Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate CCNA_01679 CCNA_01679 succinylglutamic semialdehyde dehydrogenase
Query= SwissProt::Q8ZPV0 (492 letters) >FitnessBrowser__Caulo:CCNA_01679 Length = 485 Score = 472 bits (1214), Expect = e-137 Identities = 244/471 (51%), Positives = 323/471 (68%), Gaps = 7/471 (1%) Query: 3 LWINGDWITGQGERRRKTNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQ 62 L+I+G W GQG T+P + E +W A A VA+A AAR AFP WA +P R Sbjct: 5 LFIDGKWRAGQGAGLSSTDPATGEDVWSAATATPADVADAVAAARKAFPAWADRPREERI 64 Query: 63 AIVEKFAALLEAHKAELTEVIARETGKPRWEAATEVTAMINKIAISIKAYHARTGAQKSE 122 AI+ ++ +L A E ++RETGK WE E+ +M K+ +SI+AY RTG ++ Sbjct: 65 AILRRYKDILVERAAPYAEALSRETGKALWETRAELASMAGKVDLSIRAYDERTGVTENA 124 Query: 123 LVDGAATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVIK 182 + G A LRHR HGV+AV GP+NFPGHLPNGHIVPALLAG+T++FKPSE TP G+ +++ Sbjct: 125 MPFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLMVE 184 Query: 183 LWERAGLPAGVLNLVQGGRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPEKILAL 242 E AG PAGV+NLVQGGRETGQAL + D+DGLLFTGSA+ G R + +P+ ILAL Sbjct: 185 ALEAAGAPAGVVNLVQGGRETGQALIA-QDIDGLLFTGSAAAGTYFRRYFADRPDVILAL 243 Query: 243 EMGGNNPLIIEDAANI-DAAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLARLVDV 301 E+GGNNPL++ +A + +A L +QSAFIT GQRC+CARRL+V A G A + V + Sbjct: 244 ELGGNNPLVVWNADDAPEAVAALIVQSAFITTGQRCSCARRLIVPDDASGAAIIEATVAL 303 Query: 302 AGRLQPGRWDDDPQPFIGGLISAQAAQHVMEAWRQREALGGRTLLAPRKVKE-GTSLLTP 360 A RL G W+ + +PF+G LIS +AA+ E A G+T+LA V G + L P Sbjct: 304 AERLVIGAWNAENEPFMGPLISGRAAKAAREV---ASATPGKTILALDGVAGLGDAFLKP 360 Query: 361 GIIELTGVADVPDEEVFGPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFEQLLL 420 GI+++TG+ + PDEE+F PLL V R + FDEA+ AN TR+GLS GL+S + +++ L Sbjct: 361 GIVDVTGL-ETPDEELFAPLLQVRRVSSFDEALAAANATRYGLSAGLISNESELWDKFLS 419 Query: 421 EARAGIVNWNKPLTGAASTAPFGGVGASGNHRPSAWYAADYCAWPMASLES 471 RAG+VNWN+P TGAA + PFGG+GASGNHRPSA+YAADYCA+P+AS E+ Sbjct: 420 RIRAGVVNWNRPTTGAAGSMPFGGLGASGNHRPSAYYAADYCAYPVASFEA 470 Lambda K H 0.319 0.134 0.411 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: 739 Number of extensions: 30 Number of successful extensions: 5 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: 492 Length of database: 485 Length adjustment: 34 Effective length of query: 458 Effective length of database: 451 Effective search space: 206558 Effective search space used: 206558 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate CCNA_01679 CCNA_01679 (succinylglutamic 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.19847.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-235 766.1 2.0 8.3e-235 765.9 2.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_01679 CCNA_01679 succinylglutamic semi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_01679 CCNA_01679 succinylglutamic semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 765.9 2.0 8.3e-235 8.3e-235 1 483 [. 5 484 .. 5 485 .] 0.99 Alignments for each domain: == domain 1 score: 765.9 bits; conditional E-value: 8.3e-235 TIGR03240 1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleee 73 lfidGkwraGqG+ l+s+dp+t+e++w++++a+ a+v++av+aarkafpawa+++ eeria+++r++++l+e+ lcl|FitnessBrowser__Caulo:CCNA_01679 5 LFIDGKWRAGQGAGLSSTDPATGEDVWSAATATPADVADAVAAARKAFPAWADRPREERIAILRRYKDILVER 77 59*********************************************************************** PP TIGR03240 74 keelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpG 146 ++ +ae++++etgk+lwe+r+e+asm++kv++si+ay+ertG++e++++ ++avlrhr+hGv+av+Gp+nfpG lcl|FitnessBrowser__Caulo:CCNA_01679 78 AAPYAEALSRETGKALWETRAELASMAGKVDLSIRAYDERTGVTENAMPFGRAVLRHRAHGVMAVLGPFNFPG 150 ************************************************************************* PP TIGR03240 147 hlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGs 219 hlpnGhivpallaG+tvvfkpse+tpl+++ +v+++e+aG paGv+nlvqG+retG+al+a+ didGllftGs lcl|FitnessBrowser__Caulo:CCNA_01679 151 HLPNGHIVPALLAGDTVVFKPSEETPLAGQLMVEALEAAGAPAGVVNLVQGGRETGQALIAQ-DIDGLLFTGS 222 *************************************************************9.9********* PP TIGR03240 220 sntGallhrqlagrpekilalelGGnnplvveevkd.idaavhlivqsafisaGqrctcarrllvkdgaeGda 291 +++G++++r++a+rp++ilalelGGnnplvv++++d +a+++livqsafi++Gqrc+carrl+v+d+a+G+a lcl|FitnessBrowser__Caulo:CCNA_01679 223 AAAGTYFRRYFADRPDVILALELGGNNPLVVWNADDaPEAVAALIVQSAFITTGQRCSCARRLIVPDDASGAA 295 ************************************7799999****************************** PP TIGR03240 292 llerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqlee.eaalltpgiidv 363 ++e++v++aerl++g+++ae++pf+G++is +aak aa+e ++a++gk++l+l+ ++ ++a+l+pgi+dv lcl|FitnessBrowser__Caulo:CCNA_01679 296 IIEATVALAERLVIGAWNAENEPFMGPLISGRAAK---AAREVASATPGKTILALDGVAGlGDAFLKPGIVDV 365 ***********************************...9******************99879*********** PP TIGR03240 364 tevaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGass 436 t++ e+pdee+f+pll+v r+++fdeala+an+tr+Gl+aGl+s+++el+dkfl++iraG+vnwn+p+tGa++ lcl|FitnessBrowser__Caulo:CCNA_01679 366 TGL-ETPDEELFAPLLQVRRVSSFDEALAAANATRYGLSAGLISNESELWDKFLSRIRAGVVNWNRPTTGAAG 437 **8.9******************************************************************** PP TIGR03240 437 aapfGGiGasGnhrpsayyaadycaypvasleadslalpatlspGlk 483 ++pfGG+GasGnhrpsayyaadycaypvas+ea++++ + ++++Glk lcl|FitnessBrowser__Caulo:CCNA_01679 438 SMPFGGLGASGNHRPSAYYAADYCAYPVASFEASMVVDTLKDIKGLK 484 *********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (484 nodes) Target sequences: 1 (485 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: 12.37 // [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