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

GapMind for catabolism of small carbon sources

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

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate Pf6N2E2_5668 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668
          Length = 488

 Score =  881 bits (2277), Expect = 0.0
 Identities = 441/488 (90%), Positives = 461/488 (94%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M SLYIAG WL G G+ FESLNPVTQQVLWSG GATA QVESAVQAARQAFP WARRTL+
Sbjct: 1   MNSLYIAGSWLEGQGDVFESLNPVTQQVLWSGKGATAAQVESAVQAARQAFPGWARRTLD 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ERI VLEAFAA LK+HADELA  IGEETGKPLWEAATEVT+MVNKIAISVQSYRERTGEK
Sbjct: 61  ERIQVLEAFAATLKSHADELAQCIGEETGKPLWEAATEVTTMVNKIAISVQSYRERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
           SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL
Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TVKCW+EAGLPAGVLNLLQGARETGIALAAN GIDGLFFTGSSRTGN LHQQF+GRPDKI
Sbjct: 181 TVKCWVEAGLPAGVLNLLQGARETGIALAANSGIDGLFFTGSSRTGNLLHQQFSGRPDKI 240

Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300
           LALEMGGNNPLVVD+VAD+DAAVYTIIQSAFISAGQRCTCARRLLVP+GAWGD+LLARLV
Sbjct: 241 LALEMGGNNPLVVDEVADVDAAVYTIIQSAFISAGQRCTCARRLLVPEGAWGDALLARLV 300

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
           AVSSTL VGAFDQQPAPFMG+V+SLGAAKALMDAQ HLL  GAV LL MTQPQ Q+ALLT
Sbjct: 301 AVSSTLEVGAFDQQPAPFMGAVISLGAAKALMDAQNHLLGKGAVPLLSMTQPQPQAALLT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           PGILDV+ VA+RPDEELFGPLLQVIRY DF AAI EAN+T YGLAAGLLSDS+ RYQQFW
Sbjct: 361 PGILDVTTVAERPDEELFGPLLQVIRYKDFAAAITEANNTQYGLAAGLLSDSQERYQQFW 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
           LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLV+P+A
Sbjct: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVMPAA 480

Query: 481 LTPGVKMA 488
           LTPGV+MA
Sbjct: 481 LTPGVRMA 488


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: 879
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: 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 Pf6N2E2_5668 (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.31113.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.1e-257  839.2   1.0   5.7e-257  839.0   1.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668  Succinylglutamic semialdehyde de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668  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 !  839.0   1.0  5.7e-257  5.7e-257       1     483 [.       4     486 ..       4     487 .. 1.00

  Alignments for each domain:
  == domain 1  score: 839.0 bits;  conditional E-value: 5.7e-257
                                      TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvk 64 
                                                    l+i G+w +GqG+ +esl+pvtq+vlw+gk+a+aaqve+av+aar+afp war++l+eri+v++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668   4 LYIAGSWLEGQGDVFESLNPVTQQVLWSGKGATAAQVESAVQAARQAFPGWARRTLDERIQVLE 67 
                                                    59************************************************************** PP

                                      TIGR03240  65 rfaelleeekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavl 128
                                                     fa+ l+ +++ela++i++etgkplwea+tev++mv+k+ais+++y+ertGek+ +l+da+avl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668  68 AFAATLKSHADELAQCIGEETGKPLWEAATEVTTMVNKIAISVQSYRERTGEKSGPLGDATAVL 131
                                                    **************************************************************** PP

                                      TIGR03240 129 rhrphGvlavfGpynfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvl 192
                                                    rh+phGv+avfGpynfpGhlpnGhivpallaGn+v+fkpseltp+vae tvk+w +aGlpaGvl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668 132 RHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWVEAGLPAGVL 195
                                                    **************************************************************** PP

                                      TIGR03240 193 nlvqGaretGkalaaeedidGllftGssntGallhrqlagrpekilalelGGnnplvveevkdi 256
                                                    nl+qGaretG alaa+++idGl+ftGss+tG+llh+q++grp+kilale+GGnnplvv+ev+d+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668 196 NLLQGARETGIALAANSGIDGLFFTGSSRTGNLLHQQFSGRPDKILALEMGGNNPLVVDEVADV 259
                                                    **************************************************************** PP

                                      TIGR03240 257 daavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpflGavi 320
                                                    daav++i+qsafisaGqrctcarrllv++ga+Gdall+rlv+v+++l+vg++d++p+pf+Gavi
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668 260 DAAVYTIIQSAFISAGQRCTCARRLLVPEGAWGDALLARLVAVSSTLEVGAFDQQPAPFMGAVI 323
                                                    **************************************************************** PP

                                      TIGR03240 321 sekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlry 384
                                                    s  aak+l++aq++ll +g+  ll+++q + +aalltpgi+dvt+vae+pdee+fgpll+v+ry
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668 324 SLGAAKALMDAQNHLLGKGAVPLLSMTQPQPQAALLTPGILDVTTVAERPDEELFGPLLQVIRY 387
                                                    **************************************************************** PP

                                      TIGR03240 385 kdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGn 448
                                                    kdf +a++eannt++GlaaGllsd++e+y++f+le+raGivnwnk+ltGa+s+apfGG+GasGn
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668 388 KDFAAAITEANNTQYGLAAGLLSDSQERYQQFWLESRAGIVNWNKQLTGAASSAPFGGVGASGN 451
                                                    **************************************************************** PP

                                      TIGR03240 449 hrpsayyaadycaypvasleadslalpatlspGlk 483
                                                    hr+sayyaadycaypvasle+ sl++pa l+pG++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5668 452 HRASAYYAADYCAYPVASLETPSLVMPAALTPGVR 486
                                                    *********************************97 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.36
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources