Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N2E3

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate AO353_03010 AO353_03010 succinylglutamate-semialdehyde dehydrogenase

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



>FitnessBrowser__pseudo3_N2E3:AO353_03010
          Length = 487

 Score =  904 bits (2337), Expect = 0.0
 Identities = 454/487 (93%), Positives = 469/487 (96%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M SLYIAGEWLAG G+ FESLNPVTQQVLWSG GA+A QVESAVQAARQAFP WA+R+LE
Sbjct: 1   MNSLYIAGEWLAGQGDMFESLNPVTQQVLWSGQGASAAQVESAVQAARQAFPAWAKRSLE 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           +RI VLE FAA+LK HADELAH IGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK
Sbjct: 61  DRIGVLETFAASLKKHADELAHCIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
           SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL
Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180

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

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

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
           AVS+T+ VGAFDQQPAPFMGSVVSL AAKALMDAQEHLLANGAV LL+MTQPQA +ALLT
Sbjct: 301 AVSATIDVGAFDQQPAPFMGSVVSLAAAKALMDAQEHLLANGAVPLLKMTQPQANAALLT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           PGILDVSAV DRPDEELFGPLLQVIRYADFEAAIAEAN+T YGLAAGLLSDSEARYQQFW
Sbjct: 361 PGILDVSAVTDRPDEELFGPLLQVIRYADFEAAIAEANNTQYGLAAGLLSDSEARYQQFW 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
           LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSL LP+A
Sbjct: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLTLPAA 480

Query: 481 LTPGVKM 487
           LTPGV+M
Sbjct: 481 LTPGVRM 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: 886
Number of extensions: 20
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: 487
Length adjustment: 34
Effective length of query: 454
Effective length of database: 453
Effective search space:   205662
Effective search space used:   205662
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 AO353_03010 AO353_03010 (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.1979.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.3e-257  840.3   1.6   2.5e-257  840.2   1.6    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010  AO353_03010 succinylglutamate-se


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010  AO353_03010 succinylglutamate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  840.2   1.6  2.5e-257  2.5e-257       1     483 [.       4     486 ..       4     487 .] 1.00

  Alignments for each domain:
  == domain 1  score: 840.2 bits;  conditional E-value: 2.5e-257
                                     TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkr 65 
                                                   l+i G+w aGqG+ +esl+pvtq+vlw+g++asaaqve+av+aar+afpawa++sle+ri v+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010   4 LYIAGEWLAGQGDMFESLNPVTQQVLWSGQGASAAQVESAVQAARQAFPAWAKRSLEDRIGVLET 68 
                                                   59*************************************************************** PP

                                     TIGR03240  66 faelleeekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrh 130
                                                   fa+ l+++++ela++i++etgkplwea+tev+smv+k+ais+++y+ertGek+ +l+da+avlrh
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010  69 FAASLKKHADELAHCIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEKSGPLGDATAVLRH 133
                                                   ***************************************************************** PP

                                     TIGR03240 131 rphGvlavfGpynfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlv 195
                                                   +phGv+avfGpynfpGhlpnGhivpallaGn+v+fkpseltp+vae tvk+w +aGlpaGvlnl+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010 134 KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWIEAGLPAGVLNLL 198
                                                   ***************************************************************** PP

                                     TIGR03240 196 qGaretGkalaaeedidGllftGssntGallhrqlagrpekilalelGGnnplvveevkdidaav 260
                                                   qGaretG alaa+++idGl+ftGss+tG++lh q++grp+kilale+GGnnplvv++v+d+daav
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010 199 QGARETGIALAANPGIDGLFFTGSSRTGNHLHAQFSGRPDKILALEMGGNNPLVVDQVADLDAAV 263
                                                   ***************************************************************** PP

                                     TIGR03240 261 hlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpflGavisekaa 325
                                                   ++i+qsafisaGqrctcarrllv++ga+Gd+ll+rlv+v++++ vg++d++p+pf+G+v+s  aa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010 264 YTIIQSAFISAGQRCTCARRLLVPQGAWGDTLLARLVAVSATIDVGAFDQQPAPFMGSVVSLAAA 328
                                                   ***************************************************************** PP

                                     TIGR03240 326 kellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlrykdfdea 390
                                                   k+l++aqe+lla+g+  ll+++q +++aalltpgi+dv++v+++pdee+fgpll+v+ry+df++a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010 329 KALMDAQEHLLANGAVPLLKMTQPQANAALLTPGILDVSAVTDRPDEELFGPLLQVIRYADFEAA 393
                                                   ***************************************************************** PP

                                     TIGR03240 391 laeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayy 455
                                                   +aeannt++GlaaGllsd++++y++f+le+raGivnwnk+ltGa+s+apfGG+GasGnhr+sayy
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010 394 IAEANNTQYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYY 458
                                                   ***************************************************************** PP

                                     TIGR03240 456 aadycaypvasleadslalpatlspGlk 483
                                                   aadycaypvasle+ sl+lpa l+pG++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03010 459 AADYCAYPVASLETPSLTLPAALTPGVR 486
                                                   **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (487 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: 00:00:00.03
# Mc/sec: 7.42
//
[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