Alignments for a candidate for asd in Geobacter uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Geobacter uraniireducens Rf4

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_011937976.1 GURA_RS05295 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000016745.1:WP_011937976.1
          Length = 365

 Score =  524 bits (1349), Expect = e-153
 Identities = 262/368 (71%), Positives = 300/368 (81%), Gaps = 4/368 (1%)

Query: 3   RVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDE 62
           +VGLIGWRGMVGSVL+QRM EE DF  IEPVFF+TS  G   P    +   LKDA  I E
Sbjct: 2   KVGLIGWRGMVGSVLLQRMQEENDFAGIEPVFFSTSQAGQPAP---MNAGTLKDASDIAE 58

Query: 63  LKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQA 122
           LK LDVILTCQGGDYT  + P+LR+ GWQGYWIDAAS+LRME +AVI+LDPVNR VID A
Sbjct: 59  LKKLDVILTCQGGDYTKAIHPELRKTGWQGYWIDAASTLRMEPNAVIILDPVNRNVIDAA 118

Query: 123 LDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAA 182
           L  G +++IGGNCTVSLMLMALGGLF AGLVEW+++MTYQAASGAGA NMRELL QMG  
Sbjct: 119 LAKGQKDFIGGNCTVSLMLMALGGLFRAGLVEWITSMTYQAASGAGAPNMRELLSQMGVL 178

Query: 183 HASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREE 242
           H SVA+ L NP+SAILDIDR+V  TLRS+A PT+ FGAPL G+++PWID+E+ +GQSREE
Sbjct: 179 HGSVAELLKNPSSAILDIDRQVTATLRSDALPTKEFGAPLAGNVLPWIDREVEDGQSREE 238

Query: 243 WKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNPW 302
           WK  AETNKIL     PIPVDGICVRV AMRCHSQALTIKLNKDVP+ DIE LI   N W
Sbjct: 239 WKGYAETNKILGT-TTPIPVDGICVRVSAMRCHSQALTIKLNKDVPIADIENLIKNDNQW 297

Query: 303 VKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLRR 362
           VK VPN +  S+  LTPAAV+G+L+VP+GR+RK+ MG QYL AFT GDQLLWGAAEPLRR
Sbjct: 298 VKFVPNTKADSLANLTPAAVSGSLTVPIGRVRKMKMGPQYLSAFTCGDQLLWGAAEPLRR 357

Query: 363 MLRILLER 370
           MLR+LLE+
Sbjct: 358 MLRVLLEK 365


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: 492
Number of extensions: 12
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: 370
Length of database: 365
Length adjustment: 30
Effective length of query: 340
Effective length of database: 335
Effective search space:   113900
Effective search space used:   113900
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_011937976.1 GURA_RS05295 (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.18873.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-190  618.5   0.0     2e-190  618.3   0.0    1.0  1  lcl|NCBI__GCF_000016745.1:WP_011937976.1  GURA_RS05295 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016745.1:WP_011937976.1  GURA_RS05295 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.3   0.0    2e-190    2e-190       1     366 []       1     363 [.       1     363 [. 0.99

  Alignments for each domain:
  == domain 1  score: 618.3 bits;  conditional E-value: 2e-190
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 
                                               +kvgl+gwrgmvgsvll+rmqee+df  i+pvffstsq+gq ap+ a   ++l+da di  lk+ld+i+
  lcl|NCBI__GCF_000016745.1:WP_011937976.1   1 MKVGLIGWRGMVGSVLLQRMQEENDFAGIEPVFFSTSQAGQPAPMNA---GTLKDASDIAELKKLDVIL 66 
                                               69******************************************866...57***************** PP

                                 TIGR01745  70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsl 138
                                               tcqggdytk i+p+lrk+gw+gywidaas+lrm+ +aviildpvn +vi+ a++kg ++f+ggnctvsl
  lcl|NCBI__GCF_000016745.1:WP_011937976.1  67 TCQGGDYTKAIHPELRKTGWQGYWIDAASTLRMEPNAVIILDPVNRNVIDAALAKGQKDFIGGNCTVSL 135
                                               ********************************************************************* PP

                                 TIGR01745 139 llmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkls 207
                                               +lm+lgglfr +lvew++++tyqaasg+ga  mrell+qmgvl+++v+e l +pssail+i+r+vt + 
  lcl|NCBI__GCF_000016745.1:WP_011937976.1 136 MLMALGGLFRAGLVEWITSMTYQAASGAGAPNMRELLSQMGVLHGSVAELLKNPSSAILDIDRQVTATL 204
                                               ********************************************************************* PP

                                 TIGR01745 208 rseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsqa 276
                                               rs+ lp+++f++plag+++pwid+++++gqsreewkg aetnkilgt++ i+vdg+cvr+ a+rchsqa
  lcl|NCBI__GCF_000016745.1:WP_011937976.1 205 RSDALPTKEFGAPLAGNVLPWIDREVEDGQSREEWKGYAETNKILGTTTPIPVDGICVRVSAMRCHSQA 273
                                               ********************************************************************* PP

                                 TIGR01745 277 ltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaft 345
                                               ltikl+kdv++ +ie++i+++n+wvk+vpn + ++l +ltpaav+g+l++p+gr+rk++mg++ylsaft
  lcl|NCBI__GCF_000016745.1:WP_011937976.1 274 LTIKLNKDVPIADIENLIKNDNQWVKFVPNTKADSLANLTPAAVSGSLTVPIGRVRKMKMGPQYLSAFT 342
                                               ********************************************************************* PP

                                 TIGR01745 346 vgdqllwgaaeplrrmlrill 366
                                                gdqllwgaaeplrrmlr+ll
  lcl|NCBI__GCF_000016745.1:WP_011937976.1 343 CGDQLLWGAAEPLRRMLRVLL 363
                                               ******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (365 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: 7.68
//
[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