GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asd in Pseudomonas fluorescens FW300-N2E3

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate AO353_20640 AO353_20640 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640 AO353_20640
           aspartate-semialdehyde dehydrogenase
          Length = 370

 Score =  681 bits (1758), Expect = 0.0
 Identities = 331/370 (89%), Positives = 355/370 (95%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60
           MKRVGLIGWRGMVGSVLMQRMLEE+DFDLIEPVFFTTSNVGGQGP VGKDIAPLKDAYSI
Sbjct: 1   MKRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIAPLKDAYSI 60

Query: 61  DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120
           +ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRM+DDAVIVLDPVNRKVID
Sbjct: 61  EELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIVLDPVNRKVID 120

Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180
           Q LDAGT+NYIGGNCTVSLMLM LGGLF+AGLVEWMSAMTYQAASG GAQ+MREL+KQMG
Sbjct: 121 QQLDAGTKNYIGGNCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASGGGAQHMRELIKQMG 180

Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
             HA+VAD LA+PASAILDIDR+VAE +RS+A+PTE+FG PL GSLIPWIDKELPNGQSR
Sbjct: 181 VTHAAVADQLADPASAILDIDRRVAEAMRSDAYPTENFGVPLAGSLIPWIDKELPNGQSR 240

Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300
           EEWKAQAETNKIL RFK+PIPVDGICVR+GAMRCHSQALTIKLNKDVP+ DIEGLISQHN
Sbjct: 241 EEWKAQAETNKILGRFKSPIPVDGICVRIGAMRCHSQALTIKLNKDVPIADIEGLISQHN 300

Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360
           PWVKLVPN RE+S++EL+P  VTGTL+VPVGRLRKLNMGSQ++GAFTVGDQLLWGAAEPL
Sbjct: 301 PWVKLVPNQREISMQELSPTKVTGTLNVPVGRLRKLNMGSQFVGAFTVGDQLLWGAAEPL 360

Query: 361 RRMLRILLER 370
           RRMLRILLER
Sbjct: 361 RRMLRILLER 370


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: 636
Number of extensions: 14
Number of successful extensions: 1
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: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
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 AO353_20640 AO353_20640 (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.2339.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.8e-201  653.3   0.0   5.5e-201  653.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640  AO353_20640 aspartate-semialdehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640  AO353_20640 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.1   0.0  5.5e-201  5.5e-201       1     366 []       2     368 ..       2     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 653.1 bits;  conditional E-value: 5.5e-201
                                     TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkel 65 
                                                   k+vgl+gwrgmvgsvl++rm ee+dfd+i+pvff+ts++g+++ps++k  a+l+day i+ lk l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640   2 KRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIAPLKDAYSIEELKTL 66 
                                                   68*************************************************************** PP

                                     TIGR01745  66 diiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfv 130
                                                   d+i+tcqggdyt+e++pklr+agw+gywidaasslrm+ddavi+ldpvn +vi++ ++ g+++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640  67 DVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIVLDPVNRKVIDQQLDAGTKNYI 131
                                                   ***************************************************************** PP

                                     TIGR01745 131 ggnctvslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssa 195
                                                   ggnctvsl+lm+lgglf+ +lvew+s++tyqaasggga+hmrel+kqmgv +  v+++la p+sa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640 132 GGNCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASGGGAQHMRELIKQMGVTHAAVADQLADPASA 196
                                                   ***************************************************************** PP

                                     TIGR01745 196 ileierkvtklsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgt.kdtil 259
                                                   il+i+r+v++ +rs+  p+enf+vplagslipwidk+l ngqsreewk qaetnkilg  k+ i+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640 197 ILDIDRRVAEAMRSDAYPTENFGVPLAGSLIPWIDKELPNGQSREEWKAQAETNKILGRfKSPIP 261
                                                   *********************************************************964788** PP

                                     TIGR01745 260 vdglcvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtl 324
                                                   vdg+cvriga+rchsqaltikl+kdv++ +ie +i +hn+wvk+vpn+rei+++el+p+ vtgtl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640 262 VDGICVRIGAMRCHSQALTIKLNKDVPIADIEGLISQHNPWVKLVPNQREISMQELSPTKVTGTL 326
                                                   ***************************************************************** PP

                                     TIGR01745 325 dipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366
                                                   ++pvgrlrklnmg +++ aftvgdqllwgaaeplrrmlrill
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20640 327 NVPVGRLRKLNMGSQFVGAFTVGDQLLWGAAEPLRRMLRILL 368
                                                   ****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (366 nodes)
Target sequences:                          1  (370 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: 6.96
//
[ok]

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

Links

Downloads

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:

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