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) >FitnessBrowser__BFirm:BPHYT_RS07710 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.8222.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 10.40 // [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