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.26703.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: 11.31
//
[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