Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 6938906 Sama_3009 succinylglutamic semialdehyde dehydrogenase (RefSeq)
Query= reanno::SB2B:6938906 (486 letters) >FitnessBrowser__SB2B:6938906 Length = 486 Score = 968 bits (2502), Expect = 0.0 Identities = 486/486 (100%), Positives = 486/486 (100%) Query: 1 MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG 60 MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG Sbjct: 1 MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG 60 Query: 61 RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV 120 RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV Sbjct: 61 RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV 120 Query: 121 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM Sbjct: 121 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180 Query: 181 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL Sbjct: 181 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240 Query: 241 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE 300 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE Sbjct: 241 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE 300 Query: 301 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP 360 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP Sbjct: 301 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP 360 Query: 361 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA 420 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA Sbjct: 361 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA 420 Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL 480 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL 480 Query: 481 SPGLTL 486 SPGLTL Sbjct: 481 SPGLTL 486 Lambda K H 0.317 0.133 0.393 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: 969 Number of extensions: 21 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: 486 Length of database: 486 Length adjustment: 34 Effective length of query: 452 Effective length of database: 452 Effective search space: 204304 Effective search space used: 204304 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 6938906 Sama_3009 (succinylglutamic semialdehyde dehydrogenase (RefSeq))
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.6850.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-248 810.7 1.6 2.4e-248 810.6 1.6 1.0 1 lcl|FitnessBrowser__SB2B:6938906 Sama_3009 succinylglutamic semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938906 Sama_3009 succinylglutamic semialdehyde dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 810.6 1.6 2.4e-248 2.4e-248 1 483 [. 3 485 .. 3 486 .] 1.00 Alignments for each domain: == domain 1 score: 810.6 bits; conditional E-value: 2.4e-248 TIGR03240 1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeel 77 +fi+G+w aG+G++++s++p+++ev+wqgkaa aqv++av aar+a +w l +e r+a+v+ + + le +k+el lcl|FitnessBrowser__SB2B:6938906 3 QFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQAIVEAYRNELEANKAEL 79 69*************************************************************************** PP TIGR03240 78 aeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhiv 154 aevia+etgkp+we++te a+m++k+ +s+ ay++rtG++ +e a+++avlrh+phGv+avfGpynfpGhlpnGhiv lcl|FitnessBrowser__SB2B:6938906 80 AEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIV 156 ***************************************************************************** PP TIGR03240 155 pallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqla 231 pallaGntvvfkpseltp+vae ++klwekaGlpaGv+nlvqG++etGkala+++++dGl+ftGss+tG+llh+q+a lcl|FitnessBrowser__SB2B:6938906 157 PALLAGNTVVFKPSELTPKVAELMLKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYA 233 ***************************************************************************** PP TIGR03240 232 grpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgky 308 g+p kilale+GGnnpl+v+ v+d+ aa+h+i+qsafis+Gqrctcarrl v++gaeGd+ll+ lve ++++vg + lcl|FitnessBrowser__SB2B:6938906 234 GHPGKILALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAVKAIKVGPW 310 ***************************************************************************** PP TIGR03240 309 daepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlryk 385 +a+pqpf+G++ise aak +l+aq++ll+lg+ksl+e+++l+++++l++pg+idvtev e+pdeeyfgpll+v+ry+ lcl|FitnessBrowser__SB2B:6938906 311 NADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSPGLIDVTEVIELPDEEYFGPLLQVVRYT 387 ***************************************************************************** PP TIGR03240 386 dfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycay 462 +fdea++ an+tr+Gl+aG+l+dd++ y++fl +iraGivnwnk++tGas+aapfGG+GasGnhr+sa+yaadycay lcl|FitnessBrowser__SB2B:6938906 388 SFDEAIRLANDTRYGLSAGILADDKADYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAY 464 ***************************************************************************** PP TIGR03240 463 pvasleadslalpatlspGlk 483 pvas+eads++lpa+lspGl+ lcl|FitnessBrowser__SB2B:6938906 465 PVASMEADSVTLPASLSPGLT 485 *******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (484 nodes) Target sequences: 1 (486 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: 6.33 // [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