Alignments for a candidate for asd in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Geobacter metallireducens GS-15

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_004514733.1 GMET_RS03015 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000012925.1:WP_004514733.1
          Length = 366

 Score =  514 bits (1323), Expect = e-150
 Identities = 258/369 (69%), Positives = 300/369 (81%), Gaps = 5/369 (1%)

Query: 3   RVGLIGWRGMVGSVLMQRMLEERDFDL-IEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61
           +VG++GWRGMVGSVL+QRM+EE DF+  IEPVFF+TS  G   P    +   LK A  I+
Sbjct: 2   KVGIVGWRGMVGSVLLQRMVEEGDFNTGIEPVFFSTSQAGQPAP---MNAGTLKSADDIE 58

Query: 62  ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121
           ELK LD+I+TCQGGDYT  V P+LR+ GWQGYWIDAAS+LRME +AVI+LDPVNR VID 
Sbjct: 59  ELKKLDIIVTCQGGDYTKAVHPELRKQGWQGYWIDAASTLRMEPNAVIILDPVNRNVIDA 118

Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181
           AL  G +++IGGNCTVSLMLMALGGLF AGLVEW+++MTYQAASGAGA NMRELL QMG 
Sbjct: 119 ALAKGQKDFIGGNCTVSLMLMALGGLFRAGLVEWLTSMTYQAASGAGAPNMRELLSQMGT 178

Query: 182 AHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSRE 241
            H SVAD L NP+SAILDIDR V  TLR +A PT+ FG PL GS++PWID+E+ +GQSRE
Sbjct: 179 LHGSVADLLKNPSSAILDIDRDVTATLRGDALPTKEFGFPLAGSVLPWIDREVEDGQSRE 238

Query: 242 EWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNP 301
           EWK  AETNKIL     PIPVDGICVRVGAMRCHSQALTIKLNKDVPL DIE LI   N 
Sbjct: 239 EWKGFAETNKILGT-TTPIPVDGICVRVGAMRCHSQALTIKLNKDVPLGDIEELIKNDNQ 297

Query: 302 WVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLR 361
           WVK VPN +  ++ +LTPAAV+G L+VP+GR+RK+ MG QY+ AFT GDQLLWGAAEPLR
Sbjct: 298 WVKFVPNTKADTLADLTPAAVSGLLTVPIGRVRKMKMGPQYMQAFTCGDQLLWGAAEPLR 357

Query: 362 RMLRILLER 370
           RMLRIL+E+
Sbjct: 358 RMLRILVEK 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: 516
Number of extensions: 14
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_004514733.1 GMET_RS03015 (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.8514.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-187  607.7   0.0   3.7e-187  607.6   0.0    1.0  1  lcl|NCBI__GCF_000012925.1:WP_004514733.1  GMET_RS03015 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_004514733.1  GMET_RS03015 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.6   0.0  3.7e-187  3.7e-187       1     366 []       1     364 [.       1     364 [. 0.99

  Alignments for each domain:
  == domain 1  score: 607.6 bits;  conditional E-value: 3.7e-187
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfda.ikpvffstsqlgqkapslakisailedaydidalkeldii 68 
                                               +kvg+vgwrgmvgsvll+rm+ee df++ i+pvffstsq+gq ap+ a   ++l+ a di+ lk+ldii
  lcl|NCBI__GCF_000012925.1:WP_004514733.1   1 MKVGIVGWRGMVGSVLLQRMVEEGDFNTgIEPVFFSTSQAGQPAPMNA---GTLKSADDIEELKKLDII 66 
                                               69************************866****************866...5799************** PP

                                 TIGR01745  69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137
                                               +tcqggdytk ++p+lrk+gw+gywidaas+lrm+ +aviildpvn +vi+ a++kg ++f+ggnctvs
  lcl|NCBI__GCF_000012925.1:WP_004514733.1  67 VTCQGGDYTKAVHPELRKQGWQGYWIDAASTLRMEPNAVIILDPVNRNVIDAALAKGQKDFIGGNCTVS 135
                                               ********************************************************************* PP

                                 TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206
                                               l+lm+lgglfr +lvew++++tyqaasg+ga  mrell+qmg+l+++v++ l +pssail+i+r vt +
  lcl|NCBI__GCF_000012925.1:WP_004514733.1 136 LMLMALGGLFRAGLVEWLTSMTYQAASGAGAPNMRELLSQMGTLHGSVADLLKNPSSAILDIDRDVTAT 204
                                               ********************************************************************* PP

                                 TIGR01745 207 srseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsq 275
                                                r + lp+++f+ plags++pwid+++++gqsreewkg aetnkilgt++ i+vdg+cvr+ga+rchsq
  lcl|NCBI__GCF_000012925.1:WP_004514733.1 205 LRGDALPTKEFGFPLAGSVLPWIDREVEDGQSREEWKGFAETNKILGTTTPIPVDGICVRVGAMRCHSQ 273
                                               ********************************************************************* PP

                                 TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344
                                               altikl+kdv+l +iee+i+++n+wvk+vpn + +tl +ltpaav+g l++p+gr+rk++mg++y+ af
  lcl|NCBI__GCF_000012925.1:WP_004514733.1 274 ALTIKLNKDVPLGDIEELIKNDNQWVKFVPNTKADTLADLTPAAVSGLLTVPIGRVRKMKMGPQYMQAF 342
                                               ********************************************************************* PP

                                 TIGR01745 345 tvgdqllwgaaeplrrmlrill 366
                                               t gdqllwgaaeplrrmlril+
  lcl|NCBI__GCF_000012925.1:WP_004514733.1 343 TCGDQLLWGAAEPLRRMLRILV 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.58
//
[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