GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Thioalkalivibrio thiocyanodenitrificans ARhD 1

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_026186090.1 THITHI_RS0105635 glutamate-5-semialdehyde dehydrogenase

Query= SwissProt::P07004
         (417 letters)



>NCBI__GCF_000378965.1:WP_026186090.1
          Length = 427

 Score =  375 bits (963), Expect = e-108
 Identities = 196/413 (47%), Positives = 275/413 (66%), Gaps = 4/413 (0%)

Query: 4   QMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAML 63
           +MG  A+ AS  LA+  +  K+  L  +A+ +EA++  ++  N +D+   + NGL +A+L
Sbjct: 18  EMGRRARAASRALARAETGVKDAALLGMAEIIEARAAALMAENRKDLEAGQQNGLDDALL 77

Query: 64  DRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARP 123
           DRLA TP R+  +A+ +RQ+  LADPVG + D     SG+++ R RVPLGVIG+IYE+RP
Sbjct: 78  DRLAFTPERIAVMAEGLRQIAALADPVGAISDLNYRPSGIQVGRMRVPLGVIGIIYESRP 137

Query: 124 NVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRAL 183
           NVTVD A LCLK+GNA ILRGG E   +N A    I+D L+  GLP  AVQ +   DRA 
Sbjct: 138 NVTVDAAGLCLKSGNACILRGGSEAFHSNGALADCIRDGLERAGLPMDAVQVVATTDRAA 197

Query: 184 VSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIV 243
           V  +LR+   +D+++PRGG GL     E+S IPVI    GVCH+YVD+  +  +A++V V
Sbjct: 198 VGALLRLKDSVDVIVPRGGKGLIARVSEESLIPVIKHLDGVCHVYVDDGADPDKAVRVAV 257

Query: 244 NAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKVVA 303
           NAKTQR  TCNT+ETLLV++ +A+  LP L    A+ GV L    A+ A L      +  
Sbjct: 258 NAKTQRYGTCNTMETLLVSRGVAERILPRLGDAFADKGVELRGCEASRAILSG----IKE 313

Query: 304 VKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSA 363
              +++ +E+L+  L V++V  LD AI HI  +G+ H+D+I+T D   A+RF+ EVDSS+
Sbjct: 314 ATEQDWSEEYLAPVLAVRVVDGLDAAIEHINTYGSHHTDSIVTEDYTRARRFLREVDSSS 373

Query: 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416
           V VNASTRF DG ++GLGAE+ +ST KLHARGP+GLE LTT K++ +GD  +R
Sbjct: 374 VMVNASTRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTTLKYVVLGDGHVR 426


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: 457
Number of extensions: 19
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_026186090.1 THITHI_RS0105635 (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.2392494.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-153  496.6   0.1   2.7e-153  496.4   0.1    1.0  1  NCBI__GCF_000378965.1:WP_026186090.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_026186090.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.4   0.1  2.7e-153  2.7e-153       1     398 []      23     416 ..      23     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 496.4 bits;  conditional E-value: 2.7e-153
                             TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 
                                           a+ a+  la   t  k+ al  +a+ ++a+a +++a+n+kd++a+++nGl dalldrL++t e++ ++a++++
  NCBI__GCF_000378965.1:WP_026186090.1  23 ARAASRALARAETGVKDAALLGMAEIIEARAAALMAENRKDLEAGQQNGLDDALLDRLAFTPERIAVMAEGLR 95 
                                           799********************************************************************** PP

                             TIGR00407  74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146
                                           +++ LadPvG + + + + +G+++ r+rvPlGv+g+iye+rP+v+vd+a Lclk+Gna iL+Gg+ea +sn a
  NCBI__GCF_000378965.1:WP_026186090.1  96 QIAALADPVGAISDLNYRPSGIQVGRMRVPLGVIGIIYESRPNVTVDAAGLCLKSGNACILRGGSEAFHSNGA 168
                                           ************************************************************************* PP

                             TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChi 219
                                           l++ i+d le++glp+ avq++ ++dr+ v  ll+l + vd+++PrGg++l+  + ees iPv++h dGvCh+
  NCBI__GCF_000378965.1:WP_026186090.1 169 LADCIRDGLERAGLPMDAVQVVATTDRAAVGALLRLKDSVDVIVPRGGKGLIARVSEESLIPVIKHLDGVCHV 241
                                           ************************************************************************* PP

                             TIGR00407 220 yldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekat 292
                                           y+d+ ad  ka +v v+aktqr  tCn++etLLv + +ae+ l++L ++ ++kgvelr+ ++  ++l+   ++
  NCBI__GCF_000378965.1:WP_026186090.1 242 YVDDGADPDKAVRVAVNAKTQRYGTCNTMETLLVSRGVAERILPRLGDAFADKGVELRGCEASRAILSG--IK 312
                                           ***********************************************************9999988764..45 PP

                             TIGR00407 293 eaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfa 365
                                           e  ++++d+ +e+l+++L+v++v+ l++aiehi++yg++h+d+i+ted + a++f++evds++v vnastrfa
  NCBI__GCF_000378965.1:WP_026186090.1 313 E--ATEQDWSEEYLAPVLAVRVVDGLDAAIEHINTYGSHHTDSIVTEDYTRARRFLREVDSSSVMVNASTRFA 383
                                           5..6778****************************************************************** PP

                             TIGR00407 366 dGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                           dGf++G+Gae+gist+klharGPvGLe+L++ k
  NCBI__GCF_000378965.1:WP_026186090.1 384 DGFEYGLGAEIGISTDKLHARGPVGLEGLTTLK 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: 28.05
//
[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