GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_20640
          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.9470.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: 10.11
//
[ok]

This GapMind analysis is from Apr 09 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:

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