GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Beijerinckia indica subsp. indica ATCC 9039

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_012383424.1 BIND_RS02095 glutamate-5-semialdehyde dehydrogenase

Query= BRENDA::A7Y114
         (420 letters)



>NCBI__GCF_000019845.1:WP_012383424.1
          Length = 431

 Score =  337 bits (864), Expect = 4e-97
 Identities = 181/406 (44%), Positives = 253/406 (62%), Gaps = 1/406 (0%)

Query: 16  EAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDRLS 75
           +A+ ++ +L + S + KN AL   A+ L +  + +L AN +DL   + Q    AF+DRL+
Sbjct: 25  QARASAHALSLASTEAKNLALRVAAEQLRKRTQDLLLANARDLEGAKAQDANAAFLDRLT 84

Query: 76  LSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNVTV 135
           L  +RI   A+GL ++A L DP G+ L+ +   NGL +E+V  PLGVIG+IYE+RP VT 
Sbjct: 85  LDDKRIEAIARGLDEIAALPDPVGRMLARYERPNGLVIERVATPLGVIGIIYESRPAVTA 144

Query: 136 DATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATNQL 195
           DA  L LK+GNA +L+GGS +  S   I   + + L    +P+ +V  + + DRAA  ++
Sbjct: 145 DAGALCLKAGNAAILRGGSESFFSATIIHACLTEGLRAAGLPEAAVSLVPTRDRAAVGEM 204

Query: 196 FT-MKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNAK 254
              +   +DV++PRGG  L+  V   A VPV     G  HI++ + AD+EKA  I+ NAK
Sbjct: 205 LKGLDGTIDVIVPRGGKSLVARVQAEARVPVFAHLEGVNHIFVHRAADLEKAAIIIRNAK 264

Query: 255 TDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGEDDWK 314
             RP VC AAE L+V +  +A H   L   L      + GD    TI P    A E DW+
Sbjct: 265 LRRPGVCGAAEILLVDEACMATHLAPLTRMLLDAGCAIRGDAATQTIDPRVTAAMESDWR 324

Query: 315 NEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHNAST 374
            EY    IAV+ +D L  AIAHIET+G+ H++ I+TE+QEAAD+FLA VD+A + HNAST
Sbjct: 325 TEYSDAIIAVRVIDGLNKAIAHIETHGSHHTDCIITEDQEAADRFLAEVDSAIVMHNAST 384

Query: 375 RFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
           +F DGG  GFGAEIGI+T +LHARGP+GL  LT+ K+ + G GQIR
Sbjct: 385 QFADGGEFGFGAEIGIATGRLHARGPVGLEQLTSFKYRVHGNGQIR 430


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: 470
Number of extensions: 20
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: 420
Length of database: 431
Length adjustment: 32
Effective length of query: 388
Effective length of database: 399
Effective search space:   154812
Effective search space used:   154812
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: 51 (24.3 bits)

Align candidate WP_012383424.1 BIND_RS02095 (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.2041456.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-132  427.7   0.4   2.4e-132  427.4   0.4    1.0  1  NCBI__GCF_000019845.1:WP_012383424.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019845.1:WP_012383424.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.4   0.4  2.4e-132  2.4e-132       1     398 []      26     420 ..      26     420 .. 0.98

  Alignments for each domain:
  == domain 1  score: 427.4 bits;  conditional E-value: 2.4e-132
                             TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 
                                           a+ +a  l   st+ kn al + a++L+++++ +l ana+d++ ak++    a+ldrL+L++++++ ia ++ 
  NCBI__GCF_000019845.1:WP_012383424.1  26 ARASAHALSLASTEAKNLALRVAAEQLRKRTQDLLLANARDLEGAKAQDANAAFLDRLTLDDKRIEAIARGLD 98 
                                           78889999***************************************************************** PP

                             TIGR00407  74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146
                                           +++ L+dPvG+++   e+ +GL++erv +PlGv+g+iye+rP v++d+ +Lclk+Gna+iL+Gg+e+ +s  +
  NCBI__GCF_000019845.1:WP_012383424.1  99 EIAALPDPVGRMLARYERPNGLVIERVATPLGVIGIIYESRPAVTADAGALCLKAGNAAILRGGSESFFSATI 171
                                           ************************************************************************* PP

                             TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellk.ldeyvdlliPrGgnelvklikeestiPvlehadGvCh 218
                                           + + + + l+ +glp  av l+ + dr+ v e+lk ld  +d+++PrGg++lv  ++ e+++Pv+ h +Gv h
  NCBI__GCF_000019845.1:WP_012383424.1 172 IHACLTEGLRAAGLPEAAVSLVPTRDRAAVGEMLKgLDGTIDVIVPRGGKSLVARVQAEARVPVFAHLEGVNH 244
                                           **********************************769************************************ PP

                             TIGR00407 219 iyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlklleleka 291
                                           i++ + adl+ka  +i +ak +rP +C a e LLv++a  + +l  L++ l ++g  +r+da+++ + +    
  NCBI__GCF_000019845.1:WP_012383424.1 245 IFVHRAADLEKAAIIIRNAKLRRPGVCGAAEILLVDEACMATHLAPLTRMLLDAGCAIRGDAATQTIDPRV-- 315
                                           ****************************************************************9998876.. PP

                             TIGR00407 292 teaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrf 364
                                             +++++ d+++e+++ +++v++++ l++ai+hi+++g++h+d+i+ted+++a++f+ evdsa v +nast+f
  NCBI__GCF_000019845.1:WP_012383424.1 316 --TAAMESDWRTEYSDAIIAVRVIDGLNKAIAHIETHGSHHTDCIITEDQEAADRFLAEVDSAIVMHNASTQF 386
                                           ..345678***************************************************************** PP

                             TIGR00407 365 adGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                           adG++fGfGae+gi+t +lharGPvGLe L+s+k
  NCBI__GCF_000019845.1:WP_012383424.1 387 ADGGEFGFGAEIGIATGRLHARGPVGLEQLTSFK 420
                                           ********************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (431 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: 16.59
//
[ok]

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

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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