GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pseudomonas fluorescens FW300-N2E2

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate Pf6N2E2_67 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67
          Length = 370

 Score =  687 bits (1773), Expect = 0.0
 Identities = 334/370 (90%), Positives = 357/370 (96%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60
           MKRVGLIGWRGMVGSVLMQRMLEE+DFDLIEPVFFTTSNVGGQGP VGKDI  LKDAYSI
Sbjct: 1   MKRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIGALKDAYSI 60

Query: 61  DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120
           +ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRM+DDAVI+LDPVNRKVID
Sbjct: 61  EELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIILDPVNRKVID 120

Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180
           Q LDAGT+NYIGGNCTVSLMLM LGGLF+AGLVEWMSAMTYQAASGAGAQNMREL+KQMG
Sbjct: 121 QQLDAGTKNYIGGNCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASGAGAQNMRELIKQMG 180

Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
           A HA+VADDLANPASAILDIDRKVAE +RS+A+PTE+FG PL GSLIPWIDKELPNGQSR
Sbjct: 181 ATHAAVADDLANPASAILDIDRKVAEAMRSDAYPTENFGVPLAGSLIPWIDKELPNGQSR 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 PWVKLVPNNREISMQELSPTKVTGTLNVPVGRLRKLNMGSQFVGAFTVGDQLLWGAAEPL 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: 646
Number of extensions: 15
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 Pf6N2E2_67 (Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
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.6120.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.4e-200  651.0   0.1   2.7e-200  650.8   0.1    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67  Aspartate-semialdehyde dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67  Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  650.8   0.1  2.7e-200  2.7e-200       1     366 []       2     368 ..       2     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 650.8 bits;  conditional E-value: 2.7e-200
                                    TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeld 66 
                                                  k+vgl+gwrgmvgsvl++rm ee+dfd+i+pvff+ts++g+++ps++k  ++l+day i+ lk ld
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67   2 KRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIGALKDAYSIEELKTLD 67 
                                                  68**************************************************************** PP

                                    TIGR01745  67 iiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvgg 132
                                                  +i+tcqggdyt+e++pklr+agw+gywidaasslrm+ddaviildpvn +vi++ ++ g+++++gg
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67  68 VILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIILDPVNRKVIDQQLDAGTKNYIGG 133
                                                  ****************************************************************** PP

                                    TIGR01745 133 nctvslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaile 198
                                                  nctvsl+lm+lgglf+ +lvew+s++tyqaasg+ga+ mrel+kqmg  +  v+++la+p+sail+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 134 NCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASGAGAQNMRELIKQMGATHAAVADDLANPASAILD 199
                                                  ****************************************************************** PP

                                    TIGR01745 199 ierkvtklsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgt.kdtilvdgl 263
                                                  i+rkv++ +rs+  p+enf+vplagslipwidk+l ngqsreewk qaetnkilg  k+ i+vdg+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 200 IDRKVAEAMRSDAYPTENFGVPLAGSLIPWIDKELPNGQSREEWKAQAETNKILGRfKSPIPVDGI 265
                                                  ******************************************************964788****** PP

                                    TIGR01745 264 cvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvg 329
                                                  cvriga+rchsqaltikl+kdv++ +ie +i +hn+wvk+vpn+rei+++el+p+ vtgtl++pvg
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 266 CVRIGAMRCHSQALTIKLNKDVPIADIEGLISQHNPWVKLVPNNREISMQELSPTKVTGTLNVPVG 331
                                                  ****************************************************************** PP

                                    TIGR01745 330 rlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366
                                                  rlrklnmg +++ aftvgdqllwgaaeplrrmlrill
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 332 RLRKLNMGSQFVGAFTVGDQLLWGAAEPLRRMLRILL 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.99
//
[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