Alignments for a candidate for asd in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Rhodospirillum rubrum ATCC 11170

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_011388951.1 RRU_RS06260 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>NCBI__GCF_000013085.1:WP_011388951.1
          Length = 345

 Score =  331 bits (848), Expect = 2e-95
 Identities = 182/337 (54%), Positives = 235/337 (69%), Gaps = 6/337 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFN-GKTVRVQNVEEFD 63
           + VA+ GATG VG  ML  L ER+FPV E+  LAS RS G+   F   + ++V+++E FD
Sbjct: 8   YRVAVIGATGNVGREMLSTLAERKFPVSEVIALASSRSAGREVSFGEDQVLKVRDLETFD 67

Query: 64  WSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRN 123
           ++ V IAL S G ++SA  +P AA AG VVIDNTSHFR D D+PLVVPEVNP+AIA +  
Sbjct: 68  FTGVDIALSSPGAKVSATHSPRAAAAGCVVIDNTSHFRMDRDVPLVVPEVNPQAIAGYTK 127

Query: 124 RNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKL-LNG 182
           R+IIANPNCSTIQM+VALKP++DA GI+R+ V+TYQSVSGAGK G+DEL  QT  + +N 
Sbjct: 128 RHIIANPNCSTIQMVVALKPLHDAFGIKRVVVSTYQSVSGAGKDGMDELFNQTKGIYVNQ 187

Query: 183 YPAE-TNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPV 241
            PA+    F++QIAFN IP ID FMD+G TKEE KM  ET KI  DP+I V+  C RVPV
Sbjct: 188 PPADFQQKFTKQIAFNVIPHIDIFMDDGATKEEWKMAAETCKIL-DPAIKVHANCARVPV 246

Query: 242 FYGHAEAVHVETRAPIDAEQVMDMLEQTDGIEL--FRGADFPTQVRDAGGKDHVLVGRVR 299
           F GHAE V++ET  P+  E     L+  +G+ +   R  +      +  G+D V V R+R
Sbjct: 247 FVGHAEYVNIETEKPMSEEAARRALKGGEGVIIVDHRANEGYVTPAECSGEDAVYVSRIR 306

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336
            D +  +G++ W V+DN+RKGAA NAVQIAE+L RDY
Sbjct: 307 KDTTVENGLSFWCVSDNLRKGAALNAVQIAEVLARDY 343


Lambda     K      H
   0.319    0.135    0.395 

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: 338
Number of extensions: 20
Number of successful extensions: 5
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: 337
Length of database: 345
Length adjustment: 29
Effective length of query: 308
Effective length of database: 316
Effective search space:    97328
Effective search space used:    97328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_011388951.1 RRU_RS06260 (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.3720180.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-140  453.9   0.5   1.9e-140  453.8   0.5    1.0  1  NCBI__GCF_000013085.1:WP_011388951.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013085.1:WP_011388951.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.8   0.5  1.9e-140  1.9e-140       1     338 [.       9     341 ..       9     342 .. 0.97

  Alignments for each domain:
  == domain 1  score: 453.8 bits;  conditional E-value: 1.9e-140
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkg.keleveeaekesfegidialfsaGgs 72 
                                           +va++GatG+vG+e+l +L+er+fp++++++las+rsaG++v f + + l+v+++e+++f g+dial s G+ 
  NCBI__GCF_000013085.1:WP_011388951.1   9 RVAVIGATGNVGREMLSTLAERKFPVSEVIALASSRSAGREVSFGEdQVLKVRDLETFDFTGVDIALSSPGAK 81 
                                           69******************************************762779*********************** PP

                             TIGR01296  73 vskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeakl 145
                                           vs +  p+aa+ag++viDnts fr+d+dvPLvvpevn + ++   k+ iianPnCstiq+vv+Lkpl+d++++
  NCBI__GCF_000013085.1:WP_011388951.1  82 VSATHSPRAAAAGCVVIDNTSHFRMDRDVPLVVPEVNPQAIAGYTKRHIIANPNCSTIQMVVALKPLHDAFGI 154
                                           ************************************************************************* PP

                             TIGR01296 146 krvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelk 218
                                           krvvvstYq+vsGaGk+g++eL nqtk +++ +           +kf+kqiafn+ip+id +++dG tkee k
  NCBI__GCF_000013085.1:WP_011388951.1 155 KRVVVSTYQSVSGAGKDGMDELFNQTKGIYVNQPPA-----DFQQKFTKQIAFNVIPHIDIFMDDGATKEEWK 222
                                           *****************************9865433.....3579**************************** PP

                             TIGR01296 219 llfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPlea 291
                                           ++ et kil+ + +kv a c rvPvf+gh+e v+ie+ek++s e ++  Lk+ +gv+++d+  ++ y+tP+e 
  NCBI__GCF_000013085.1:WP_011388951.1 223 MAAETCKILD-PAIKVHANCARVPVFVGHAEYVNIETEKPMSEEAARRALKGGEGVIIVDHRANEGYVTPAEC 294
                                           **********.************************************************************** PP

                             TIGR01296 292 vgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                           +g+d+v+v+rirkD + e+gl+ ++v+DnlrkGaalnavqiae l +
  NCBI__GCF_000013085.1:WP_011388951.1 295 SGEDAVYVSRIRKDTTVENGLSFWCVSDNLRKGAALNAVQIAEVLAR 341
                                           *******************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (345 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.16
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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