Alignments for a candidate for asd in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Teredinibacter turnerae T7901

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_015818862.1 TERTU_RS11080 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>NCBI__GCF_000023025.1:WP_015818862.1
          Length = 368

 Score =  536 bits (1381), Expect = e-157
 Identities = 268/367 (73%), Positives = 299/367 (81%), Gaps = 1/367 (0%)

Query: 3   RVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDE 62
           +VG +GWRGMVGSVLM RMLEE DF  IEPVFFTTSNVGG  P+VG +   LKDAYSIDE
Sbjct: 2   KVGFVGWRGMVGSVLMGRMLEENDFAGIEPVFFTTSNVGGTAPDVGVEAPALKDAYSIDE 61

Query: 63  LKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQA 122
           LK LD I++CQGGDYT EVF KLR AGWQGYWIDAASSLRM+ DA+IVLDPVN  VI   
Sbjct: 62  LKQLDAIISCQGGDYTGEVFGKLRAAGWQGYWIDAASSLRMDKDALIVLDPVNDNVIRDG 121

Query: 123 LDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAA 182
           L  G +NYIGGNCTVSLMLM LGGLF   LVEW SAMTYQAASGAGAQNMREL+ QMG  
Sbjct: 122 LAKGIKNYIGGNCTVSLMLMGLGGLFRENLVEWTSAMTYQAASGAGAQNMRELITQMGQI 181

Query: 183 HASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREE 242
             SVA +LA+PASAILDIDRKV E +RS+    + FGAPL GSL+P+IDK+L N QS+EE
Sbjct: 182 RDSVATELADPASAILDIDRKVVEAMRSD-LTVDRFGAPLAGSLLPYIDKQLENFQSKEE 240

Query: 243 WKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNPW 302
           WK   ETNKIL    +PIP+DGICVR+GAMRCHSQALTIKL KDVPL D+E LI+  N W
Sbjct: 241 WKGGVETNKILGTSDSPIPIDGICVRIGAMRCHSQALTIKLKKDVPLADVESLIANANSW 300

Query: 303 VKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLRR 362
           VK++PN R+ ++ ELTP  VTGTLSVPVGRLRK+ MG +YL AFTVGDQLLWGAAEPLRR
Sbjct: 301 VKVIPNDRDATLEELTPTKVTGTLSVPVGRLRKMAMGPEYLSAFTVGDQLLWGAAEPLRR 360

Query: 363 MLRILLE 369
           MLRIL E
Sbjct: 361 MLRILRE 367


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: 483
Number of extensions: 8
Number of successful extensions: 2
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_015818862.1 TERTU_RS11080 (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.21112.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-193  628.2   0.1   2.3e-193  628.0   0.1    1.0  1  lcl|NCBI__GCF_000023025.1:WP_015818862.1  TERTU_RS11080 aspartate-semialde


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015818862.1  TERTU_RS11080 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  628.0   0.1  2.3e-193  2.3e-193       1     365 [.       1     365 [.       1     366 [. 0.99

  Alignments for each domain:
  == domain 1  score: 628.0 bits;  conditional E-value: 2.3e-193
                                 TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 
                                               +kvg+vgwrgmvgsvl+ rm ee+df  i+pvff+ts++g+ ap ++  + +l+day id lk+ld ii
  lcl|NCBI__GCF_000023025.1:WP_015818862.1   1 MKVGFVGWRGMVGSVLMGRMLEENDFAGIEPVFFTTSNVGGTAPDVGVEAPALKDAYSIDELKQLDAII 69 
                                               69*********************************************9999****************** PP

                                 TIGR01745  70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsl 138
                                               +cqggdyt e++ klr+agw+gywidaasslrm++da+i+ldpvn +vi+d+++kgi++++ggnctvsl
  lcl|NCBI__GCF_000023025.1:WP_015818862.1  70 SCQGGDYTGEVFGKLRAAGWQGYWIDAASSLRMDKDALIVLDPVNDNVIRDGLAKGIKNYIGGNCTVSL 138
                                               ********************************************************************* PP

                                 TIGR01745 139 llmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkls 207
                                               +lm+lgglfr++lvew s++tyqaasg+ga+ mrel++qmg +  +v++ela p+sail+i+rkv + +
  lcl|NCBI__GCF_000023025.1:WP_015818862.1 139 MLMGLGGLFRENLVEWTSAMTYQAASGAGAQNMRELITQMGQIRDSVATELADPASAILDIDRKVVEAM 207
                                               ********************************************************************* PP

                                 TIGR01745 208 rseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdt.ilvdglcvrigalrchsq 275
                                               r ++l v+ f++plagsl+p+idkql+n qs+eewkg  etnkilgt+d  i++dg+cvriga+rchsq
  lcl|NCBI__GCF_000023025.1:WP_015818862.1 208 R-SDLTVDRFGAPLAGSLLPYIDKQLENFQSKEEWKGGVETNKILGTSDSpIPIDGICVRIGAMRCHSQ 275
                                               *.79*******************************************9755****************** PP

                                 TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344
                                               altiklkkdv+l ++e++i++ n wvkv+pn+r+ tl+eltp+ vtgtl++pvgrlrk+ mg+eylsaf
  lcl|NCBI__GCF_000023025.1:WP_015818862.1 276 ALTIKLKKDVPLADVESLIANANSWVKVIPNDRDATLEELTPTKVTGTLSVPVGRLRKMAMGPEYLSAF 344
                                               ********************************************************************* PP

                                 TIGR01745 345 tvgdqllwgaaeplrrmlril 365
                                               tvgdqllwgaaeplrrmlril
  lcl|NCBI__GCF_000023025.1:WP_015818862.1 345 TVGDQLLWGAAEPLRRMLRIL 365
                                               *******************98 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: 8.79
//
[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