Alignments for a candidate for proA in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for proA in Thermithiobacillus tepidarius DSM 3134

Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_028989441.1 G579_RS0105865 glutamate-5-semialdehyde dehydrogenase

Query= BRENDA::A7Y114
         (420 letters)



>NCBI__GCF_000423825.1:WP_028989441.1
          Length = 422

 Score =  367 bits (941), Expect = e-106
 Identities = 191/417 (45%), Positives = 270/417 (64%)

Query: 4   TKDNVNVEAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGRE 63
           T     V   A  A+ A++ L     + KN+AL  +A+ + RD E I  AN KDLRN   
Sbjct: 5   TPVETQVRGLAERARAAARVLQQADTRAKNEALLGMAEFIVRDSEEIQKANRKDLRNAEA 64

Query: 64  QGFTEAFMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVI 123
            G   A +DRL+LS+ R++  A+GLR++A L DP G+        +G+QV K+ +P+GVI
Sbjct: 65  AGLDAASLDRLTLSEPRLQAMAEGLREIAALPDPVGEIADLKFRPSGIQVGKMRMPIGVI 124

Query: 124 GMIYEARPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQF 183
           GMIYE+RPNVT DA GL LKSGNA++L+GGS A +SNQAI E +  AL   ++P +++Q 
Sbjct: 125 GMIYESRPNVTADAAGLCLKSGNAVILRGGSEAFHSNQAIAERLRAALGRARLPLDAIQV 184

Query: 184 IASTDRAATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADV 243
           + + DRAA   +  M+  +D++IPRGG  LI+ +   ATVPV++   GNCH+Y+D+ A++
Sbjct: 185 LDTPDRAAVGAMIRMRGLIDIIIPRGGKSLIERISAEATVPVIKHLHGNCHVYVDEFANL 244

Query: 244 EKAISILVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIP 303
           +KA+ I+VNAK  R   CN AE+L+VH+         + +AL+++ I + G    L ++P
Sbjct: 245 DKAVRIVVNAKVQRLGTCNTAESLLVHQAVAGDMLPPIAAALREKGIELRGCPETLKLLP 304

Query: 304 DAVPAGEDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIV 363
           D   A E+D+  EYL   I+VK VD L  A+ HI  YG+ HSEAIVTE+   A +FL  V
Sbjct: 305 DLAVATEEDYYTEYLGPIISVKVVDSLDAAMDHIAQYGSGHSEAIVTEDYSHARRFLREV 364

Query: 364 DAAAIYHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420
           D++++  NASTRF DG   G GAEIGIST KLH RGP+GL  LTT K+++ G G +R
Sbjct: 365 DSSSVMVNASTRFADGFEYGLGAEIGISTDKLHVRGPVGLEGLTTQKWIVLGDGHVR 421


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: 435
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: 420
Length of database: 422
Length adjustment: 32
Effective length of query: 388
Effective length of database: 390
Effective search space:   151320
Effective search space used:   151320
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 WP_028989441.1 G579_RS0105865 (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.151316.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-146  473.5   0.1   2.9e-146  473.3   0.1    1.0  1  NCBI__GCF_000423825.1:WP_028989441.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000423825.1:WP_028989441.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.3   0.1  2.9e-146  2.9e-146       1     398 []      18     411 ..      18     411 .. 0.99

  Alignments for each domain:
  == domain 1  score: 473.3 bits;  conditional E-value: 2.9e-146
                             TIGR00407   1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 
                                           a+ aa  l+q  t+ kneal  +a+ + +++e+i +an+kd+ +a++ Gl  a ldrL+L+e +l+ +a++++
  NCBI__GCF_000423825.1:WP_028989441.1  18 ARAAARVLQQADTRAKNEALLGMAEFIVRDSEEIQKANRKDLRNAEAAGLDAASLDRLTLSEPRLQAMAEGLR 90 
                                           899********************************************************************** PP

                             TIGR00407  74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146
                                           +++ L+dPvG++ + + + +G+++ ++r+P+Gv+g+iye+rP+v++d+a Lclk+GnaviL+Gg+ea +sn+a
  NCBI__GCF_000423825.1:WP_028989441.1  91 EIAALPDPVGEIADLKFRPSGIQVGKMRMPIGVIGMIYESRPNVTADAAGLCLKSGNAVILRGGSEAFHSNQA 163
                                           ************************************************************************* PP

                             TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChi 219
                                           ++e ++ al ++ lp  a+q++++pdr+ v  ++++   +d++iPrGg++l++ i  e+t+Pv++h  G+Ch+
  NCBI__GCF_000423825.1:WP_028989441.1 164 IAERLRAALGRARLPLDAIQVLDTPDRAAVGAMIRMRGLIDIIIPRGGKSLIERISAEATVPVIKHLHGNCHV 236
                                           ************************************************************************* PP

                             TIGR00407 220 yldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekat 292
                                           y+de a+l ka +++v+ak qr  tCn+ e+LLv++a+a + l+ ++ +l ekg+elr+   +lkll+     
  NCBI__GCF_000423825.1:WP_028989441.1 237 YVDEFANLDKAVRIVVNAKVQRLGTCNTAESLLVHQAVAGDMLPPIAAALREKGIELRGCPETLKLLPDL--- 306
                                           ***********************************************************99999999876... PP

                             TIGR00407 293 eaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfa 365
                                            a +++ed+ +e+l +++svk+v++l++a++hi qyg+ hs+ai+ted + a++f++evds++v vnastrfa
  NCBI__GCF_000423825.1:WP_028989441.1 307 -AVATEEDYYTEYLGPIISVKVVDSLDAAMDHIAQYGSGHSEAIVTEDYSHARRFLREVDSSSVMVNASTRFA 378
                                           .456789****************************************************************** PP

                             TIGR00407 366 dGfrfGfGaevgistqklharGPvGLeaLvsyk 398
                                           dGf++G+Gae+gist+klh rGPvGLe+L++ k
  NCBI__GCF_000423825.1:WP_028989441.1 379 DGFEYGLGAEIGISTDKLHVRGPVGLEGLTTQK 411
                                           ******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (422 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: 14.19
//
[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:

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 2024 update 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 original 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