GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Pseudomonas fluorescens FW300-N1B4

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate Pf1N1B4_3444 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974
         (488 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 Succinylglutamic
           semialdehyde dehydrogenase (EC 1.2.1.71)
          Length = 488

 Score =  926 bits (2393), Expect = 0.0
 Identities = 465/487 (95%), Positives = 477/487 (97%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M SLYIAGEWLAG GE+F+S+NPVTQQVLW+G GAT GQVESAVQAARQAFP WARRTLE
Sbjct: 1   MNSLYIAGEWLAGQGESFQSVNPVTQQVLWAGEGATTGQVESAVQAARQAFPGWARRTLE 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ERI VLEAFAAALKNHADELA TIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK
Sbjct: 61  ERIGVLEAFAAALKNHADELARTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
           SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL
Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLH+QF+GRPDKI
Sbjct: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHKQFSGRPDKI 240

Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300
           LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGD+LLARLV
Sbjct: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDTLLARLV 300

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
           AVSST+ VGAFDQQPAPFMGSV+SLGAAKALMDAQEHLLANGAVALLEMTQPQAQ+ALLT
Sbjct: 301 AVSSTIEVGAFDQQPAPFMGSVISLGAAKALMDAQEHLLANGAVALLEMTQPQAQAALLT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           PGILDV+AVADRPDEELFGPLLQVIRYADFEAAIAEANDT YGLAAGLLSDSEARYQQFW
Sbjct: 361 PGILDVTAVADRPDEELFGPLLQVIRYADFEAAIAEANDTDYGLAAGLLSDSEARYQQFW 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
           LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLP+ 
Sbjct: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPAT 480

Query: 481 LTPGVKM 487
           LTPGVKM
Sbjct: 481 LTPGVKM 487


Lambda     K      H
   0.316    0.132    0.388 

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: 934
Number of extensions: 23
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: 488
Length of database: 488
Length adjustment: 34
Effective length of query: 454
Effective length of database: 454
Effective search space:   206116
Effective search space used:   206116
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate Pf1N1B4_3444 (Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

# 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.carbon/TIGR03240.hmm
# target sequence database:        /tmp/gapView.8633.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03240  [M=484]
Accession:   TIGR03240
Description: arg_catab_astD: succinylglutamate-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     1e-257  841.5   1.7   1.1e-257  841.3   1.7    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444  Succinylglutamic semialdehyde de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444  Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  841.3   1.7  1.1e-257  1.1e-257       1     484 []       4     487 ..       4     487 .. 1.00

  Alignments for each domain:
  == domain 1  score: 841.3 bits;  conditional E-value: 1.1e-257
                                      TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvk 64 
                                                    l+i G+w aGqGes++s++pvtq+vlw g++a++ qve+av+aar+afp war++leeri v++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444   4 LYIAGEWLAGQGESFQSVNPVTQQVLWAGEGATTGQVESAVQAARQAFPGWARRTLEERIGVLE 67 
                                                    59************************************************************** PP

                                      TIGR03240  65 rfaelleeekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavl 128
                                                     fa+ l+++++ela++i++etgkplwea+tev+smv+k+ais+++y+ertGek+ +l+da+avl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444  68 AFAAALKNHADELARTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEKSGPLGDATAVL 131
                                                    **************************************************************** PP

                                      TIGR03240 129 rhrphGvlavfGpynfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvl 192
                                                    rh+phGv+avfGpynfpGhlpnGhivpallaGn+v+fkpseltp+vae tvk+w +aGlpaGvl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 132 RHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWIEAGLPAGVL 195
                                                    **************************************************************** PP

                                      TIGR03240 193 nlvqGaretGkalaaeedidGllftGssntGallhrqlagrpekilalelGGnnplvveevkdi 256
                                                    nl+qGaretG alaa+++idGl+ftGss+tG++lh+q++grp+kilale+GGnnplvv++v+d+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 196 NLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHKQFSGRPDKILALEMGGNNPLVVDQVADL 259
                                                    **************************************************************** PP

                                      TIGR03240 257 daavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpflGavi 320
                                                    daav++i+qsafisaGqrctcarrllv++ga+Gd+ll+rlv+v+++++vg++d++p+pf+G+vi
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 260 DAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDTLLARLVAVSSTIEVGAFDQQPAPFMGSVI 323
                                                    **************************************************************** PP

                                      TIGR03240 321 sekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlry 384
                                                    s  aak+l++aqe+lla+g+ +lle++q +++aalltpgi+dvt+va++pdee+fgpll+v+ry
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 324 SLGAAKALMDAQEHLLANGAVALLEMTQPQAQAALLTPGILDVTAVADRPDEELFGPLLQVIRY 387
                                                    **************************************************************** PP

                                      TIGR03240 385 kdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGn 448
                                                    +df++a+aean+t +GlaaGllsd++++y++f+le+raGivnwnk+ltGa+s+apfGG+GasGn
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 388 ADFEAAIAEANDTDYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLTGAASSAPFGGVGASGN 451
                                                    **************************************************************** PP

                                      TIGR03240 449 hrpsayyaadycaypvasleadslalpatlspGlkl 484
                                                    hr+sayyaadycaypvasle+ sl+lpatl+pG+k+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 452 HRASAYYAADYCAYPVASLETPSLVLPATLTPGVKM 487
                                                    *********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (488 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: 00:00:00.02
# Mc/sec: 10.17
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint on GapMind for carbon sources, or view the source code.

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