Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Ga0059261_4132 Ga0059261_4132 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
Query= SwissProt::Q8ZPV0 (492 letters) >FitnessBrowser__Korea:Ga0059261_4132 Length = 471 Score = 472 bits (1214), Expect = e-137 Identities = 247/457 (54%), Positives = 314/457 (68%), Gaps = 6/457 (1%) Query: 20 TNPVSAEILWQGNDANAAQVAEACQAARAAFPRWARQPFAARQAIVEKFAALLEAHKAEL 79 TNP + E LW+G A+A A A + AR AFP WA Q AR AI+ ++AA+L K L Sbjct: 8 TNPATGETLWEGPVASAEDCARAVERARTAFPAWAAQSPDARAAILTRYAAVLGERKDAL 67 Query: 80 TEVIARETGKPRWEAATEVTAMINKIAISIKAYHARTGAQKSELVDGAATLRHRPHGVLA 139 E IARETGKP WE ATEV +MI K+AISI+A AR G ++S + G A L HRPHGV+A Sbjct: 68 AEAIARETGKPLWETATEVASMIGKVAISIEAMAARAGTRESAMPFGRAVLAHRPHGVMA 127 Query: 140 VFGPYNFPGHLPNGHIVPALLAGNTLIFKPSELTPWTGETVIKLWERAGLPAGVLNLVQG 199 V GPYNFPGHLPNGHIVPALLAGNTL+FKPSE TP G+ +++ AG+P V L+QG Sbjct: 128 VLGPYNFPGHLPNGHIVPALLAGNTLVFKPSEETPLVGQLMVEALHAAGIPEDVAILLQG 187 Query: 200 GRETGQALSSLDDLDGLLFTGSASTGYQLHRQLSGQPEKILALEMGGNNPLIIEDAANID 259 GRETG AL S D+DGLLFTGSA G R + +P ILALE+GGNNPL+ D + Sbjct: 188 GRETGAALVS-QDIDGLLFTGSAGAGMHFRRSFAERPAVILALELGGNNPLVAWD-GEPE 245 Query: 260 AAVHLTLQSAFITAGQRCTCARRLLVKQGAQGDAFLARLVDVAGRLQPGRWDDDPQPFIG 319 A + + S FIT GQRC+CARRL+V +GA GDA + + ++ RL+ GRWD+ P+PF+G Sbjct: 246 AVASIVVASTFITTGQRCSCARRLIVPEGAAGDAIVDAVAALSDRLRIGRWDETPEPFMG 305 Query: 320 GLISAQAAQHVMEAWRQREALGGRTLLAPRKVKEGTS--LLTPGIIELTGVADVPDEEVF 377 L+S AA+ LG R + P EG S + P I+++TG+ +VPDEE+F Sbjct: 306 PLVSTGAAERAAAQVAALVGLGARE-IRPFGGVEGRSGAFVRPAILDVTGL-EVPDEEIF 363 Query: 378 GPLLNVWRYAHFDEAIRLANNTRFGLSCGLVSTDRAQFEQLLLEARAGIVNWNKPLTGAA 437 P+L V R A FD A+ AN TRFGL+ GL+S D A + + +ARAG+VN N+P TGAA Sbjct: 364 APVLQVRRVADFDAALAAANQTRFGLAAGLISDDDALWARFQAQARAGVVNRNRPTTGAA 423 Query: 438 STAPFGGVGASGNHRPSAWYAADYCAWPMASLESPEL 474 S+ PFGG+G SGNHRPSA+YAADYCA+P+ASLE+ + Sbjct: 424 SSMPFGGLGDSGNHRPSAYYAADYCAYPVASLEAERI 460 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: 711 Number of extensions: 32 Number of successful extensions: 4 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: 471 Length adjustment: 34 Effective length of query: 458 Effective length of database: 437 Effective search space: 200146 Effective search space used: 200146 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 Ga0059261_4132 Ga0059261_4132 (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.20552.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-203 663.2 3.3 1.5e-203 662.8 3.3 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_4132 Ga0059261_4132 succinylglutamic Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_4132 Ga0059261_4132 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 ! 662.8 3.3 1.5e-203 1.5e-203 15 475 .. 5 463 .. 2 470 .. 0.98 Alignments for each domain: == domain 1 score: 662.8 bits; conditional E-value: 1.5e-203 TIGR03240 15 lesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeelaeviak 83 ++s++p+t+e+lw+g asa++ ++av+ ar+afpawa+ s ++r+a+++r+a++l e+k++lae+ia+ lcl|FitnessBrowser__Korea:Ga0059261_4132 5 FASTNPATGETLWEGPVASAEDCARAVERARTAFPAWAAQSPDARAAILTRYAAVLGERKDALAEAIAR 73 789****************************************************************** PP TIGR03240 84 etgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGh 152 etgkplwe++tevasm++kvaisi+a + r+G++es+++ ++avl hrphGv+av+GpynfpGhlpnGh lcl|FitnessBrowser__Korea:Ga0059261_4132 74 ETGKPLWETATEVASMIGKVAISIEAMAARAGTRESAMPFGRAVLAHRPHGVMAVLGPYNFPGHLPNGH 142 ********************************************************************* PP TIGR03240 153 ivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssn 221 ivpallaGnt+vfkpse+tplv++ +v+++++aG+p+ v l+qG+retG al+++ didGllftGs+ lcl|FitnessBrowser__Korea:Ga0059261_4132 143 IVPALLAGNTLVFKPSEETPLVGQLMVEALHAAGIPEDVAILLQGGRETGAALVSQ-DIDGLLFTGSAG 210 ******************************************************98.9*********** PP TIGR03240 222 tGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGd 290 +G++++r +a+rp +ilalelGGnnplv ++ + +a++ +v s+fi++Gqrc+carrl+v++ga Gd lcl|FitnessBrowser__Korea:Ga0059261_4132 211 AGMHFRRSFAERPAVILALELGGNNPLVAWDG-EPEAVASIVVASTFITTGQRCSCARRLIVPEGAAGD 278 ****************************9996.589********************************* PP TIGR03240 291 allerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqlee.eaalltp 358 a+++++ ++++rl++g++d+ p+pf+G+++s+ aa++ a + l+ lg++++ + +e + a+++p lcl|FitnessBrowser__Korea:Ga0059261_4132 279 AIVDAVAALSDRLRIGRWDETPEPFMGPLVSTGAAERAAAQVAALVGLGAREIRPFGGVEGrSGAFVRP 347 *************************************999999***************9984568**** PP TIGR03240 359 giidvtevaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivnw 427 +i+dvt++ evpdee f+p+l+v r++dfd+ala+an+trfGlaaGl+sdd++l+ +f ++raG+vn lcl|FitnessBrowser__Korea:Ga0059261_4132 348 AILDVTGL-EVPDEEIFAPVLQVRRVADFDAALAAANQTRFGLAAGLISDDDALWARFQAQARAGVVNR 415 *******8.9*********************************************************** PP TIGR03240 428 nkpltGassaapfGGiGasGnhrpsayyaadycaypvasleadslalp 475 n+p+tGa+s++pfGG+G sGnhrpsayyaadycaypvaslea+++a lcl|FitnessBrowser__Korea:Ga0059261_4132 416 NRPTTGAASSMPFGGLGDSGNHRPSAYYAADYCAYPVASLEAERIADQ 463 *******************************************99865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (484 nodes) Target sequences: 1 (471 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: 00:00:00.02 # Mc/sec: 9.58 // [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