Alignments for a candidate for asd in Cupriavidus basilensis FW507-4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Cupriavidus basilensis FW507-4G11

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate RR42_RS14380 RR42_RS14380 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__Cup4G11:RR42_RS14380
          Length = 378

 Score =  511 bits (1316), Expect = e-149
 Identities = 254/375 (67%), Positives = 299/375 (79%), Gaps = 9/375 (2%)

Query: 4   VGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDEL 63
           VGL+GWRGMVGSVLMQRM EERDFD IEPVFF+TSN GGQ P + K+   LKDA  I+ L
Sbjct: 3   VGLVGWRGMVGSVLMQRMQEERDFDHIEPVFFSTSNAGGQAPAMAKNETKLKDANDIEAL 62

Query: 64  KTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQAL 123
           K  DV+LT QGGDYT+E+FP+LR AGW+GYWIDAASSLRM+DDA+IVLDPVN  VI  AL
Sbjct: 63  KKCDVVLTAQGGDYTNEIFPQLRAAGWKGYWIDAASSLRMKDDAIIVLDPVNLGVIKDAL 122

Query: 124 DAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAH 183
             G +N+IGGNCTVS M+M LGGLF   L++WM++MTYQAASG GAQ+MRELL Q G  +
Sbjct: 123 AKGVKNFIGGNCTVSCMMMGLGGLFQHDLIDWMTSMTYQAASGGGAQHMRELLTQFGTLN 182

Query: 184 ASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKELPNGQSREE 242
           ASV   L NPASAIL+IDR +  T     A  T+ FG PL G+LIPWIDK+L NG S+EE
Sbjct: 183 ASVKSLLDNPASAILEIDRTILATQHGLSADETKQFGVPLAGNLIPWIDKDLGNGVSKEE 242

Query: 243 WKAQAETNKILARFKN--------PIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEG 294
           WKA AETNKIL R +         PI VDG+CVR+GAMRCHSQALTIKL +DVPL +IE 
Sbjct: 243 WKAGAETNKILGRGEGFLGATGAAPIAVDGLCVRIGAMRCHSQALTIKLRRDVPLDEIEA 302

Query: 295 LISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLW 354
           +++++N W K+VPN RE S+ +LTPAAVTGTL++PVGRLRK+ MG +YL AFTVGDQLLW
Sbjct: 303 MLAENNQWAKVVPNTREASMTDLTPAAVTGTLTIPVGRLRKMQMGGEYLSAFTVGDQLLW 362

Query: 355 GAAEPLRRMLRILLE 369
           GAAEPLRRMLRIL+E
Sbjct: 363 GAAEPLRRMLRILIE 377


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: 518
Number of extensions: 14
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: 378
Length adjustment: 30
Effective length of query: 340
Effective length of database: 348
Effective search space:   118320
Effective search space used:   118320
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: 50 (23.9 bits)

Align candidate RR42_RS14380 RR42_RS14380 (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.2738766.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.5e-190  617.5   0.4     4e-190  617.4   0.4    1.0  1  FitnessBrowser__Cup4G11:RR42_RS14380  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Cup4G11:RR42_RS14380  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.4   0.4    4e-190    4e-190       1     366 []       1     376 [.       1     376 [. 0.96

  Alignments for each domain:
  == domain 1  score: 617.4 bits;  conditional E-value: 4e-190
                             TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqg 73 
                                           ++vglvgwrgmvgsvl++rmqee+dfd+i+pvffsts++g++ap++ak ++ l+da+di+alk++d+++t qg
  FitnessBrowser__Cup4G11:RR42_RS14380   1 MIVGLVGWRGMVGSVLMQRMQEERDFDHIEPVFFSTSNAGGQAPAMAKNETKLKDANDIEALKKCDVVLTAQG 73 
                                           68*********************************************************************** PP

                             TIGR01745  74 gdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslggl 146
                                           gdyt+ei+p+lr+agwkgywidaasslrmkdda+i+ldpvnl vikda++kg+++f+ggnctvs ++m+lggl
  FitnessBrowser__Cup4G11:RR42_RS14380  74 GDYTNEIFPQLRAAGWKGYWIDAASSLRMKDDAIIVLDPVNLGVIKDALAKGVKNFIGGNCTVSCMMMGLGGL 146
                                           ************************************************************************* PP

                             TIGR01745 147 frdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseel.pvenfs 218
                                           f+++l++w++++tyqaasggga+hmrell+q+g+l  +v++ l +p+sailei+r +  +        +++f+
  FitnessBrowser__Cup4G11:RR42_RS14380 147 FQHDLIDWMTSMTYQAASGGGAQHMRELLTQFGTLNASVKSLLDNPASAILEIDRTILATQHGLSAdETKQFG 219
                                           ********************************************************98877754432699*** PP

                             TIGR01745 219 vplagslipwidkqldngqsreewkgqaetnkilg.........tkdtilvdglcvrigalrchsqaltiklk 282
                                           vplag+lipwidk+l ng s+eewk  aetnkilg          +  i vdglcvriga+rchsqaltikl+
  FitnessBrowser__Cup4G11:RR42_RS14380 220 VPLAGNLIPWIDKDLGNGVSKEEWKAGAETNKILGrgegflgatGAAPIAVDGLCVRIGAMRCHSQALTIKLR 292
                                           *********************************98333333221245699*********************** PP

                             TIGR01745 283 kdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaa 355
                                           +dv+l+eie +++++n+w+kvvpn re ++ +ltpaavtgtl+ipvgrlrk++mg eylsaftvgdqllwgaa
  FitnessBrowser__Cup4G11:RR42_RS14380 293 RDVPLDEIEAMLAENNQWAKVVPNTREASMTDLTPAAVTGTLTIPVGRLRKMQMGGEYLSAFTVGDQLLWGAA 365
                                           ************************************************************************* PP

                             TIGR01745 356 eplrrmlrill 366
                                           eplrrmlril+
  FitnessBrowser__Cup4G11:RR42_RS14380 366 EPLRRMLRILI 376
                                           *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (378 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: 13.06
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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