GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Burkholderia phytofirmans PsJN

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate BPHYT_RS07710 BPHYT_RS07710 succinylglutamate-semialdehyde dehydrogenase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS07710 BPHYT_RS07710
           succinylglutamate-semialdehyde dehydrogenase
          Length = 487

 Score =  592 bits (1527), Expect = e-174
 Identities = 292/486 (60%), Positives = 362/486 (74%)

Query: 1   MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60
           M  L+I GEW AG G AF S NP T   +W G  A+A  V+ AV++AR+AFP W+  +L+
Sbjct: 1   MSELFIDGEWAAGTGPAFASHNPGTGAAVWEGNSASADDVDRAVRSARRAFPAWSALSLD 60

Query: 61  ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120
           ER  V+  FAA +    + LA  IG ETGKPLWEA TE  SM  K+ IS+Q+Y ERTGEK
Sbjct: 61  ERCGVVRRFAALVTERKEALAEAIGRETGKPLWEARTEAASMAAKVEISIQAYNERTGEK 120

Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180
              + D TAVLRH+PHGVVAVFGPYNFPGHLPNGHIVPAL+AGN+V+FKPSEL P VA L
Sbjct: 121 RSAMADGTAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNAVVFKPSELAPGVAAL 180

Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240
           TV+ W +AGLP GVLNL+QG ++TGIALA +  IDGLFFTGSS TG  LH+QF GRP+ +
Sbjct: 181 TVQIWRDAGLPTGVLNLVQGEKDTGIALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIV 240

Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300
           LALEMGGNNPLV+  VAD+DAAV+  IQSAF+SAGQRCTCARR+ VP  A GD  + R  
Sbjct: 241 LALEMGGNNPLVIGPVADVDAAVHHTIQSAFLSAGQRCTCARRIFVPNDAGGDRFMERFT 300

Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360
            V+S ++VG ++  P PFMG+V+S  AA  L+ AQE LLA+GA ALL+M Q   +   +T
Sbjct: 301 EVTSRITVGEYNADPQPFMGAVISARAASRLVAAQERLLADGAKALLKMEQRDPKLGFVT 360

Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
           P ILDV+ V + PDEE FGPL Q+IRY  F  A+ +ANDT +GL+AGLL+D EA +  F 
Sbjct: 361 PAILDVTNVKNLPDEEHFGPLAQIIRYGSFNEALEQANDTEFGLSAGLLADDEALWTHFQ 420

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480
              RAGIVNWN+   GA+S APFGG G SGNHR SAYYAADYCA+P+AS+E+  L +P++
Sbjct: 421 RTIRAGIVNWNRPTNGASSGAPFGGPGRSGNHRPSAYYAADYCAFPMASVESAQLQMPAS 480

Query: 481 LTPGVK 486
           ++PG++
Sbjct: 481 VSPGLQ 486


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: 730
Number of extensions: 31
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 BPHYT_RS07710 BPHYT_RS07710 (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.3651.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.8e-254  830.8   0.6     2e-254  830.6   0.6    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07710  BPHYT_RS07710 succinylglutamate-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07710  BPHYT_RS07710 succinylglutamate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  830.6   0.6    2e-254    2e-254       1     484 []       4     487 .]       4     487 .] 1.00

  Alignments for each domain:
  == domain 1  score: 830.6 bits;  conditional E-value: 2e-254
                                TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaell 70 
                                              lfidG+w aG+G +++s++p t++++w+g++asa++v++av++ar+afpaw++lsl+er+ vv+rfa+l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07710   4 LFIDGEWAAGTGPAFASHNPGTGAAVWEGNSASADDVDRAVRSARRAFPAWSALSLDERCGVVRRFAALV 73 
                                              59******************************************************************** PP

                                TIGR03240  71 eeekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfG 140
                                              +e+ke+lae+i++etgkplwearte asm+akv+isi+ay+ertGek+s++ad++avlrhrphGv+avfG
  lcl|FitnessBrowser__BFirm:BPHYT_RS07710  74 TERKEALAEAIGRETGKPLWEARTEAASMAAKVEISIQAYNERTGEKRSAMADGTAVLRHRPHGVVAVFG 143
                                              ********************************************************************** PP

                                TIGR03240 141 pynfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeed 210
                                              pynfpGhlpnGhivpal+aGn+vvfkpsel+p va  tv++w++aGlp+GvlnlvqG+++tG ala++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07710 144 PYNFPGHLPNGHIVPALIAGNAVVFKPSELAPGVAALTVQIWRDAGLPTGVLNLVQGEKDTGIALANHRQ 213
                                              ********************************************************************** PP

                                TIGR03240 211 idGllftGssntGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarr 280
                                              idGl+ftGss+tG+llh+q++grpe++lale+GGnnplv+  v+d+daavh+++qsaf+saGqrctcarr
  lcl|FitnessBrowser__BFirm:BPHYT_RS07710 214 IDGLFFTGSSDTGTLLHKQFGGRPEIVLALEMGGNNPLVIGPVADVDAAVHHTIQSAFLSAGQRCTCARR 283
                                              ********************************************************************** PP

                                TIGR03240 281 llvkdgaeGdallerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqle 350
                                              ++v+++a Gd+++er++ev++r+tvg+y+a+pqpf+Gavis++aa++l+aaqe+lla g+k+ll+++q +
  lcl|FitnessBrowser__BFirm:BPHYT_RS07710 284 IFVPNDAGGDRFMERFTEVTSRITVGEYNADPQPFMGAVISARAASRLVAAQERLLADGAKALLKMEQRD 353
                                              ********************************************************************** PP

                                TIGR03240 351 eeaalltpgiidvtevaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkfllei 420
                                               + +++tp+i+dvt+v+++pdee+fgpl +++ry +f+eal++an+t+fGl+aGll+dd++l+ +f ++i
  lcl|FitnessBrowser__BFirm:BPHYT_RS07710 354 PKLGFVTPAILDVTNVKNLPDEEHFGPLAQIIRYGSFNEALEQANDTEFGLSAGLLADDEALWTHFQRTI 423
                                              ********************************************************************** PP

                                TIGR03240 421 raGivnwnkpltGassaapfGGiGasGnhrpsayyaadycaypvasleadslalpatlspGlkl 484
                                              raGivnwn+p++Gass apfGG G+sGnhrpsayyaadyca+p+as+e+++l++pa++spGl++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07710 424 RAGIVNWNRPTNGASSGAPFGGPGRSGNHRPSAYYAADYCAFPMASVESAQLQMPASVSPGLQF 487
                                              **************************************************************87 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: 00:00:00.02
# Mc/sec: 8.99
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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