GapMind for Amino acid biosynthesis

 

Alignments 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)



>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.11913.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.59
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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