Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate Pf1N1B4_3444 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 Length = 488 Score = 926 bits (2393), Expect = 0.0 Identities = 465/487 (95%), Positives = 477/487 (97%) Query: 1 MKSLYIAGEWLAGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLE 60 M SLYIAGEWLAG GE+F+S+NPVTQQVLW+G GAT GQVESAVQAARQAFP WARRTLE Sbjct: 1 MNSLYIAGEWLAGQGESFQSVNPVTQQVLWAGEGATTGQVESAVQAARQAFPGWARRTLE 60 Query: 61 ERISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120 ERI VLEAFAAALKNHADELA TIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK Sbjct: 61 ERIGVLEAFAAALKNHADELARTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK 120 Query: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL Sbjct: 121 SGPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAEL 180 Query: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKI 240 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLH+QF+GRPDKI Sbjct: 181 TVKCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHKQFSGRPDKI 240 Query: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLV 300 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGD+LLARLV Sbjct: 241 LALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDTLLARLV 300 Query: 301 AVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLT 360 AVSST+ VGAFDQQPAPFMGSV+SLGAAKALMDAQEHLLANGAVALLEMTQPQAQ+ALLT Sbjct: 301 AVSSTIEVGAFDQQPAPFMGSVISLGAAKALMDAQEHLLANGAVALLEMTQPQAQAALLT 360 Query: 361 PGILDVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420 PGILDV+AVADRPDEELFGPLLQVIRYADFEAAIAEANDT YGLAAGLLSDSEARYQQFW Sbjct: 361 PGILDVTAVADRPDEELFGPLLQVIRYADFEAAIAEANDTDYGLAAGLLSDSEARYQQFW 420 Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPSA 480 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLP+ Sbjct: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPAT 480 Query: 481 LTPGVKM 487 LTPGVKM Sbjct: 481 LTPGVKM 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: 934 Number of extensions: 23 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 Pf1N1B4_3444 (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.12042.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-257 841.5 1.7 1.1e-257 841.3 1.7 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 Succinylglutamic semialdehyde de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 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 ! 841.3 1.7 1.1e-257 1.1e-257 1 484 [] 4 487 .. 4 487 .. 1.00 Alignments for each domain: == domain 1 score: 841.3 bits; conditional E-value: 1.1e-257 TIGR03240 1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvk 64 l+i G+w aGqGes++s++pvtq+vlw g++a++ qve+av+aar+afp war++leeri v++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 4 LYIAGEWLAGQGESFQSVNPVTQQVLWAGEGATTGQVESAVQAARQAFPGWARRTLEERIGVLE 67 59************************************************************** PP TIGR03240 65 rfaelleeekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavl 128 fa+ l+++++ela++i++etgkplwea+tev+smv+k+ais+++y+ertGek+ +l+da+avl lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 68 AFAAALKNHADELARTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEKSGPLGDATAVL 131 **************************************************************** PP TIGR03240 129 rhrphGvlavfGpynfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvl 192 rh+phGv+avfGpynfpGhlpnGhivpallaGn+v+fkpseltp+vae tvk+w +aGlpaGvl lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 132 RHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWIEAGLPAGVL 195 **************************************************************** PP TIGR03240 193 nlvqGaretGkalaaeedidGllftGssntGallhrqlagrpekilalelGGnnplvveevkdi 256 nl+qGaretG alaa+++idGl+ftGss+tG++lh+q++grp+kilale+GGnnplvv++v+d+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 196 NLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHKQFSGRPDKILALEMGGNNPLVVDQVADL 259 **************************************************************** PP TIGR03240 257 daavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgkydaepqpflGavi 320 daav++i+qsafisaGqrctcarrllv++ga+Gd+ll+rlv+v+++++vg++d++p+pf+G+vi lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 260 DAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDTLLARLVAVSSTIEVGAFDQQPAPFMGSVI 323 **************************************************************** PP TIGR03240 321 sekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlry 384 s aak+l++aqe+lla+g+ +lle++q +++aalltpgi+dvt+va++pdee+fgpll+v+ry lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 324 SLGAAKALMDAQEHLLANGAVALLEMTQPQAQAALLTPGILDVTAVADRPDEELFGPLLQVIRY 387 **************************************************************** PP TIGR03240 385 kdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGn 448 +df++a+aean+t +GlaaGllsd++++y++f+le+raGivnwnk+ltGa+s+apfGG+GasGn lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 388 ADFEAAIAEANDTDYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLTGAASSAPFGGVGASGN 451 **************************************************************** PP TIGR03240 449 hrpsayyaadycaypvasleadslalpatlspGlkl 484 hr+sayyaadycaypvasle+ sl+lpatl+pG+k+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 452 HRASAYYAADYCAYPVASLETPSLVLPATLTPGVKM 487 *********************************985 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: 00:00:00.03 # Mc/sec: 7.84 // [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