  KN  L  +A  L      +  ANAQD+A A A GL   
Sbjct: 10  MQALGLQAKTASAQMARADAATKNVALRALARRLREAGPALAEANAQDLARAEAAGLPAP 69

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           M DRL LTP  ++ +A    Q+  + D +G+VI     +SG+R+ + RVP+GV G+IYE+
Sbjct: 70  MQDRLRLTPKVIETVALGCEQLAAMPDVIGEVIGMKQQESGIRVGQMRVPIGVFGMIYES 129

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVT++ ASL +K+GNA ILRGG E   +N A  A+++ AL   GLP  AVQ +   DR
Sbjct: 130 RPNVTIEAASLAIKSGNAAILRGGSEAIDSNKALAALVRAALAEAGLPEDAVQLVQTTDR 189

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
             V  ++ M +++D++IPRGG GL +     + +PVI    G CH+YVD++ ++  A+KV
Sbjct: 190 EAVGHLIAMPQFVDVIIPRGGKGLIERISRDAKVPVIKHLDGNCHVYVDDTADLDMAVKV 249

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHAD--AAALAQLQAGPA 299
             NAKTQ+ S CN  E LLV + +A  FLP +    A  GV +  D  AAAL Q  AG  
Sbjct: 250 ADNAKTQKYSPCNAAEGLLVARAVAAQFLPRIGAVFAAKGVEMRCDGEAAALLQGLAGQP 309

Query: 300 KVVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEV 359
           KVV    +++ +E+L+  +++K+V+ LD+AI HI  + + H+DAILTRD  NAQRF+ EV
Sbjct: 310 KVVPATEQDWSEEYLAPIISIKVVAGLDEAIDHINRYSSHHTDAILTRDHVNAQRFLREV 369

Query: 360 DSSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIRA 417
           DS++V VNASTRF DG ++GLGAE+ +ST K HARGP+G+E LT+ K+I +G   IRA
Sbjct: 370 DSASVMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGIEGLTSLKYIVLGQGEIRA 427


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: 431
Number of extensions: 12
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: 427
Length adjustment: 32
Effective length of query: 385
Effective length of database: 395
Effective search space:   152075
Effective search space used:   152075
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_038203754.1 Q392_RS07075 (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.2735878.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.9e-150  485.2   1.0   7.8e-150  485.0   1.0    1.0  1  NCBI__GCF_000745855.1:WP_038203754.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038203754.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.0   1.0  7.8e-150  7.8e-150       1     398 []      17     416 ..      17     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 485.0 bits;  conditional E-value: 7.8e-150
                             TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 
                                           ak a++++a   +a kn al ++a  L+++ +++ +ana+d+a a++ Gl  ++ drL Lt + ++++a + +
  NCBI__GCF_000745855.1:WP_038203754.1  17 AKTASAQMARADAATKNVALRALARRLREAGPALAEANAQDLARAEAAGLPAPMQDRLRLTPKVIETVALGCE 89 
                                           899********************************************************************** PP

                             TIGR00407  74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146
                                           +++ ++d +G+vi  ++ ++G+++ ++rvP+Gv g+iye+rP+v++++asL++k+Gna+iL+Gg+ea+ snka
  NCBI__GCF_000745855.1:WP_038203754.1  90 QLAAMPDVIGEVIGMKQQESGIRVGQMRVPIGVFGMIYESRPNVTIEAASLAIKSGNAAILRGGSEAIDSNKA 162
                                           ************************************************************************* PP

                             TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChi 219
                                           l+++++ al+++glp  avql++++dre v +l+ + ++vd++iPrGg++l++ i +++++Pv++h dG+Ch+
  NCBI__GCF_000745855.1:WP_038203754.1 163 LAALVRAALAEAGLPEDAVQLVQTTDREAVGHLIAMPQFVDVIIPRGGKGLIERISRDAKVPVIKHLDGNCHV 235
                                           ************************************************************************* PP

                             TIGR00407 220 yldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlklle..lek 290
                                           y+d++adl +a kv ++aktq+ s Cna e LLv +a+a++fl+++    ++kgve+r d  + +ll+  +++
  NCBI__GCF_000745855.1:WP_038203754.1 236 YVDDTADLDMAVKVADNAKTQKYSPCNAAEGLLVARAVAAQFLPRIGAVFAAKGVEMRCDGEAAALLQglAGQ 308
                                           ***********************************************************98888887744678 PP

                             TIGR00407 291 ateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastr 363
                                            +++ ++++d+ +e+l++++s+k+v  l+eai+hi++y+++h+dailt+d+ na++f++evdsa+v vnastr
  NCBI__GCF_000745855.1:WP_038203754.1 309 PKVVPATEQDWSEEYLAPIISIKVVAGLDEAIDHINRYSSHHTDAILTRDHVNAQRFLREVDSASVMVNASTR 381
                                           89999******************************************************************** PP

                             TIGR00407 364 fadGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                           fadGf++G+Gae+gist+k+harGPvG+e+L+s k
  NCBI__GCF_000745855.1:WP_038203754.1 382 FADGFEYGLGAEIGISTDKFHARGPVGIEGLTSLK 416
                                           ********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (427 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: 00:00:00.00
# Mc/sec: 28.91
//
[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