Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N2C3

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate AO356_18740 AO356_18740 succinylglutamate-semialdehyde dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_18740
          Length = 488

 Score =  889 bits (2298), Expect = 0.0
 Identities = 444/488 (90%), Positives = 466/488 (95%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M SLYIAG WL G G+ FESLNPVTQQVLWSG GATA QVESAVQAARQAFPDWARR+L+
Sbjct: 1   MNSLYIAGSWLEGQGDLFESLNPVTQQVLWSGNGATAAQVESAVQAARQAFPDWARRSLD 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ERI VLEAFAAALK+HADELA  IGEETGKPLWEAATEVTSMVNK+AISVQSYRERTGEK
Sbjct: 61  ERIQVLEAFAAALKSHADELAQCIGEETGKPLWEAATEVTSMVNKVAISVQSYRERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
           SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL
Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TVKCW+EAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGN LHQQF+GRPDKI
Sbjct: 181 TVKCWVEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNLLHQQFSGRPDKI 240

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

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
           AVSSTL VGAFDQQPAPFMGSV+SLGAAKALMDAQ HLL  GAV LL MTQPQ Q+ALLT
Sbjct: 301 AVSSTLEVGAFDQQPAPFMGSVISLGAAKALMDAQNHLLGKGAVPLLAMTQPQPQAALLT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           PGILDV+AVA+RPDEELFGPLLQVIRY DF AAI EAN+T YGLAAGLLSDS+ARYQQFW
Sbjct: 361 PGILDVTAVAERPDEELFGPLLQVIRYTDFAAAITEANNTQYGLAAGLLSDSQARYQQFW 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
           L+SRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLV+P+A
Sbjct: 421 LQSRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVMPAA 480

Query: 481 LTPGVKMA 488
           LTPGV+M+
Sbjct: 481 LTPGVRMS 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: 890
Number of extensions: 16
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 AO356_18740 AO356_18740 (succinylglutamate-semialdehyde dehydrogenase)
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.4225.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.5e-257  841.0   1.2   1.7e-257  840.8   1.2    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740  AO356_18740 succinylglutamate-se


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740  AO356_18740 succinylglutamate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  840.8   1.2  1.7e-257  1.7e-257       1     483 [.       4     486 ..       4     487 .. 1.00

  Alignments for each domain:
  == domain 1  score: 840.8 bits;  conditional E-value: 1.7e-257
                                       TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavv 63 
                                                     l+i G+w +GqG+ +esl+pvtq+vlw+g++a+aaqve+av+aar+afp+war+sl+eri+v+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740   4 LYIAGSWLEGQGDLFESLNPVTQQVLWSGNGATAAQVESAVQAARQAFPDWARRSLDERIQVL 66 
                                                     59************************************************************* PP

                                       TIGR03240  64 krfaelleeekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladaka 126
                                                     + fa+ l+ +++ela++i++etgkplwea+tev+smv+kvais+++y+ertGek+ +l+da+a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740  67 EAFAAALKSHADELAQCIGEETGKPLWEAATEVTSMVNKVAISVQSYRERTGEKSGPLGDATA 129
                                                     *************************************************************** PP

                                       TIGR03240 127 vlrhrphGvlavfGpynfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpa 189
                                                     vlrh+phGv+avfGpynfpGhlpnGhivpallaGn+v+fkpseltp+vae tvk+w +aGlpa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740 130 VLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWVEAGLPA 192
                                                     *************************************************************** PP

                                       TIGR03240 190 GvlnlvqGaretGkalaaeedidGllftGssntGallhrqlagrpekilalelGGnnplvvee 252
                                                     Gvlnl+qGaretG alaa+++idGl+ftGss+tG+llh+q++grp+kilale+GGnnplvv+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740 193 GVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNLLHQQFSGRPDKILALEMGGNNPLVVDE 255
                                                     *************************************************************** PP

                                       TIGR03240 253 vkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpf 315
                                                     v+d+daav++i+qsafisaGqrctcarrllv++ga+Gdall+rlv+v+++l+vg++d++p+pf
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740 256 VADVDAAVYTIIQSAFISAGQRCTCARRLLVPEGAWGDALLARLVAVSSTLEVGAFDQQPAPF 318
                                                     *************************************************************** PP

                                       TIGR03240 316 lGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpl 378
                                                     +G+vis  aak+l++aq++ll +g+  ll+++q + +aalltpgi+dvt+vae+pdee+fgpl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740 319 MGSVISLGAAKALMDAQNHLLGKGAVPLLAMTQPQPQAALLTPGILDVTAVAERPDEELFGPL 381
                                                     *************************************************************** PP

                                       TIGR03240 379 lkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfG 441
                                                     l+v+ry+df +a++eannt++GlaaGllsd++++y++f+l++raGivnwnk+ltGa+s+apfG
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740 382 LQVIRYTDFAAAITEANNTQYGLAAGLLSDSQARYQQFWLQSRAGIVNWNKQLTGAASSAPFG 444
                                                     *************************************************************** PP

                                       TIGR03240 442 GiGasGnhrpsayyaadycaypvasleadslalpatlspGlk 483
                                                     G+GasGnhr+sayyaadycaypvasle+ sl++pa l+pG++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18740 445 GVGASGNHRASAYYAADYCAYPVASLETPSLVMPAALTPGVR 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.40
//
[ok]

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

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Candidates (tab-delimited)
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