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.12399.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.55
//
[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:

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. 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:

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:

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