Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_072907554.1 BUB13_RS07785 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_900142125.1:WP_072907554.1 Length = 418 Score = 392 bits (1007), Expect = e-113 Identities = 197/409 (48%), Positives = 279/409 (68%) Query: 12 AQAIEAKKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFM 71 A AIEA+KAS+ + +LS KN+ L +A LE + NEKDL+ RE+G A + Sbjct: 9 ALAIEAQKASRKMAVLSSGVKNELLLKMATALETAESELQRENEKDLQAAREKGMAAAMV 68 Query: 72 DRLSLSQERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARP 131 DRL+L+ ERI+ A GLR+VA L DP G+ W NG+QV + +PLGVIG+IYE+RP Sbjct: 69 DRLALTPERIKGMADGLREVAALPDPVGEVTGMWLRPNGIQVGRQRIPLGVIGIIYESRP 128 Query: 132 NVTVDATGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAA 191 NVT DA GL LKSGNA+VL+GGS AI+SN AI ++ +A+ E +P+ ++Q + ++DR A Sbjct: 129 NVTADAAGLCLKSGNAVVLRGGSEAIHSNTAIGSILQQAMQEMGLPKAALQVVTTSDRNA 188 Query: 192 TNQLFTMKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILV 251 +L +++ +D++IPRGG LI+ V EN+ +PV++ G CH Y+DK AD++ A I + Sbjct: 189 VTELLKLEDQIDLIIPRGGEGLIRFVSENSRIPVIKHYKGVCHTYVDKAADLQMAEDICI 248 Query: 252 NAKTDRPAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDEHVLTIIPDAVPAGED 311 N K RP VCNA ETL++H+D A+ ++ +A++KE + + G E L I+PD V A E+ Sbjct: 249 NEKVQRPGVCNAMETLLIHQDIAAEFLPQITAAMRKEGVELRGCEKSLQIVPDLVAATEE 308 Query: 312 DWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHN 371 DW EYL +AV+ V+ A HIETYG+ H+E IVT + E + +FL ++++ + N Sbjct: 309 DWPAEYLELILAVRVVESFEQAKEHIETYGSLHTEVIVTNDYELSQRFLKEINSSVVMVN 368 Query: 372 ASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 AS+RF+DG LG GAEIGIST KLH+ GPMGL LTT KF++ G+GQIR Sbjct: 369 ASSRFSDGNQLGLGAEIGISTTKLHSFGPMGLEDLTTRKFVVLGSGQIR 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: 422 Number of extensions: 15 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_072907554.1 BUB13_RS07785 (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.25763.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-148 479.5 0.5 4.1e-148 479.4 0.5 1.0 1 lcl|NCBI__GCF_900142125.1:WP_072907554.1 BUB13_RS07785 glutamate-5-semial Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900142125.1:WP_072907554.1 BUB13_RS07785 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.4 0.5 4.1e-148 4.1e-148 1 398 [] 14 407 .. 14 407 .. 0.99 Alignments for each domain: == domain 1 score: 479.4 bits; conditional E-value: 4.1e-148 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a++a+ k+a ls+ kne+l k+a +L+ + +++ +n+kd++aa+e+G+a a++drL+Lt e++k++a lcl|NCBI__GCF_900142125.1:WP_072907554.1 14 AQKASRKMAVLSSGVKNELLLKMATALETAESELQRENEKDLQAAREKGMAAAMVDRLALTPERIKGMA 82 799****************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 d++++v+ L+dPvG+v+ + +G+++ r r+PlGv+g+iye+rP+v++d+a Lclk+Gnav+L+Gg+ lcl|NCBI__GCF_900142125.1:WP_072907554.1 83 DGLREVAALPDPVGEVTGMWLRPNGIQVGRQRIPLGVIGIIYESRPNVTADAAGLCLKSGNAVVLRGGS 151 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 ea++sn a+ +++q+a+++ glp+ a+q+++++dr+ v+ellkl++ +dl+iPrGg++l++ + e+s+i lcl|NCBI__GCF_900142125.1:WP_072907554.1 152 EAIHSNTAIGSILQQAMQEMGLPKAALQVVTTSDRNAVTELLKLEDQIDLIIPRGGEGLIRFVSENSRI 220 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pv++h +GvCh+y+d+ adl++a+ + ++ k qrP +Cna+etLL++++ia+efl++++ ++ ++gvel lcl|NCBI__GCF_900142125.1:WP_072907554.1 221 PVIKHYKGVCHTYVDKAADLQMAEDICINEKVQRPGVCNAMETLLIHQDIAAEFLPQITAAMRKEGVEL 289 ********************************************************************* PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+ ++ l++++ +++++ed+ e+l+l+L+v++ve+ e+a ehi++yg+ h++ i+t+d + ++ lcl|NCBI__GCF_900142125.1:WP_072907554.1 290 RGCEKSLQIVPDL----VAATEEDWPAEYLELILAVRVVESFEQAKEHIETYGSLHTEVIVTNDYELSQ 354 **99999988766....577889********************************************** PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f+ke++s+ v vnas rf+dG + G+Gae+gist klh+ GP+GLe L++ k lcl|NCBI__GCF_900142125.1:WP_072907554.1 355 RFLKEINSSVVMVNASSRFSDGNQLGLGAEIGISTTKLHSFGPMGLEDLTTRK 407 **************************************************976 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.38 // [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