Alignments for a candidate for asd in Thiothrix lacustris DSM 21227

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Thiothrix lacustris DSM 21227

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_028488727.1 Q394_RS0107450 aspartate-semialdehyde dehydrogenase

Query= BRENDA::P44801
         (371 letters)



>NCBI__GCF_000621325.1:WP_028488727.1
          Length = 372

 Score =  508 bits (1308), Expect = e-148
 Identities = 259/372 (69%), Positives = 298/372 (80%), Gaps = 4/372 (1%)

Query: 1   MKNVGFIGWRGMVGSVLMDRMSQENDFENLNPVFFTTSQAGQKAPVFGGKDAGDLKSAFD 60
           M  VGF+GWRGMVGSVLM+RM  ENDF+   PVFFTTSQ+G+  P  G   A  L+ A +
Sbjct: 1   MLKVGFVGWRGMVGSVLMERMRAENDFQGFEPVFFTTSQSGKPGPDVG-MGAQPLEDAMN 59

Query: 61  IEELKKLDIIVTCQGGDYTNEVYPKLKATGWDGYWVDAASALRMKDDAIIVLDPVNQHVI 120
           +++L ++DII++CQGGDYT  VY  L+A  W+GYW+DAAS LRM DDAIIVLDPVN+ VI
Sbjct: 60  LDKLAEMDIILSCQGGDYTTAVYENLRAN-WNGYWIDAASTLRMADDAIIVLDPVNRAVI 118

Query: 121 SEGLKKGIKTFVGGNCTVSLMLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQM 180
             GLK+GIK ++GGNCTVSLMLMA+GGLFEK LVEWIS  TYQAASGAGAKNMRELL+QM
Sbjct: 119 DAGLKRGIKNYIGGNCTVSLMLMALGGLFEKGLVEWISSMTYQAASGAGAKNMRELLTQM 178

Query: 181 GLLEQAVSSELKDPASSILDIERKVTAKMRADNFPTDNFGAALGGSLIPWIDKLLPETGQ 240
           G L   V   L DPA++ILDI+ KVTAK+      T NFGA L GSLIPWIDKL  E GQ
Sbjct: 179 GELNGEVGDLLADPAAAILDIDTKVTAKLNDGTLSTANFGAPLAGSLIPWIDKLW-ENGQ 237

Query: 241 TKEEWKGYAETNKILG-LSDNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIA 299
           TKEEWKG AETNKILG  + N IPVDG CVRIGA+RCHSQ FTIKLK+DLPL +IE IIA
Sbjct: 238 TKEEWKGIAETNKILGKTAANIIPVDGQCVRIGAMRCHSQGFTIKLKQDLPLADIEAIIA 297

Query: 300 SHNEWVKVIPNDKEITLRELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAA 359
           SHNEWVKVIPNDK  TL  LTP + +GTL+VPVGR+RK+ +GPEYL AFTVGDQLLWGAA
Sbjct: 298 SHNEWVKVIPNDKASTLNGLTPVQASGTLTVPVGRIRKMNLGPEYLTAFTVGDQLLWGAA 357

Query: 360 EPVRRILKQLVA 371
           EPVRR+LK  +A
Sbjct: 358 EPVRRMLKIALA 369


Lambda     K      H
   0.317    0.136    0.402 

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: 487
Number of extensions: 13
Number of successful extensions: 5
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: 371
Length of database: 372
Length adjustment: 30
Effective length of query: 341
Effective length of database: 342
Effective search space:   116622
Effective search space used:   116622
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_028488727.1 Q394_RS0107450 (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.3085.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-181  587.6   0.3   5.3e-181  587.3   0.3    1.0  1  lcl|NCBI__GCF_000621325.1:WP_028488727.1  Q394_RS0107450 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000621325.1:WP_028488727.1  Q394_RS0107450 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  587.3   0.3  5.3e-181  5.3e-181       2     364 ..       3     366 ..       2     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 587.3 bits;  conditional E-value: 5.3e-181
                                 TIGR01745   2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 
                                               kvg+vgwrgmvgsvl++rm+ e+df+  +pvff+tsq g+ +p ++  +++leda+++d l e+dii++
  lcl|NCBI__GCF_000621325.1:WP_028488727.1   3 KVGFVGWRGMVGSVLMERMRAENDFQGFEPVFFTTSQSGKPGPDVGMGAQPLEDAMNLDKLAEMDIILS 71 
                                               79******************************************************************* PP

                                 TIGR01745  71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsll 139
                                               cqggdyt+ +y +lr++ w+gywidaas+lrm dda+i+ldpvn  vi+ ++++gi++++ggnctvsl+
  lcl|NCBI__GCF_000621325.1:WP_028488727.1  72 CQGGDYTTAVYENLRAN-WNGYWIDAASTLRMADDAIIVLDPVNRAVIDAGLKRGIKNYIGGNCTVSLM 139
                                               ***************76.*************************************************** PP

                                 TIGR01745 140 lmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsr 208
                                               lm+lgglf+++lvew+s++tyqaasg+ga+ mrell+qmg l +ev + la p+ ail+i+ kvt    
  lcl|NCBI__GCF_000621325.1:WP_028488727.1 140 LMALGGLFEKGLVEWISSMTYQAASGAGAKNMRELLTQMGELNGEVGDLLADPAAAILDIDTKVTAKLN 208
                                               ********************************************************************* PP

                                 TIGR01745 209 seelpvenfsvplagslipwidkqldngqsreewkgqaetnkilg..tkdtilvdglcvrigalrchsq 275
                                                + l + nf++plagslipwidk  +ngq++eewkg aetnkilg  ++++i+vdg cvriga+rchsq
  lcl|NCBI__GCF_000621325.1:WP_028488727.1 209 DGTLSTANFGAPLAGSLIPWIDKLWENGQTKEEWKGIAETNKILGktAANIIPVDGQCVRIGAMRCHSQ 277
                                               ********************************************8434689****************** PP

                                 TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344
                                               ++tiklk+d++l +ie ii++hn+wvkv+pn++  tl+ ltp   +gtl++pvgr+rk+n+g+eyl+af
  lcl|NCBI__GCF_000621325.1:WP_028488727.1 278 GFTIKLKQDLPLADIEAIIASHNEWVKVIPNDKASTLNGLTPVQASGTLTVPVGRIRKMNLGPEYLTAF 346
                                               ********************************************************************* PP

                                 TIGR01745 345 tvgdqllwgaaeplrrmlri 364
                                               tvgdqllwgaaep+rrml+i
  lcl|NCBI__GCF_000621325.1:WP_028488727.1 347 TVGDQLLWGAAEPVRRMLKI 366
                                               ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (372 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.15
//
[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