Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_012536144.1 AFE_RS02145 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_000021485.1:WP_012536144.1 Length = 418 Score = 355 bits (910), Expect = e-102 Identities = 187/404 (46%), Positives = 259/404 (64%) Query: 17 AKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDRLSL 76 A+ A + L K+ AL +A+ L RD + + AN KDLR+ E G AF+DRL L Sbjct: 14 ARSAQRRLQSADSAAKDSALRAMAEFLRRDADNLQRANRKDLRSAEEAGKDAAFIDRLRL 73 Query: 77 SQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNVTVD 136 + RI A+GL ++A L DP G+ +G+QV ++ PLGVI MIYE+RPNVT D Sbjct: 74 DEARIEAMARGLEEIAALPDPVGEITDLRYRPSGIQVGRMRAPLGVIAMIYESRPNVTAD 133 Query: 137 ATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATNQLF 196 A GL KSGNA++L+GGS +++SN AI E + AL +P + VQ++ + +R A L Sbjct: 134 AAGLCAKSGNAVILRGGSESLHSNMAIAERLRAALGRANLPLDLVQYVNTAEREAVGILV 193 Query: 197 TMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNAKTD 256 M +VDV+IPRGG LI V +ATVPV+ GNCH+Y+D DAD KA+ +++N+KT Sbjct: 194 GMDRYVDVVIPRGGKGLISRVKADATVPVIMHLHGNCHVYVDADADPRKALRVVLNSKTQ 253 Query: 257 RPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGEDDWKNE 316 R CN AE+L++H++ + + +AL+++ I V E L IP A+ A E+D+ E Sbjct: 254 RLGTCNTAESLLIHQERMDDLLGPIAAALQEKGIEVRACERGLPRIPGAIAATEEDYGAE 313 Query: 317 YLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHNASTRF 376 YL I++K VDDL AIAHI YG++H+E+IVTEN A +FL VDA+++ NASTRF Sbjct: 314 YLGPIISLKVVDDLDAAIAHINRYGSQHTESIVTENYTQARRFLREVDASSVMVNASTRF 373 Query: 377 TDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 DG G GAEIGIST +LH RGP+GL LT K+++ G G IR Sbjct: 374 ADGFEYGLGAEIGISTNRLHVRGPVGLEGLTLQKWIVLGDGHIR 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: 409 Number of extensions: 14 Number of successful extensions: 2 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_012536144.1 AFE_RS02145 (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.31163.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-142 458.6 0.1 9.5e-142 458.4 0.1 1.0 1 lcl|NCBI__GCF_000021485.1:WP_012536144.1 AFE_RS02145 glutamate-5-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_012536144.1 AFE_RS02145 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.4 0.1 9.5e-142 9.5e-142 1 396 [. 14 405 .. 14 407 .. 0.98 Alignments for each domain: == domain 1 score: 458.4 bits; conditional E-value: 9.5e-142 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a+ a +l++ +a k++al ++a+ L+++a+ + an+kd+ +a+e G a++drL L+e++++ +a lcl|NCBI__GCF_000021485.1:WP_012536144.1 14 ARSAQRRLQSADSAAKDSALRAMAEFLRRDADNLQRANRKDLRSAEEAGKDAAFIDRLRLDEARIEAMA 82 79999**************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 ++++++ L+dPvG++++ r + +G+++ r+r+PlGv+ +iye+rP+v++d+a Lc k+GnaviL+Gg+ lcl|NCBI__GCF_000021485.1:WP_012536144.1 83 RGLEEIAALPDPVGEITDLRYRPSGIQVGRMRAPLGVIAMIYESRPNVTADAAGLCAKSGNAVILRGGS 151 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 e+ +sn a++e ++ al ++ lp vq +++++re v l+ +d+yvd++iPrGg++l++ +k ++t+ lcl|NCBI__GCF_000021485.1:WP_012536144.1 152 ESLHSNMAIAERLRAALGRANLPLDLVQYVNTAEREAVGILVGMDRYVDVVIPRGGKGLISRVKADATV 220 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pv+ h G+Ch+y+d++ad ka +v++++ktqr tCn+ e+LL++++ ++ l ++ +l+ekg+e+ lcl|NCBI__GCF_000021485.1:WP_012536144.1 221 PVIMHLHGNCHVYVDADADPRKALRVVLNSKTQRLGTCNTAESLLIHQERMDDLLGPIAAALQEKGIEV 289 ********************************************************************* PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 ra + l ++ + +++++ed+ e+l +++s+k+v+dl++ai+hi++yg++h+++i+te+ ++a+ lcl|NCBI__GCF_000021485.1:WP_012536144.1 290 RACERGLPRIPGA----IAATEEDYGAEYLGPIISLKVVDDLDAAIAHINRYGSQHTESIVTENYTQAR 354 **98887777766....567789********************************************** PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvs 396 +f++evd+++v vnastrfadGf++G+Gae+gist++lh rGPvGLe+L+ lcl|NCBI__GCF_000021485.1:WP_012536144.1 355 RFLREVDASSVMVNASTRFADGFEYGLGAEIGISTNRLHVRGPVGLEGLTL 405 *************************************************96 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: 00:00:00.02 # Mc/sec: 7.14 // [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