Alignments for a candidate for asd in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Desulfobacter vibrioformis DSM 8776

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_035239144.1 Q366_RS11925 aspartate-semialdehyde dehydrogenase

Query= BRENDA::Q9KQG2
         (370 letters)



>NCBI__GCF_000745975.1:WP_035239144.1
          Length = 368

 Score =  504 bits (1297), Expect = e-147
 Identities = 239/366 (65%), Positives = 295/366 (80%)

Query: 2   RVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIES 61
           +VG+VGWRGMVGSVLM+RM  + DF    PVFF+TSQ G PAP+ G+ A  L DAFDI++
Sbjct: 3   KVGIVGWRGMVGSVLMERMSSQNDFQKFTPVFFTTSQAGQPAPDVGRGASNLIDAFDIDT 62

Query: 62  LKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHG 121
           L ++D ++TCQGGSYTE V P L + GW G+WIDAASTLRMD ++II LDPVNL  I   
Sbjct: 63  LMEMDILVTCQGGSYTEAVRPKLAERGWNGFWIDAASTLRMDGQSIIVLDPVNLPVIEEA 122

Query: 122 IHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVI 181
           I  G K F+GGNCTVSLMLMALGGL+E   VEWM++MTYQAASGAGA+NMREL++QM  I
Sbjct: 123 ISRGIKNFIGGNCTVSLMLMALGGLFENDWVEWMTSMTYQAASGAGAKNMRELVAQMRTI 182

Query: 182 NDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEE 241
            D  +  L NPA++ILD+D+KV +T+RS ++P +N+GVPL  SLIPWID   DNGQ++EE
Sbjct: 183 GDQAAPILDNPAAAILDLDQKVTDTLRSDAYPVENWGVPLGASLIPWIDRAMDNGQTREE 242

Query: 242 WKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDW 301
           WK  VE NKILG  D+P+PIDG C+RIG+MRCHSQA TIKLK+++PLDEI   +A +NDW
Sbjct: 243 WKGFVETNKILGRSDNPIPIDGQCIRIGSMRCHSQAFTIKLKKDVPLDEINAALAANNDW 302

Query: 302 VKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRR 361
           V+VIPN ++ + RELTPA VTGTL+VPVGR+RKM +G++FL AF+VGDQLLWGAAEPLRR
Sbjct: 303 VRVIPNNKEDSIRELTPAAVTGTLNVPVGRIRKMNIGENFLTAFSVGDQLLWGAAEPLRR 362

Query: 362 TLRIIL 367
            L IIL
Sbjct: 363 ILNIIL 368


Lambda     K      H
   0.319    0.135    0.405 

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: 484
Number of extensions: 14
Number of successful extensions: 1
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: 368
Length adjustment: 30
Effective length of query: 340
Effective length of database: 338
Effective search space:   114920
Effective search space used:   114920
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_035239144.1 Q366_RS11925 (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.31168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-179  583.1   0.3   1.1e-179  583.0   0.3    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035239144.1  Q366_RS11925 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035239144.1  Q366_RS11925 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.0   0.3  1.1e-179  1.1e-179       1     365 [.       2     367 ..       2     368 .] 0.99

  Alignments for each domain:
  == domain 1  score: 583.0 bits;  conditional E-value: 1.1e-179
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 
                                               kkvg+vgwrgmvgsvl++rm  ++df++  pvff+tsq+gq ap +++ ++ l da+did+l e+di++
  lcl|NCBI__GCF_000745975.1:WP_035239144.1   2 KKVGIVGWRGMVGSVLMERMSSQNDFQKFTPVFFTTSQAGQPAPDVGRGASNLIDAFDIDTLMEMDILV 70 
                                               69******************************************************************* PP

                                 TIGR01745  70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsl 138
                                               tcqgg+yt+ + pkl + gw+g+widaas+lrm+ +++i+ldpvnl vi++a+++gi++f+ggnctvsl
  lcl|NCBI__GCF_000745975.1:WP_035239144.1  71 TCQGGSYTEAVRPKLAERGWNGFWIDAASTLRMDGQSIIVLDPVNLPVIEEAISRGIKNFIGGNCTVSL 139
                                               ********************************************************************* PP

                                 TIGR01745 139 llmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkls 207
                                               +lm+lgglf+++ vew++++tyqaasg+ga+ mrel+ qm ++  + +  l +p+ ail++++kvt + 
  lcl|NCBI__GCF_000745975.1:WP_035239144.1 140 MLMALGGLFENDWVEWMTSMTYQAASGAGAKNMRELVAQMRTIGDQAAPILDNPAAAILDLDQKVTDTL 208
                                               ********************************************************************* PP

                                 TIGR01745 208 rseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkd.tilvdglcvrigalrchsq 275
                                               rs+  pven++vpl +slipwid+ +dngq+reewkg  etnkilg +d  i++dg c+rig++rchsq
  lcl|NCBI__GCF_000745975.1:WP_035239144.1 209 RSDAYPVENWGVPLGASLIPWIDRAMDNGQTREEWKGFVETNKILGRSDnPIPIDGQCIRIGSMRCHSQ 277
                                               **********************************************87626****************** PP

                                 TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344
                                               a+tiklkkdv+l+ei+  ++a+n+wv+v+pn++e+++reltpaavtgtl++pvgr+rk+n+g+++l+af
  lcl|NCBI__GCF_000745975.1:WP_035239144.1 278 AFTIKLKKDVPLDEINAALAANNDWVRVIPNNKEDSIRELTPAAVTGTLNVPVGRIRKMNIGENFLTAF 346
                                               ********************************************************************* PP

                                 TIGR01745 345 tvgdqllwgaaeplrrmlril 365
                                                vgdqllwgaaeplrr+l+i+
  lcl|NCBI__GCF_000745975.1:WP_035239144.1 347 SVGDQLLWGAAEPLRRILNII 367
                                               *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (368 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: 9.15
//
[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