Alignments for a candidate for astD in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Pseudomonas simiae WCS417

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate GFF4235 PS417_21695 succinylglutamate-semialdehyde dehydrogenase

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



>FitnessBrowser__WCS417:GFF4235
          Length = 488

 Score =  874 bits (2258), Expect = 0.0
 Identities = 436/487 (89%), Positives = 461/487 (94%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M SLYIAG WLAG GE FES NPVTQQVLW+G GATA QVESAVQAARQAFP WA+R LE
Sbjct: 1   MNSLYIAGSWLAGQGELFESRNPVTQQVLWAGNGATAEQVESAVQAARQAFPAWAKRPLE 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ERISVLE FAA LK  AD++A  IGEETGKPLWE+ATEVTSM NKIAISVQSYRERTGEK
Sbjct: 61  ERISVLETFAATLKRRADDIARCIGEETGKPLWESATEVTSMANKIAISVQSYRERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
           SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGN+VLFKPSELTPKVAEL
Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVLFKPSELTPKVAEL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TV+CW+EAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQF+GRPDKI
Sbjct: 181 TVQCWVEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFSGRPDKI 240

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

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
           AVSST+ VGAFDQQPAPFMGSV+SL AAKALMDAQE +LANGAVALLEMTQPQ Q+ALLT
Sbjct: 301 AVSSTIEVGAFDQQPAPFMGSVISLAAAKALMDAQELMLANGAVALLEMTQPQDQAALLT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           PGI+DV+ V +R DEELFGPLLQVIRYADFEAAIAEAN+T YGLAAGLLSDSEARYQQFW
Sbjct: 361 PGIIDVTGVTEREDEELFGPLLQVIRYADFEAAIAEANNTQYGLAAGLLSDSEARYQQFW 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
           LESRAGIVNWNKQLTGAAS+APFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLP+ 
Sbjct: 421 LESRAGIVNWNKQLTGAASTAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPAT 480

Query: 481 LTPGVKM 487
           LTPG+ +
Sbjct: 481 LTPGITL 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: 875
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: 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 GFF4235 PS417_21695 (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.5371.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.9e-257  839.6   1.4   4.4e-257  839.4   1.4    1.0  1  lcl|FitnessBrowser__WCS417:GFF4235  PS417_21695 succinylglutamate-se


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4235  PS417_21695 succinylglutamate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  839.4   1.4  4.4e-257  4.4e-257       1     483 [.       4     486 ..       4     487 .. 1.00

  Alignments for each domain:
  == domain 1  score: 839.4 bits;  conditional E-value: 4.4e-257
                           TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeeke 75 
                                         l+i G+w aGqGe +es++pvtq+vlw g++a+a+qve+av+aar+afpawa+++leeri+v+++fa+ l+++++
  lcl|FitnessBrowser__WCS417:GFF4235   4 LYIAGSWLAGQGELFESRNPVTQQVLWAGNGATAEQVESAVQAARQAFPAWAKRPLEERISVLETFAATLKRRAD 78 
                                         59************************************************************************* PP

                           TIGR03240  76 elaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpn 150
                                         ++a++i++etgkplwe++tev+sm++k+ais+++y+ertGek+ +l+da+avlrh+phGv+avfGpynfpGhlpn
  lcl|FitnessBrowser__WCS417:GFF4235  79 DIARCIGEETGKPLWESATEVTSMANKIAISVQSYRERTGEKSGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPN 153
                                         *************************************************************************** PP

                           TIGR03240 151 GhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGal 225
                                         GhivpallaGntv+fkpseltp+vae tv++w +aGlpaGvlnl+qGaretG alaa+++idGl+ftGss+tG++
  lcl|FitnessBrowser__WCS417:GFF4235 154 GHIVPALLAGNTVLFKPSELTPKVAELTVQCWVEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNH 228
                                         *************************************************************************** PP

                           TIGR03240 226 lhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlveva 300
                                         lh+q++grp+kilale+GGnnplvv+ev+d+daav++i+qsafisaGqrctcarrllv++ga+Gdall+rlv+v+
  lcl|FitnessBrowser__WCS417:GFF4235 229 LHQQFSGRPDKILALEMGGNNPLVVDEVADVDAAVYTIIQSAFISAGQRCTCARRLLVPEGAWGDALLARLVAVS 303
                                         *************************************************************************** PP

                           TIGR03240 301 erltvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyf 375
                                         ++++vg++d++p+pf+G+vis  aak+l++aqe +la+g+ +lle++q + +aalltpgiidvt+v+e+ dee+f
  lcl|FitnessBrowser__WCS417:GFF4235 304 STIEVGAFDQQPAPFMGSVISLAAAKALMDAQELMLANGAVALLEMTQPQDQAALLTPGIIDVTGVTEREDEELF 378
                                         *************************************************************************** PP

                           TIGR03240 376 gpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhr 450
                                         gpll+v+ry+df++a+aeannt++GlaaGllsd++++y++f+le+raGivnwnk+ltGa+s+apfGG+GasGnhr
  lcl|FitnessBrowser__WCS417:GFF4235 379 GPLLQVIRYADFEAAIAEANNTQYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLTGAASTAPFGGVGASGNHR 453
                                         *************************************************************************** PP

                           TIGR03240 451 psayyaadycaypvasleadslalpatlspGlk 483
                                         +sayyaadycaypvasle+ sl+lpatl+pG++
  lcl|FitnessBrowser__WCS417:GFF4235 454 ASAYYAADYCAYPVASLETPSLVLPATLTPGIT 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: 00:00:00.01
# Mc/sec: 12.42
//
[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