Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate PP_4478 PP_4478 N-succinylglutamate 5-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >FitnessBrowser__Putida:PP_4478 Length = 487 Score = 814 bits (2102), Expect = 0.0 Identities = 406/487 (83%), Positives = 437/487 (89%) Query: 1 MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60 M + YIAG W AG GE +SLNPVTQ V+W G GA A QV++AVQAARQAFP WA+ +LE Sbjct: 1 MTTHYIAGNWQAGQGETLQSLNPVTQAVIWQGQGADASQVDAAVQAARQAFPAWAQLSLE 60 Query: 61 ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120 RI VLE FAA LK HA+ +A IGEETGKPLWE+ATEVTSM+NK+AISVQSYRERTGEK Sbjct: 61 ARIDVLEKFAAQLKVHAEAMAQCIGEETGKPLWESATEVTSMINKVAISVQSYRERTGEK 120 Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180 SGPL DATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGN V+FKPSELTPKVAEL Sbjct: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAEL 180 Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240 TV CWI AGLPAGVLNL+QGARETG+ALAANPGIDGLFFTGSSRTGN LHQQFAGRPDKI Sbjct: 181 TVNCWIAAGLPAGVLNLVQGARETGVALAANPGIDGLFFTGSSRTGNLLHQQFAGRPDKI 240 Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300 LALEMGGNNPLVVD+V DLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGD+L+ARLV Sbjct: 241 LALEMGGNNPLVVDEVKDLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALIARLV 300 Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360 V T++VGAFD+QPAPFMGSV+SL AA+AL+ AQ L A G V LLEMTQPQA +ALLT Sbjct: 301 EVCKTITVGAFDEQPAPFMGSVISLQAARALLAAQVELAAKGGVKLLEMTQPQADAALLT 360 Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420 PGI+DV+AVADRPDEE FGPLLQVIRYADF+AAI EAN+T YGLAAGLLSDS ARYQ FW Sbjct: 361 PGIVDVTAVADRPDEEFFGPLLQVIRYADFDAAIDEANNTQYGLAAGLLSDSRARYQYFW 420 Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480 L SRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLET SL LP+ Sbjct: 421 LRSRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETASLALPAT 480 Query: 481 LTPGVKM 487 LTPGV + Sbjct: 481 LTPGVTL 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: 802 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: 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 PP_4478 PP_4478 (N-succinylglutamate 5-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.9610.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-266 870.3 4.0 2.1e-266 870.1 4.0 1.0 1 lcl|FitnessBrowser__Putida:PP_4478 PP_4478 N-succinylglutamate 5-se Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4478 PP_4478 N-succinylglutamate 5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 870.1 4.0 2.1e-266 2.1e-266 1 483 [. 4 486 .. 4 487 .] 1.00 Alignments for each domain: == domain 1 score: 870.1 bits; conditional E-value: 2.1e-266 TIGR03240 1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeeke 75 ++i G+w+aGqGe+l+sl+pvtq+v+wqg++a+a+qv++av+aar+afpawa+lsle+ri+v+++fa++l+ ++e lcl|FitnessBrowser__Putida:PP_4478 4 HYIAGNWQAGQGETLQSLNPVTQAVIWQGQGADASQVDAAVQAARQAFPAWAQLSLEARIDVLEKFAAQLKVHAE 78 69************************************************************************* PP TIGR03240 76 elaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpn 150 ++a++i++etgkplwe++tev+sm++kvais+++y+ertGek+ +lada+avlrh+phGv+avfGpynfpGhlpn lcl|FitnessBrowser__Putida:PP_4478 79 AMAQCIGEETGKPLWESATEVTSMINKVAISVQSYRERTGEKSGPLADATAVLRHKPHGVVAVFGPYNFPGHLPN 153 *************************************************************************** PP TIGR03240 151 GhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGal 225 GhivpallaGn+vvfkpseltp+vae tv++w +aGlpaGvlnlvqGaretG+alaa+++idGl+ftGss+tG+l lcl|FitnessBrowser__Putida:PP_4478 154 GHIVPALLAGNCVVFKPSELTPKVAELTVNCWIAAGLPAGVLNLVQGARETGVALAANPGIDGLFFTGSSRTGNL 228 *************************************************************************** PP TIGR03240 226 lhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlveva 300 lh+q+agrp+kilale+GGnnplvv+evkd+daav++i+qsafisaGqrctcarrllv++ga+Gdal++rlvev+ lcl|FitnessBrowser__Putida:PP_4478 229 LHQQFAGRPDKILALEMGGNNPLVVDEVKDLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALIARLVEVC 303 *************************************************************************** PP TIGR03240 301 erltvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyf 375 +++tvg++d++p+pf+G+vis +aa++llaaq +l+a+gg +lle++q +++aalltpgi+dvt+va++pdee+f lcl|FitnessBrowser__Putida:PP_4478 304 KTITVGAFDEQPAPFMGSVISLQAARALLAAQVELAAKGGVKLLEMTQPQADAALLTPGIVDVTAVADRPDEEFF 378 *************************************************************************** PP TIGR03240 376 gpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhr 450 gpll+v+ry+dfd+a++eannt++GlaaGllsd+r++y++f+l++raGivnwnk+ltGa+s+apfGG+GasGnhr lcl|FitnessBrowser__Putida:PP_4478 379 GPLLQVIRYADFDAAIDEANNTQYGLAAGLLSDSRARYQYFWLRSRAGIVNWNKQLTGAASSAPFGGVGASGNHR 453 *************************************************************************** PP TIGR03240 451 psayyaadycaypvasleadslalpatlspGlk 483 +sayyaadycaypvasle++slalpatl+pG++ lcl|FitnessBrowser__Putida:PP_4478 454 ASAYYAADYCAYPVASLETASLALPATLTPGVT 486 *******************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.87 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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