GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pseudomonas putida KT2440

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate PP_1989 PP_1989 Aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q51344
         (370 letters)



>FitnessBrowser__Putida:PP_1989
          Length = 370

 Score =  696 bits (1795), Expect = 0.0
 Identities = 338/370 (91%), Positives = 358/370 (96%)

Query: 1   MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60
           MKRVGLIGWRGMVGSVLMQRMLEE+DFDLIEPVFFTTSNVGGQGP VGKD APLKDAYSI
Sbjct: 1   MKRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPNVGKDTAPLKDAYSI 60

Query: 61  DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120
           +ELKTLDVILTCQGGDYT+EVFPKLREAGWQGYWIDAASSLRM+DDAVI+LDPVNRKVID
Sbjct: 61  EELKTLDVILTCQGGDYTNEVFPKLREAGWQGYWIDAASSLRMQDDAVIILDPVNRKVID 120

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

Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240
           A HA+VADDLANPASAILDIDRKVAET+RSEAFPTE+FG PL GSLIPWIDKELPNGQSR
Sbjct: 181 ATHAAVADDLANPASAILDIDRKVAETMRSEAFPTENFGVPLAGSLIPWIDKELPNGQSR 240

Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300
           EEWKAQAETNKIL RFK+PIPVDGICVR+GAMRCHSQALTIKLNKDVP+ DIEG+ISQHN
Sbjct: 241 EEWKAQAETNKILGRFKSPIPVDGICVRIGAMRCHSQALTIKLNKDVPIADIEGMISQHN 300

Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360
           PWVKLVPN RE+S++ELTP  VTGTL++PVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL
Sbjct: 301 PWVKLVPNQREISMQELTPTKVTGTLNIPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 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: 652
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 PP_1989 PP_1989 (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.3331.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.6e-203  660.3   0.1   4.1e-203  660.1   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_1989  PP_1989 Aspartate-semialdehyde d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1989  PP_1989 Aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  660.1   0.1  4.1e-203  4.1e-203       1     366 []       2     368 ..       2     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 660.1 bits;  conditional E-value: 4.1e-203
                           TIGR01745   1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqggd 75 
                                         k+vgl+gwrgmvgsvl++rm ee+dfd+i+pvff+ts++g+++p ++k +a+l+day i+ lk ld+i+tcqggd
  lcl|FitnessBrowser__Putida:PP_1989   2 KRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPNVGKDTAPLKDAYSIEELKTLDVILTCQGGD 76 
                                         68************************************************************************* PP

                           TIGR01745  76 ytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrde 150
                                         yt+e++pklr+agw+gywidaasslrm+ddaviildpvn +vi++ ++ g+++++ggnctvsl+lm+lgglf+ +
  lcl|FitnessBrowser__Putida:PP_1989  77 YTNEVFPKLREAGWQGYWIDAASSLRMQDDAVIILDPVNRKVIDQQLDAGTKNYIGGNCTVSLMLMGLGGLFEAG 151
                                         *************************************************************************** PP

                           TIGR01745 151 lvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplagsl 225
                                         lvew+s++tyqaasg+ga+ mrel+kqmg  +  v+++la+p+sail+i+rkv++++rse +p+enf+vplagsl
  lcl|FitnessBrowser__Putida:PP_1989 152 LVEWMSAMTYQAASGAGAQNMRELIKQMGATHAAVADDLANPASAILDIDRKVAETMRSEAFPTENFGVPLAGSL 226
                                         *************************************************************************** PP

                           TIGR01745 226 ipwidkqldngqsreewkgqaetnkilgt.kdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnk 299
                                         ipwidk+l ngqsreewk qaetnkilg  k+ i+vdg+cvriga+rchsqaltikl+kdv++ +ie +i +hn+
  lcl|FitnessBrowser__Putida:PP_1989 227 IPWIDKELPNGQSREEWKAQAETNKILGRfKSPIPVDGICVRIGAMRCHSQALTIKLNKDVPIADIEGMISQHNP 301
                                         ***************************964788****************************************** PP

                           TIGR01745 300 wvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366
                                         wvk+vpn+rei+++eltp+ vtgtl+ipvgrlrklnmg +yl aftvgdqllwgaaeplrrmlrill
  lcl|FitnessBrowser__Putida:PP_1989 302 WVKLVPNQREISMQELTPTKVTGTLNIPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLRRMLRILL 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: 11.95
//
[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