Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_066918355.1 ACG33_RS02275 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_001579945.1:WP_066918355.1 Length = 427 Score = 356 bits (913), Expect = e-103 Identities = 184/412 (44%), Positives = 269/412 (65%), Gaps = 3/412 (0%) Query: 10 VEAQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEA 69 ++A A +A++ L S K+ AL A + + ILAAN DLR E+G + A Sbjct: 17 MDALGRAAVQAARLLARASSASKDAALLGAAAAVRAQRDDILAANALDLRQAGERGLSAA 76 Query: 70 FMDRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEA 129 +DRL+L +R+ A+G+ ++A L DP G ++ W NGL++ +V VPLGVIG+IYE+ Sbjct: 77 LLDRLALDDKRVEAMARGIEEIAALADPVGTVMASWERPNGLRIARVRVPLGVIGIIYES 136 Query: 130 RPNVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDR 189 RPNVT DA L LKSGNA++L+GGS + +S++AI + L E +P+ ++Q + +TDR Sbjct: 137 RPNVTADAGALCLKSGNAVILRGGSESSHSSRAIHACLVSGLREAGLPEAAIQRVPTTDR 196 Query: 190 AATNQLFT-MKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAIS 248 AA L + M +++DVL+PRGG L++ V A VPV+ GNCH+Y+D+DAD + A Sbjct: 197 AAVGLLLSGMTQYIDVLVPRGGRSLVERVQREARVPVIGHLEGNCHVYVDRDADADMARE 256 Query: 249 ILVNAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPA 308 +++NAK R +C AAET++ +D A + +++AL + V GDE V + V A Sbjct: 257 VVLNAKMRRTGICGAAETVLFDRDCPA--AAGVVAALLEAGCEVRGDEAVQALDARVVAA 314 Query: 309 GEDDWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAI 368 E DW EYL+ IA + VD + A+AHIE YG+ H+E+IVT N + A++FLA VD+A + Sbjct: 315 NEQDWMTEYLAPIIAARVVDTVEGAMAHIERYGSGHTESIVTGNPQTAERFLAGVDSAIV 374 Query: 369 YHNASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 HNAST+F DGG G GAEIGIST K HARGP+G+ LT+ K+++ G+GQ+R Sbjct: 375 LHNASTQFADGGEFGMGAEIGISTDKFHARGPVGVEQLTSYKYVVHGSGQLR 426 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: 440 Number of extensions: 20 Number of successful extensions: 3 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: 427 Length adjustment: 32 Effective length of query: 388 Effective length of database: 395 Effective search space: 153260 Effective search space used: 153260 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: 51 (24.3 bits)
Align candidate WP_066918355.1 ACG33_RS02275 (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.6378.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-135 438.0 0.3 1.8e-135 437.8 0.3 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066918355.1 ACG33_RS02275 glutamate-5-semial Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066918355.1 ACG33_RS02275 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.8 0.3 1.8e-135 1.8e-135 1 398 [] 24 416 .. 24 416 .. 0.98 Alignments for each domain: == domain 1 score: 437.8 bits; conditional E-value: 1.8e-135 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a +aa la s+a k+ al a +++a+ + ilaana d+ +a e Gl+ alldrL+L++++++ +a lcl|NCBI__GCF_001579945.1:WP_066918355.1 24 AVQAARLLARASSASKDAALLGAAAAVRAQRDDILAANALDLRQAGERGLSAALLDRLALDDKRVEAMA 92 5699***************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 ++++++ LadPvG v+ + e+ +GL++ rvrvPlGv+g+iye+rP+v++d+ +Lclk+GnaviL+Gg+ lcl|NCBI__GCF_001579945.1:WP_066918355.1 93 RGIEEIAALADPVGTVMASWERPNGLRIARVRVPLGVIGIIYESRPNVTADAGALCLKSGNAVILRGGS 161 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellk.ldeyvdlliPrGgnelvklikeest 206 e+ +s +a+ + + + l+++glp a+q + ++dr+ v ll+ + +y+d+l+PrGg++lv+ +++e++ lcl|NCBI__GCF_001579945.1:WP_066918355.1 162 ESSHSSRAIHACLVSGLREAGLPEAAIQRVPTTDRAAVGLLLSgMTQYIDVLVPRGGRSLVERVQREAR 230 ***************************************999549************************ PP TIGR00407 207 iPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgve 275 +Pv++h +G+Ch+y+d++ad +a++v+++ak +r C a et+L +++ ++ +l e+g e lcl|NCBI__GCF_001579945.1:WP_066918355.1 231 VPVIGHLEGNCHVYVDRDADADMAREVVLNAKMRRTGICGAAETVLFDRDCP--AAAGVVAALLEAGCE 297 *************************************************998..46778999******* PP TIGR00407 276 lradalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkkna 344 +r+d++v++l a+++++ ++d+ +e+l++++++++v+ +e a++hi++yg+ h+++i+t + ++a lcl|NCBI__GCF_001579945.1:WP_066918355.1 298 VRGDEAVQALD----ARVVAANEQDWMTEYLAPIIAARVVDTVEGAMAHIERYGSGHTESIVTGNPQTA 362 ******99885....456788899********************************************* PP TIGR00407 345 ekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 e+f+ vdsa v +nast+fadG++fG+Gae+gist+k+harGPvG+e L+syk lcl|NCBI__GCF_001579945.1:WP_066918355.1 363 ERFLAGVDSAIVLHNASTQFADGGEFGMGAEIGISTDKFHARGPVGVEQLTSYK 416 *****************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (427 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: 7.53 // [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