Alignments for a candidate for astD in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Pseudomonas fluorescens GW456-L13

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate PfGW456L13_1974 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974
          Length = 488

 Score =  962 bits (2487), Expect = 0.0
 Identities = 488/488 (100%), Positives = 488/488 (100%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE
Sbjct: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK
Sbjct: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
           SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL
Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI
Sbjct: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240

Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300
           LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV
Sbjct: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
           AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT
Sbjct: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW
Sbjct: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
           LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA
Sbjct: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480

Query: 481 LTPGVKMA 488
           LTPGVKMA
Sbjct: 481 LTPGVKMA 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: 955
Number of extensions: 24
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 PfGW456L13_1974 (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.9743.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   8.6e-256  835.1   1.8   9.8e-256  834.9   1.8    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974  Succinylglutamic semialdehyde de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974  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 !  834.9   1.8  9.8e-256  9.8e-256       1     484 []       4     487 ..       4     487 .. 1.00

  Alignments for each domain:
  == domain 1  score: 834.9 bits;  conditional E-value: 9.8e-256
                                               TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarls 55 
                                                             l+i G+w aG Ge++esl+pvtq+vlw+g +a+a qve+av+aar+afp+war++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974   4 LYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRT 58 
                                                             59***************************************************** PP

                                               TIGR03240  56 leeriavvkrfaelleeekeelaeviaketgkplweartevasmvakvaisikay 110
                                                             leeri+v++ fa+ l+++++ela++i++etgkplwea+tev+smv+k+ais+++y
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974  59 LEERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSY 113
                                                             ******************************************************* PP

                                               TIGR03240 111 eertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhivpallaGntvvf 165
                                                             +ertGek+ +l+da+avlrh+phGv+avfGpynfpGhlpnGhivpallaGn+v+f
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 114 RERTGEKSGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLF 168
                                                             ******************************************************* PP

                                               TIGR03240 166 kpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGss 220
                                                             kpseltp+vae tvk+w +aGlpaGvlnl+qGaretG alaa+++idGl+ftGss
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 169 KPSELTPKVAELTVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSS 223
                                                             ******************************************************* PP

                                               TIGR03240 221 ntGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrc 275
                                                             +tG++lh+q+agrp+kilale+GGnnplvv++v+d+daav++i+qsafisaGqrc
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 224 RTGNHLHQQFAGRPDKILALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRC 278
                                                             ******************************************************* PP

                                               TIGR03240 276 tcarrllvkdgaeGdallerlvevaerltvgkydaepqpflGavisekaakella 330
                                                             tcarrllv++ga+Gd+ll+rlv+v+++l vg++d++p+pf+G+v+s  aak+l++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 279 TCARRLLVPQGAWGDSLLARLVAVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMD 333
                                                             ******************************************************* PP

                                               TIGR03240 331 aqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlryk 385
                                                             aqe+lla+g+ +lle++q ++++alltpgi+dv++va++pdee+fgpll+v+ry+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 334 AQEHLLANGAVALLEMTQPQAQSALLTPGILDVSAVADRPDEELFGPLLQVIRYA 388
                                                             ******************************************************* PP

                                               TIGR03240 386 dfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapf 440
                                                             df++a+aean+t++GlaaGllsd++++y++f+le+raGivnwnk+ltGa+s+apf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 389 DFEAAIAEANDTAYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLTGAASSAPF 443
                                                             ******************************************************* PP

                                               TIGR03240 441 GGiGasGnhrpsayyaadycaypvasleadslalpatlspGlkl 484
                                                             GG+GasGnhr+sayyaadycaypvasle+ sl+lp  l+pG+k+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1974 444 GGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSALTPGVKM 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: 10.84
//
[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 (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