Alignments for a candidate for asd in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Geobacter lovleyi SZ

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_012468432.1 GLOV_RS01640 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000020385.1:WP_012468432.1
          Length = 366

 Score =  496 bits (1276), Expect = e-145
 Identities = 251/369 (68%), Positives = 295/369 (79%), Gaps = 5/369 (1%)

Query: 3   RVGLIGWRGMVGSVLMQRMLEERDFDL-IEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61
           +VG++GWRGMVGSVLMQRM EE DF L  EPVFFTTS  G   P        LK A  I+
Sbjct: 2   KVGIVGWRGMVGSVLMQRMQEENDFALGFEPVFFTTSQAGQPAP---MGAGTLKKADDIE 58

Query: 62  ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121
           ELK LDVI+TCQGGDYT  V P+LR+ GW GYWIDAAS+LRMED+AVI+LDPVNR VID+
Sbjct: 59  ELKKLDVIITCQGGDYTKAVHPELRKQGWNGYWIDAASTLRMEDNAVIILDPVNRNVIDK 118

Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181
           AL  G +++IGGNCTVSLMLM LGGLF AGLVEW+S+MTYQAASGAGA NMRELL QMG 
Sbjct: 119 ALANGQKDFIGGNCTVSLMLMGLGGLFRAGLVEWISSMTYQAASGAGAPNMRELLSQMGV 178

Query: 182 AHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSRE 241
               VA +L +  SAIL+ID+KV +TLR  + PT+ FG PL G+++PWID+E+ +GQSRE
Sbjct: 179 LQGVVAKELKDAGSAILEIDKKVTQTLRDGSMPTKEFGFPLAGNVLPWIDREVEDGQSRE 238

Query: 242 EWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNP 301
           E K   ETNKIL     PIPVDGICVRVGAMRCHSQA+TIKLNKD+PL +IE LI+  N 
Sbjct: 239 ELKGFQETNKILGT-SAPIPVDGICVRVGAMRCHSQAITIKLNKDLPLAEIEQLIANDNQ 297

Query: 302 WVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLR 361
           WVKL+PN++  ++  LTPAAV+GTL+VPVGR+RK+ MG QY+ AFT GDQLLWGAAEPLR
Sbjct: 298 WVKLIPNNKADTLAGLTPAAVSGTLTVPVGRVRKMKMGPQYVQAFTCGDQLLWGAAEPLR 357

Query: 362 RMLRILLER 370
           RMLRILLE+
Sbjct: 358 RMLRILLEK 366


Lambda     K      H
   0.319    0.136    0.409 

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: 512
Number of extensions: 17
Number of successful extensions: 4
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: 370
Length of database: 366
Length adjustment: 30
Effective length of query: 340
Effective length of database: 336
Effective search space:   114240
Effective search space used:   114240
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_012468432.1 GLOV_RS01640 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (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/TIGR01745.hmm
# target sequence database:        /tmp/gapView.1986.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01745  [M=366]
Accession:   TIGR01745
Description: asd_gamma: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-185  601.6   0.1   2.8e-185  601.4   0.1    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012468432.1  GLOV_RS01640 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012468432.1  GLOV_RS01640 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.4   0.1  2.8e-185  2.8e-185       1     366 []       1     364 [.       1     364 [. 0.99

  Alignments for each domain:
  == domain 1  score: 601.4 bits;  conditional E-value: 2.8e-185
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfda.ikpvffstsqlgqkapslakisailedaydidalkeldii 68 
                                               +kvg+vgwrgmvgsvl++rmqee+df +  +pvff+tsq+gq ap+ a   ++l++a di+ lk+ld+i
  lcl|NCBI__GCF_000020385.1:WP_012468432.1   1 MKVGIVGWRGMVGSVLMQRMQEENDFALgFEPVFFTTSQAGQPAPMGA---GTLKKADDIEELKKLDVI 66 
                                               69************************9758***************866...579*************** PP

                                 TIGR01745  69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137
                                               itcqggdytk ++p+lrk+gw+gywidaas+lrm+d+aviildpvn +vi+ a+++g ++f+ggnctvs
  lcl|NCBI__GCF_000020385.1:WP_012468432.1  67 ITCQGGDYTKAVHPELRKQGWNGYWIDAASTLRMEDNAVIILDPVNRNVIDKALANGQKDFIGGNCTVS 135
                                               ********************************************************************* PP

                                 TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206
                                               l+lm+lgglfr +lvew+s++tyqaasg+ga  mrell+qmgvl + v++el  + sailei++kvt++
  lcl|NCBI__GCF_000020385.1:WP_012468432.1 136 LMLMGLGGLFRAGLVEWISSMTYQAASGAGAPNMRELLSQMGVLQGVVAKELKDAGSAILEIDKKVTQT 204
                                               ********************************************************************* PP

                                 TIGR01745 207 srseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsq 275
                                                r + +p+++f+ plag+++pwid+++++gqsree kg  etnkilgt+  i+vdg+cvr+ga+rchsq
  lcl|NCBI__GCF_000020385.1:WP_012468432.1 205 LRDGSMPTKEFGFPLAGNVLPWIDREVEDGQSREELKGFQETNKILGTSAPIPVDGICVRVGAMRCHSQ 273
                                               ********************************************************************* PP

                                 TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344
                                               a+tikl+kd++l eie++i+++n+wvk++pn++ +tl  ltpaav+gtl++pvgr+rk++mg++y+ af
  lcl|NCBI__GCF_000020385.1:WP_012468432.1 274 AITIKLNKDLPLAEIEQLIANDNQWVKLIPNNKADTLAGLTPAAVSGTLTVPVGRVRKMKMGPQYVQAF 342
                                               ********************************************************************* PP

                                 TIGR01745 345 tvgdqllwgaaeplrrmlrill 366
                                               t gdqllwgaaeplrrmlrill
  lcl|NCBI__GCF_000020385.1:WP_012468432.1 343 TCGDQLLWGAAEPLRRMLRILL 364
                                               ********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (366 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: 8.17
//
[ok]

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