Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_013706340.1 DESAC_RS06840 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_000195295.1:WP_013706340.1 Length = 418 Score = 365 bits (936), Expect = e-105 Identities = 194/411 (47%), Positives = 260/411 (63%) Query: 10 VEAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEA 69 V+ A EAK A++SL +L KN AL +A LE+ E I N+KD+ ++Q + A Sbjct: 7 VKHMAQEAKAAARSLAVLPTAVKNQALAGLAQSLEQHRELIQEENQKDIVEAKKQNYPAA 66 Query: 70 FMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEA 129 F+DRL+LS + ++ QGL DV L DP G S W NGL V + +PLGVIG IYE+ Sbjct: 67 FIDRLTLSDKVLKSMVQGLHDVIHLPDPVGAVTSMWRRPNGLLVGRQRIPLGVIGFIYES 126 Query: 130 RPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDR 189 RPNVTVDA L LKSGNA++LKGG AI SN A+ ++ +AL+E P +VQ I +T+R Sbjct: 127 RPNVTVDAGALCLKSGNAVILKGGKEAIRSNLALSRLMAQALSEVGAPAAAVQVIPTTER 186 Query: 190 AATNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISI 249 A +L + E +D++IPRGG LI+ V EN+ +PVL+ G CHI +D DAD+E A +I Sbjct: 187 EAVVELLKLDELIDIVIPRGGEGLIRFVAENSRIPVLKHYKGVCHILVDADADLEMAETI 246 Query: 250 LVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAG 309 NAK RP VCNA ETL++H+D + + + ++ + + G + P PA Sbjct: 247 CFNAKVQRPGVCNAMETLLIHQDVARRFIPRMFARFREAGVELRGCPETCALDPQVKPAV 306 Query: 310 EDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIY 369 DW E+ +AVK V DL A+ HI YG+ H+EAIVT+N A +FL VD++ + Sbjct: 307 ATDWGYEFSDLILAVKVVPDLEAALDHIARYGSYHTEAIVTQNYGHAQRFLNEVDSSVVL 366 Query: 370 HNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 NASTRF DGG LG GAEIGI+T KLHA GPM L LTT KF++ G+GQIR Sbjct: 367 VNASTRFNDGGELGLGAEIGINTSKLHAFGPMSLEELTTTKFIVYGSGQIR 417 Lambda K H 0.315 0.131 0.365 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: 451 Number of extensions: 23 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: 420 Length of database: 418 Length adjustment: 32 Effective length of query: 388 Effective length of database: 386 Effective search space: 149768 Effective search space used: 149768 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: 42 (22.0 bits) S2: 50 (23.9 bits)
Align candidate WP_013706340.1 DESAC_RS06840 (glutamate-5-semialdehyde dehydrogenase)
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))
# 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.aa/TIGR00407.hmm # target sequence database: /tmp/gapView.24345.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00407 [M=398] Accession: TIGR00407 Description: proA: glutamate-5-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-149 482.7 0.0 4.5e-149 482.5 0.0 1.0 1 lcl|NCBI__GCF_000195295.1:WP_013706340.1 DESAC_RS06840 glutamate-5-semial Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195295.1:WP_013706340.1 DESAC_RS06840 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.5 0.0 4.5e-149 4.5e-149 1 398 [] 14 407 .. 14 407 .. 0.99 Alignments for each domain: == domain 1 score: 482.5 bits; conditional E-value: 4.5e-149 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 ak aa la l ta kn+al+ +a++L+++ eli ++n+kdi++ak++ a++drL+L+++ lks++ lcl|NCBI__GCF_000195295.1:WP_013706340.1 14 AKAAARSLAVLPTAVKNQALAGLAQSLEQHRELIQEENQKDIVEAKKQNYPAAFIDRLTLSDKVLKSMV 82 899****************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 ++++dvi+L+dPvG v++ ++ +GL + r r+PlGv+g iye+rP+v+vd+ +Lclk+GnaviLkGgk lcl|NCBI__GCF_000195295.1:WP_013706340.1 83 QGLHDVIHLPDPVGAVTSMWRRPNGLLVGRQRIPLGVIGFIYESRPNVTVDAGALCLKSGNAVILKGGK 151 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 ea+rsn al +++ +al + g p+ avq+i +++re v ellklde +d++iPrGg++l++ + e+s+i lcl|NCBI__GCF_000195295.1:WP_013706340.1 152 EAIRSNLALSRLMAQALSEVGAPAAAVQVIPTTEREAVVELLKLDELIDIVIPRGGEGLIRFVAENSRI 220 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pvl+h +GvChi +d++adl++a+++ +ak qrP +Cna+etLL+++++a++f++++ + e+gvel lcl|NCBI__GCF_000195295.1:WP_013706340.1 221 PVLKHYKGVCHILVDADADLEMAETICFNAKVQRPGVCNAMETLLIHQDVARRFIPRMFARFREAGVEL 289 ********************************************************************* PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+ +++l ++ k ++d+ ef++l+L+vk+v dle+a++hi +yg+ h++ai+t++ a+ lcl|NCBI__GCF_000195295.1:WP_013706340.1 290 RGCPETCALDPQVKPA----VATDWGYEFSDLILAVKVVPDLEAALDHIARYGSYHTEAIVTQNYGHAQ 354 *********9988443....3589********************************************* PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f++evds+ v vnastrf dG++ G+Gae+gi t+klha GP+ Le L+++k lcl|NCBI__GCF_000195295.1:WP_013706340.1 355 RFLNEVDSSVVLVNASTRFNDGGELGLGAEIGINTSKLHAFGPMSLEELTTTK 407 **************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (418 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: 11.22 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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