Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BWI76_RS11680 BWI76_RS11680 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__Koxy:BWI76_RS11680 Length = 492 Score = 784 bits (2024), Expect = 0.0 Identities = 384/489 (78%), Positives = 424/489 (86%) Query: 1 MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60 M+LWINGDW +G+G +R K NPVS +LWQGNDADA QV A AARAAFP WAR FA Sbjct: 1 MSLWINGDWQSGRGPARSKHNPVSQTLLWQGNDADADQVALAVSAARAAFPAWARQPFAA 60 Query: 61 RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120 R A+ E+FA+LLE+NK+ELTA+IARETGKPRWEAATE+TAMINKIAIS+ AYH RTGE + Sbjct: 61 RKAIAEKFASLLEANKSELTAVIARETGKPRWEAATEITAMINKIAISVNAYHSRTGEAQ 120 Query: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180 + M DG A+LRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNT++FKPSELTP SGEAV Sbjct: 121 TAMADGEATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPQSGEAV 180 Query: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240 ++LW +AGLPPGVLNL+QGGRETG+ALS D+DGLLFTGS+ TG+QLHRQL+GQPEKIL Sbjct: 181 VKLWAEAGLPPGVLNLLQGGRETGEALSGQADIDGLLFTGSSATGFQLHRQLAGQPEKIL 240 Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300 ALEMGGNNPLI+D+ DIDAAVHLTIQSAF+TAGQRCTCARRLL+K G GDAFL RLV Sbjct: 241 ALEMGGNNPLIVDDPQDIDAAVHLTIQSAFITAGQRCTCARRLLVKRGEAGDAFLQRLVT 300 Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360 VSQ L P WD EPQPFIGGLIS QAAQ+V AW A GG+ LL PRLLQAGTSLLTP Sbjct: 301 VSQTLIPAAWDAEPQPFIGGLISAQAAQKVHQAWLAHVASGGKTLLEPRLLQAGTSLLTP 360 Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420 GIIEM+ VA V DEEVFGPLL VWRYD FDEAI +AN TRFGLSCGL+S ER+KFDQLLL Sbjct: 361 GIIEMSAVAQVADEEVFGPLLCVWRYDHFDEAIALANATRFGLSCGLISAERDKFDQLLL 420 Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480 EARAGIVNWNKPLTGAASTAPFGG GASGNHRP AWYAADYCAWPMASLES L+LPATL Sbjct: 421 EARAGIVNWNKPLTGAASTAPFGGTGASGNHRPGAWYAADYCAWPMASLESPELSLPATL 480 Query: 481 NPGLDFSDE 489 +PGL+F E Sbjct: 481 SPGLNFRQE 489 Lambda K H 0.318 0.134 0.412 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: 949 Number of extensions: 38 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: 492 Length of database: 492 Length adjustment: 34 Effective length of query: 458 Effective length of database: 458 Effective search space: 209764 Effective search space used: 209764 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 BWI76_RS11680 BWI76_RS11680 (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.13497.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-248 810.2 0.8 3.5e-248 810.0 0.8 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS11680 BWI76_RS11680 succinylglutamate- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS11680 BWI76_RS11680 succinylglutamate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 810.0 0.8 3.5e-248 3.5e-248 1 484 [] 3 486 .. 3 486 .. 1.00 Alignments for each domain: == domain 1 score: 810.0 bits; conditional E-value: 3.5e-248 TIGR03240 1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelle 71 l+i+G+w++G+G + ++++pv+q lwqg++a+a+qv+ av aar+afpawar ++++r a+ ++fa+lle lcl|FitnessBrowser__Koxy:BWI76_RS11680 3 LWINGDWQSGRGPARSKHNPVSQTLLWQGNDADADQVALAVSAARAAFPAWARQPFAARKAIAEKFASLLE 73 59********************************************************************* PP TIGR03240 72 eekeelaeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpy 142 +k+el++via+etgkp+wea+te+++m++k+ais++ay++rtGe ++++ad++a lrhrphGvlavfGpy lcl|FitnessBrowser__Koxy:BWI76_RS11680 74 ANKSELTAVIARETGKPRWEAATEITAMINKIAISVNAYHSRTGEAQTAMADGEATLRHRPHGVLAVFGPY 144 *********************************************************************** PP TIGR03240 143 nfpGhlpnGhivpallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidG 213 nfpGhlpnGhivpallaGntvvfkpseltp+++e++vklw++aGlp Gvlnl+qG+retG+al+ + didG lcl|FitnessBrowser__Koxy:BWI76_RS11680 145 NFPGHLPNGHIVPALLAGNTVVFKPSELTPQSGEAVVKLWAEAGLPPGVLNLLQGGRETGEALSGQADIDG 215 *********************************************************************** PP TIGR03240 214 llftGssntGallhrqlagrpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvk 284 llftGss+tG++lhrqlag+pekilale+GGnnpl+v++ +didaavhl++qsafi+aGqrctcarrllvk lcl|FitnessBrowser__Koxy:BWI76_RS11680 216 LLFTGSSATGFQLHRQLAGQPEKILALEMGGNNPLIVDDPQDIDAAVHLTIQSAFITAGQRCTCARRLLVK 286 *********************************************************************** PP TIGR03240 285 dgaeGdallerlvevaerltvgkydaepqpflGavisekaakellaaqekllalggksllelkqleeeaal 355 +g+ Gda+l+rlv v+++l ++daepqpf+G++is++aa+++ +a+ +a ggk+lle + l+++++l lcl|FitnessBrowser__Koxy:BWI76_RS11680 287 RGEAGDAFLQRLVTVSQTLIPAAWDAEPQPFIGGLISAQAAQKVHQAWLAHVASGGKTLLEPRLLQAGTSL 357 *********************************************************************** PP TIGR03240 356 ltpgiidvtevaevpdeeyfgpllkvlrykdfdealaeanntrfGlaaGllsddrelydkflleiraGivn 426 ltpgii++++va+v dee+fgpll v+ry++fdea+a an+trfGl++Gl+s +r+++d++lle+raGivn lcl|FitnessBrowser__Koxy:BWI76_RS11680 358 LTPGIIEMSAVAQVADEEVFGPLLCVWRYDHFDEAIALANATRFGLSCGLISAERDKFDQLLLEARAGIVN 428 *********************************************************************** PP TIGR03240 427 wnkpltGassaapfGGiGasGnhrpsayyaadycaypvasleadslalpatlspGlkl 484 wnkpltGa+s+apfGG GasGnhrp a+yaadyca+p+asle+ +l+lpatlspGl++ lcl|FitnessBrowser__Koxy:BWI76_RS11680 429 WNKPLTGAASTAPFGGTGASGNHRPGAWYAADYCAWPMASLESPELSLPATLSPGLNF 486 *******************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (484 nodes) Target sequences: 1 (492 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: 00:00:00.02 # Mc/sec: 11.34 // [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