Alignments for a candidate for asd in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Trichormus variabilis ATCC 29413

Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_011320317.1 AVA_RS18285 aspartate-semialdehyde dehydrogenase

Query= metacyc::AT1G14810-MONOMER
         (375 letters)



>NCBI__GCF_000204075.1:WP_011320317.1
          Length = 347

 Score =  350 bits (897), Expect = e-101
 Identities = 173/335 (51%), Positives = 239/335 (71%), Gaps = 8/335 (2%)

Query: 41  LAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTVEELTADSFNG 100
           +A++G TGAVG E L +L  R+FP + +K+LAS+RS G+ + F G    VE ++  +   
Sbjct: 7   VAILGATGAVGTELLELLESRNFPVAELKLLASERSVGRSLPFKGENIIVEAVSDRALEN 66

Query: 101 VDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPEAMKGIKVGMG 160
           VDI L SAGGS SK +  +A EKG +V+DNSSAFRM   VPL++PEVNP+A    K    
Sbjct: 67  VDIVLASAGGSTSKAWASVAVEKGAVVIDNSSAFRMNPDVPLIVPEVNPQAAADHK---- 122

Query: 161 KGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEELVQQTREVLEG 220
              +IANPNC+TI+  +AV PLH    V+R+V +TYQ+ASGAGA AM E+  Q+  +L+G
Sbjct: 123 --GIIANPNCTTILMTLAVWPLHQVRPVQRIVAATYQSASGAGAKAMAEVKTQSSAILKG 180

Query: 221 KPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKVTATCIRVPVM 280
           + P   +     AFNLF HN+P+ D+GY EEE+K+V ETRKI+   E+++TATC+RVPV+
Sbjct: 181 EEPVAEVLPYPLAFNLFPHNSPLTDSGYCEEELKMVNETRKIFGTQEIRITATCVRVPVL 240

Query: 281 RAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNKDDVAVGRIRR 340
           RAH+E++NL+F  P   + AREIL  APGV +++D   N FP P++ S +D+V VGRIR+
Sbjct: 241 RAHSEAINLEFAEPFSPDEAREILSHAPGVKLLEDWGKNYFPMPIEASGRDEVLVGRIRQ 300

Query: 341 DVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375
           D+S     GL++++CGDQIRKGAALNAVQIAE+L+
Sbjct: 301 DISHP--CGLELWLCGDQIRKGAALNAVQIAELLV 333


Lambda     K      H
   0.318    0.133    0.380 

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: 321
Number of extensions: 9
Number of successful extensions: 3
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: 375
Length of database: 347
Length adjustment: 29
Effective length of query: 346
Effective length of database: 318
Effective search space:   110028
Effective search space used:   110028
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: 49 (23.5 bits)

Align candidate WP_011320317.1 AVA_RS18285 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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/TIGR01296.hmm
# target sequence database:        /tmp/gapView.19610.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: aspartate-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-128  412.7   0.0   6.9e-128  412.4   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011320317.1  AVA_RS18285 aspartate-semialdehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011320317.1  AVA_RS18285 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.4   0.0  6.9e-128  6.9e-128       1     338 [.       6     334 ..       6     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.4 bits;  conditional E-value: 6.9e-128
                                 TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 
                                               +vai+GatGavG ell++Le rnfp+ +l+llasers G+ + fkg+++ ve+++    e++di l sa
  lcl|NCBI__GCF_000204075.1:WP_011320317.1   6 RVAILGATGAVGTELLELLESRNFPVAELKLLASERSVGRSLPFKGENIIVEAVSDRALENVDIVLASA 74 
                                               69******************************************************************* PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                               Ggs+sk++a+ a+++g++viDn+safr+++dvPL+vpevn +  +++k  giianPnC+ti ++ ++ p
  lcl|NCBI__GCF_000204075.1:WP_011320317.1  75 GGSTSKAWASVAVEKGAVVIDNSSAFRMNPDVPLIVPEVNPQAAADHK--GIIANPNCTTILMTLAVWP 141
                                               ********************************************9998..******************* PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207
                                               l++   ++r+v +tYq+ sGaG+k+++e+k q  a+l+g+e         a+  ++++afn++p+   l
  lcl|NCBI__GCF_000204075.1:WP_011320317.1 142 LHQVRPVQRIVAATYQSASGAGAKAMAEVKTQSSAILKGEEPV-------AEVLPYPLAFNLFPHNSPL 203
                                               *************************************999866.......7999*************** PP

                                 TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276
                                               ++ Gy +eelk+++etrki+g+++++++atcvrvPv+++hse++++ef++++s++e++e+L +apgv++
  lcl|NCBI__GCF_000204075.1:WP_011320317.1 204 TDSGYCEEELKMVNETRKIFGTQEIRITATCVRVPVLRAHSEAINLEFAEPFSPDEAREILSHAPGVKL 272
                                               ********************************************************************* PP

                                 TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                               ++d  +n +p+P+ea+g+dev+vgrir+D+s+  gl+l++ +D++rkGaalnavqiaell++
  lcl|NCBI__GCF_000204075.1:WP_011320317.1 273 LEDWGKNYFPMPIEASGRDEVLVGRIRQDISHPCGLELWLCGDQIRKGAALNAVQIAELLVE 334
                                               ***********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (347 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: 7.77
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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 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 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