GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asd in Cupriavidus basilensis 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)



>lcl|FitnessBrowser__Cup4G11:RR42_RS14380 RR42_RS14380
           aspartate-semialdehyde dehydrogenase
          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.14843.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  lcl|FitnessBrowser__Cup4G11:RR42_RS14380  RR42_RS14380 aspartate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS14380  RR42_RS14380 aspartate-semialdehyde dehydrogenase
   #    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 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 
                                               ++vglvgwrgmvgsvl++rmqee+dfd+i+pvffsts++g++ap++ak ++ l+da+di+alk++d+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14380   1 MIVGLVGWRGMVGSVLMQRMQEERDFDHIEPVFFSTSNAGGQAPAMAKNETKLKDANDIEALKKCDVVL 69 
                                               68******************************************************************* PP

                                 TIGR01745  70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsl 138
                                               t qggdyt+ei+p+lr+agwkgywidaasslrmkdda+i+ldpvnl vikda++kg+++f+ggnctvs 
  lcl|FitnessBrowser__Cup4G11:RR42_RS14380  70 TAQGGDYTNEIFPQLRAAGWKGYWIDAASSLRMKDDAIIVLDPVNLGVIKDALAKGVKNFIGGNCTVSC 138
                                               ********************************************************************* PP

                                 TIGR01745 139 llmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkls 207
                                               ++m+lgglf+++l++w++++tyqaasggga+hmrell+q+g+l  +v++ l +p+sailei+r +  + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS14380 139 MMMGLGGLFQHDLIDWMTSMTYQAASGGGAQHMRELLTQFGTLNASVKSLLDNPASAILEIDRTILATQ 207
                                               ****************************************************************98877 PP

                                 TIGR01745 208 rseel.pvenfsvplagslipwidkqldngqsreewkgqaetnkilg.........tkdtilvdglcvr 266
                                                      +++f+vplag+lipwidk+l ng s+eewk  aetnkilg          +  i vdglcvr
  lcl|FitnessBrowser__Cup4G11:RR42_RS14380 208 HGLSAdETKQFGVPLAGNLIPWIDKDLGNGVSKEEWKAGAETNKILGrgegflgatGAAPIAVDGLCVR 276
                                               754432699************************************98333333221245699******* PP

                                 TIGR01745 267 igalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrkln 335
                                               iga+rchsqaltikl++dv+l+eie +++++n+w+kvvpn re ++ +ltpaavtgtl+ipvgrlrk++
  lcl|FitnessBrowser__Cup4G11:RR42_RS14380 277 IGAMRCHSQALTIKLRRDVPLDEIEAMLAENNQWAKVVPNTREASMTDLTPAAVTGTLTIPVGRLRKMQ 345
                                               ********************************************************************* PP

                                 TIGR01745 336 mgkeylsaftvgdqllwgaaeplrrmlrill 366
                                               mg eylsaftvgdqllwgaaeplrrmlril+
  lcl|FitnessBrowser__Cup4G11:RR42_RS14380 346 MGGEYLSAFTVGDQLLWGAAEPLRRMLRILI 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: 00:00:00.02
# Mc/sec: 6.90
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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, or view the source code, or see 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